2013 BFng2569 MOESM20 ESM

The draft genome of the fast growing non-timber forest species Moso
Bamboo (Phyllostachys heterocycla)
Zhenhua Peng1,4, Ying Lu2,4, Lubin Li1,4, Qiang Zhao2,4, Qi Feng2,4, Zhimin Gao3,4,
Hengyun Lu2, Tao Hu3, Na Yao1, Kunyan Liu2, Yan Li2, Danlin Fan2, Yunli Guo2,
Wenjun Li2, Yiqi Lu2, Qijun Weng2, Congcong Zhou2, Lei Zhang2, Tao Huang2, Yan
Zhao2, Chuanrang Zhu2, Xinge Liu3, Xuewen Yang3, Tao Wang1, Kun Miao1, Caiyun
Zhuang1, Xiaolu Cao1, Wenli Tang3, Guanshui Liu3, Yingli Liu3, Jie Chen1, Zhenjing
Liu1, Licai Yuan3, Zhenhua Liu1, Xuehui Huang2, Tingting Lu2, Benhua Fei3, Zemin
Ning2, Bin Han2* & Zehui Jiang1,3*
1
Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree
Breeding and Cultivation, State Forestry Administration, Beijing 100091, China.
2
National Center for Gene Research，Shanghai Institute of Plant Physiology and
Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences,
500 Caobao Road, Shanghai 200233, China.
3
International Center for Bamboo and Rattan, 8 Fu Tong Dong Da Jie, Chaoyang
District, Beijing 100102, China.
4
These authors contributed equally to this work.
*
Correspondence should be addressed to B.H. (bhan@ncgr.ac.cn); Z.J.
(jiangzehui@icbr.ac.cn).
Nature Genetics: doi:10.1038/ng.2569

Supplementary Notes
Bamboo and the individual subjected to genome sequencing.

Bamboo is the general name of plants which belong to a Bambusoideae in
Gramineae family, about 1,250 species and 90 genera widely distributed in the
tropical and subtropical areas of Asia, Africa, America, and Pacific islands, and a few
in the temperate and frigid zone1.
According to the statistics, there are about 500 species of bamboo and totally
53,800 km2 of bamboo forest in China, the largest cultivation area and the
maximum gross output value of bamboo industry in the world. The export volume
of bamboo products was US$ 14 billion in 2009 and the gross output value of
bamboo industry was about US$ 130 billion in 2010. Bamboo is one of the most
important non-timber forest resources and forest products in terms of their
ecological conservation, feasible economic profit and social benefit, increasingly
playing an important role in increasing farmer income and promoting local
economic development. Fast growing, high productivity, strongly regeneration
capability and various benefits of bamboo attracted attention in countries, where it
was a sustainable material to supply works of the planting and industry to billions of
people.
Moso bamboo is a large woody bamboo with the highest ecological, economic,
and cultural values of all bamboos in Asia and accounting for ~70% of total area of
bamboo growth and 5 billion US dollars of annual forest production in China1. The
moso bamboo is one of the plants with an incredible growth speed in the world.
The height growth of its shoot is rapid and steady in suitable condition in spring
depended on its strong rhizome-dependent system. At the growth peak, the shoot
of the moso Bamboo can grow as long as 100-cm within 24 hours, and reach to its
maximum height about 20 meters in shortly 45 to 60 days. It grows predominantly
by vegetative propagation due to its unique rhizome-dependent system. Bamboo
has a very term flowering interval as long as 60 to 120 years. All of these mysteries

attracted our interesting in its biological research.
The moso bamboo genome contains 24 pairs of chromosomes, as well as basic
number of chromosomes characters in other bamboos. Prior to the whole genome
sequencing, we checked different moso bamboo communities growing in main
planting areas, crossing Eastern, Southeastern, and Southern China. We finally
chose the individual growing in the Tianmu-Mountain National Nature Reserve in
Zhejiang Province of Eastern China (119º26'55.0”E, 30º19'13.4”N; 480-meter in
elevation) where its growth had not been interrupted by human activities for a long
time.
The tissues for the transcriptome sequencing.

Five vegetative tissues (young leaves, rhizome, root, tip of the 20cm-high shoot, and
tip of the 50cm-high shoot) were collected in the Tianmu-Mountain National Nature
Reserve in Zhejiang Province of China in spring, which was from the same individual
used in genome sequencing. To perform the transcriptome sequencing of floral
tissues, we spent over two years to look for the floral tissues of moso bamboo in 8
provinces of China because its flowering was too rare. Finally, in early summer of
2010, two reproductive tissues (panicles at early stage and panicles at flowering
stage) were obtained in suburban Guilin (110º31'20.2”E, 25º10'42.7”N; 216 meter
in elevation), Guangxi Province of Southern China, more than 1800 kilometers
(1,100 miles) from our institute. The collected panicles from plant with no flowering
or post-flowering spikelet were considered as panicle at early stage, while those
from the plant growing at least 50% of flowering or post-flowering spikelet were
considered as that at flowering stage.
Cytogenetic analysis of moso bamboo chromosomes.

Fluorescence In situ hybridization.
Meiotic pachytene chromosomes were prepared from the root tip of freshly
germinated seedling. Individual pachytene chromosomes were identified by
fluorescence in situ hybridization using rice 45s rDNA probe2, according the method
3

described in Jiang et al.3. Digital images were recorded from an Olympus BX60
fluorescence microscope.
Estimation of genome size of the moso bamboo by the flow cytometry.

We put 2-month-old leaves from the sequenced bamboo individual into a flow
cytometric analysis to estimate genome size as mentioned by Galbraith4. Finally,
over 10,000 nuclei were analyzed per sample with a FACSAria flow cytometer
(Becton, Dickinson and Company), equipped with 488 nm argon laser. 24 samples
were analyzed using rice as the standard species. The software BDFACSDiva was
used for data analysis with the coefficient variation controlled in 5%. The peak
values of the fluorescence intensity of 24 bamboo and rice samples, the genome
size of moso bamboo was estimated to be about 2,075.025 ± 13.08 Mb, or 2C DNA
about 4.24 pg (1 pg DNA = 0.978×109 bp 5).
Estimation of genome size of the moso bamboo by the frequency of k-mer

occurency.
Values of K-mers were plotted against the frequency at their occurency
(Supplementary Fig.3). At a K-mer size of 51, the peak occurrency is at 36. Study of
the panda genome used K-mer frequency to estimate the genome size6. To avoid
potential over-estimation of genome sized introduced by base errors, we turned to
the modified method as described in the paper of the Tasmanian devil genome7 to
estimate the genome size of the moso bamboo. As the definition of genome size,
the total number of effective K-mer words divided by the K-mer depth or the K-mer
occurrence number at the peak kmer frequency Dp, Gs = (Kn – Ks)/Dp. Here Kn is the
total number of K-mer words and Ks is the number of single or unique K-mer words.
So we estimated the genome size to be (80477036861 - 9537946584) / 36 = 1.97
Gb.
BAC and BAC-end sequencing.

The moso bamboo BAC library was constructed by Amplicon Express, USA,
4

composed of 165,888 clones harvested from a Hind-III BAC library with epicenter
pCC1BAC Cloning-Ready Vector. The nuclear DNA was isolated from the same
individual as used in genome sequencing. Average insert size of bamboo BAC is
about 135 Kb. Eight randomly selected BACs were sequenced by using subcloning
and standard Sanger sequencing methods. A total of 10,327 BACs were isolated
with MACHEREY-NAGEL plasmid and large-construct DNA purification kit
(NucleoSpin○
R 96 Flash, Cat. No.740618.24). Both ends of all these BACs were
sequenced by the dideoxy chain termination method using BigDye Terminator Cycle
sequencing kit V3.1 (Applied Biosystems, Life Technologies). BAC end sequencing
was carried out on ABI3730xl DNA analyzer. The assembling of the BACs and
re-basecalling of raw BAC-end sequences were performed by the PHRED and PHRAP
programs8. Manual editing was utilized to validate the accuracy of the re-basecalled
reads.
Prediction of protein-coding genes.

We build a 7-step pipeline to construct the gene model set (Supplementary Fig. 7).
1) The prediction software program, FgeneSH++ with gene model parameters
trained from monocots, was used in ab initio gene prediction to build the
preliminary gene models.
2) Coding sequences of each predicted gene model were aligned to both the
Repbase TE library and the moso bamboo TE library created by RepeatModeler,
using the Blastn at E-value of 1e-5.
3) The Illumina RNA-seq sequences from five vegetative and two reproductive
tissues were mapped onto the coding sequences of FgeneSH gene models by the
aligner SMALT with parameters set to minimum Smith-Waterman (-m) at 80 (for
2*120 bp reads) or 60 (for 2*100 bp reads), maximum insert size (-i) at 1,500, and
minimum insert size (-j) at 20. Only uniquely matched reads were selected in
assistance with gene prediction. Information between unique matches and
corresponding gene models were collected by using 2 thresholds to screen SMALT
cigar outputs: A) cigar:S and cigar:A items with score at 50 or more were selected. B)
5

for the selected cigar:A items, the available paired-end insert size should be at least
200 bp.
4) A total of 8,253 moso bamboo cDNAs, carrying entire coding sequences but
not TE-derived, were selected from the 10,608 putative full-length cDNAs and were
then mapped to the scaffolds by an mRNA/EST genome mapping program of GMAP9
with the parameters set to “-n 1 -f 2 -B 1 -A -t 4”.
5) The gene models were screened by integrating the information from outputs
of the step 2), 3), and 4), using the following 4 thresholds.
A, the gene models coding TE-elements or overlapping TE-elements greater than
10% of gene coding region were firstly discarded.
B, the models aligned to the full-length cDNAs were preferentially collected. The
splicing sites were manually adjusted according to the alignment.
C, the models detected not by the FgeneSH++ but by the cDNAs were created and
their coding information was added into gene model set.
D, candidate gene models without the evidence of full-length cDNAs should be
supported by 2 different uniquely matched RNA-seq sequences. And at least 20% of
their coding region was covered by RNA-seq reads. A pair of PE reads was treated as
a single RNA-seq sequence when counting number of the mapped transcriptome
reads for each model.
6) Information of cDNA-supporting UTR ends was attached to the gene model set.
7) The single-exon genes were manually checked by experts and the genes with
no hits to homologs of grass genes were also discarded.
8) For the gene with different transcripts, the longest one was selected.
Comparison of parameters of gene models among plant genomes.

We did comparative analysis between the bamboo genes and the genes identified
from Arabidopsis, Brachypodium, rice, sorghum, and maize. The bamboo gene
models exhibited very high similarity to other grass species in all of these
parameters, such as the distribution of gene length, coding sequences (CDS), exon
length, intron length, GC content in coding region, and exon number per gene
6

(Supplementary Fig. 8). Of compared species, only dicot Arabidopsis is obviously
different from any other species in gene length, CDS GC content, and intron length.
Comparison of the assembled scaffolds to the available moso bamboo sequences

in database.
The assemblies were compared with available sequences in the public database to
assess the genomic coverage and assembling accuracy. In the GenBank till October
of 2011, there have been 1,086 genome survey sequences, and 18 gene sequences.
Alignment of the known genomic sequences with the length over 2 Kb to our
assemblies showed that over 98% of sequence region were covered by the
assembled scaffolds and 91% covered by a single best match (Supplementary Table
2). Similar coverage, 96% of all matches and 94% of the single best match, was
observed in alignment of the rest 996 genome survey sequences less than 2 Kb.
Most of the sequences with low coverage have putative sequencing errors because
of more biases distribution within them. The known 18 gene coding sequences with
total length of 28,741 bp were parallelly mapped onto the assemblies. Almost each
one had a perfect match located on a single scaffold except unmatched bases at the
end of the genes (Supplementary Table 3). The average sequence identities in
aligned region were over 98%. Our manual check revealed that most unmatched
bases at the end should be the low quality bases introduced by sequencing of
amplified DNA fragments. Prior to this study, over ten thousand putative full-length
cDNAs were cloned and sequenced for the moso bamboo. Of them, 8,253 cDNA
sequences were picked up when those TE-derived, false ORF-coding, and
non-moso-bamboo items were removed. We mapped the cDNAs onto the
assemblies by means of GMAP. A total of 8118 (98.4% of 8,253) cDNAs were
uniquely aligned to the assembled scaffolds with very high identities (averagely at
99.1%, Supplementary Fig. 4). All of the sequence comparison consisted with the
estimated 98% coverage of genome assembly.
To evaluate the quality of whole genome shotgun assembly, the assembled
scaffolds were aligned to 8 finished bacterial artificial chromosomes (BACs)
7

sequences with average length 133 Kb by Sanger sequencing technology. Seven
BACs were well aligned to a single scaffold and 1 BACs were aligned to 2 scaffolds
each (Supplementary Fig. 5). The coverage of the scaffolds and initial contigs on the
BACs were up to 88.8% and 98.8% (Supplementary Table 4), which supported our
estimation of whole genome coverage of the assemblies. The frequency of
single-base difference and insertion/deletion were approximately 0.19 and 0.09 per
Kb, without regard to heterozygous single nucleotide polymorphisms (SNPs) and
short indels detected by the annotation. The average PE read depth in aligned
regions was at 100- to 132-fold coverage. The incompatible bases were inclined to
located near the unclosed gaps, indicative of assembling quality were lower at the
end of the initial contigs. Prior to sequence alignment, we have removed most of
the sequence errors in assembly of the Sanger BACs. The detected SNPs or short
indels were probably derived from potential heterozygosity or low rate assembling
errors.
Repeat annotation.
The de novo repeat annotation revealed that the moso bamboo genome comprised
approximately 59% transposable elements (TEs). Detection of the TEs in the
Sanger-BACs showed 53% of TE content, similar with that in whole genome. With
comparison to other grass species, the moso bamboo genome had similar TE
content to that of the sorghum (62%) (main text ref. 36), and more TE content than
rice (40%) (main text ref.18) and Brachypodium (28%)10, but lower than maize (84%)
(main text ref.36, 26). Of the observed TEs, retrotransposons were the dominating
repetitive sequences (39%), as well as 9.5% of DNA transposons. Like the rice,
sorghum and maize genomes, the most abundant repeats in bamboo were
long-terminal repeat elements (LTRs), 24.6% of Gypsy-type LTRs and 12.3% of
Copia-type LTRs.
Bamboo genome has the highest copy numbers of TEs, Gypsy/Copia-type LTR
retrotransposons and En/Spm transposons. Rice and sorghum have the highest copy
numbers of MITE transposons (Tourist & Stowaway), and Harbinger transposons
8

and Gypsy/Copia-type LTR retrotransposons, respectively (Supplementary Table
10b and 10c). It was inferred that insertion of the LTR retrotransposons played the
most important role in expansion of the higher plant genome size, though some
DNA transposons also had very high copies. The TEs covering approximately 11% of
the bamboo genome were not classified. However, their average unit length was
within the range of the LTRs, implying that there should still be some unknown TEs
active in the bamboo. A total of 9,412 intact LTR retrotransposons were predicted in
our genome assemblies. The average length was approximately 10.3 Kb, 3 times of
the average gene length.
We performed de novo prediction for LTR retrotransposons with LTRharvest and
LTR_FINDER on the large-sized scaffolds (>10 Kb), using default parameter but
-maxdistltr set at 30,000. The quality criteria were the existence of one or more
typical retrotransposon protein domains and the simple-repeat/tandem-repeat
content less than 35%. A total of 9,142 remaining candidates were considered as
the full-length LTRs, including 3,103 Gypsy-type (PR-RT-INT), 2,677 Copia-type
(PR-INT-RT), and 3,632 unclassified.
Identification of gene synteny and whole-genome duplication.

Detection of syntenic genes between bamboo and rice and between bamboo and
sorghum.
To generate a pair-wise alignment of gene models between bamboo and rice (MSU
RGAP 6.1) and between bamboo and sorghum (v1.4), 30,379 bamboo genes located
on the larger scaffolds (>50 Kb) were aligned to the reference gene models by Blastp
with E-value < 1e-20. The evidence-based gene prediction approach scarcely
concerned gene colinearity between bamboo and other grasses and also expected
to miss some genes. So two criteria were used to call syntenic gene blocks in
bamboo scaffolds: i) number of the genes in one syntenic block >= 5; ii) number of
non-syntenic bamboo genes between two adjacent syntenic genes <5. A perl script
and following manual check was applied to determine the syntenic blocks and
breakpoints between the blocks.
9

Identification of the WGD by investigating the collinear orthologous genes between
bamboo and rice.
According the location of rice genes in chromosome, the collinear gene blocks of
bamboo were mapped to the rice chromosomes. The overlapped gene blocks were
manually checked to remove redundancy. As shown in Supplemental Fig. 10a, moso
bamboo seemed to carry as two duplicates as that of rice gene model sets, though
lots of bamboo gene lost within these regions during the duplication. It was
suggested that the large-scale genome duplication in bamboo resulted from whole
genome duplication not from segmental duplication, which supported a tetraploid
origin of bamboo. Interestingly, rice chromosomes are characteristic of diploid
(2n=24) while moso bamboo chromosomes are 2n=48. There might be unknown
connection between them. We collected the orthologous pairs of bamboo, which
share unique rice ortholog in collinear blocks, to estimate the divergence time with
universal substitution rate of 6.5 × 10-9 mutations per site per year. Thus, estimated
7 to 15 mya was the potential time when two bamboo porgenitors diverged
(Supplemental Fig.10b), and the WGD should occur more recent. However, the
moso bamboo chromosomes now exhibit to be a diploid according to the FISH
analysis. Consequently, we speculated that there is a long progress from
tetraploidization to diploidization in moso bamboo since approximately 7-12 mya.
But for the bamboo species with different chromosome number or ploidy number,
the process should be variable.
Annotation of gene function and comparison of fundamental pathways.

Prediction of gene function motifs and domains were performed by Interpro11
against available databases, including ProDom, PRINTS, Pfam, Panther, Profile, PIR,
Smart, and Pattern. The gene functional ontology was retrieved from the outputs of
InterPro using Gene Ontology12
The bamboo gene models were aligned to entries of sorghum, rice, and maize
from the KEGG database (release till April 2011) by Blastp under E-value 1e-10 to
find the best hit for each gene. The similarity of each pathway is the ratio of number
of shared enzymatic steps and sum of referenced enzymatic steps. For instance,
similarity (bamboo vs. rice) = number of the enzymatic steps shared by rice and
10

bamboo / sum of the rice-gene-involved enzymatic steps.
Annotation of conserved non-coding RNA (ncRNA) genes.

Identification of transfer RNAs (tRNA).
The tRNAScan-SE13 algorithms with default parameters were applied to prediction
of tRNA genes in the Arabidopsis, sorghum, maize, rice, Brachypodium, and bamboo
genomes. Bamboo had 1,167 tRNA genes in the assemblies, nearly 0.5 times as
many as that of maize because most of bamboo pseudogenes were not detected in
the current assemblies (containing 10% unclosed gaps). The same analysis of the
Arabidopsis14 and Brachypodium10 found 699 and 615 tRNA loci, respectively, very
closed to 711 and 614 identified by their Genome Initiatives, suggesting that most
of bamboo tRNAs had been found. Of all conserved tRNA genes, selenocysteine and
suppressor tRNAs were involved in a special coding way by the stop codens. It was
interesting that 6 Selenocysteine and 1 suppressor tRNAs were detected in the
bamboo genome, which were only found in maize and sorghum of Panicoideae but
not in its sister groups, Brachypodium of Pooideae and rice of Ehrhartoideae.
Identification of rRNA genes.

The rRNA fragments were identified by aligning the rRNA template sequences (Rfam
database15, release 10.0) of Arabidopsis thaliana, Oryza sativa, Sorghum bicolor,
and Zea mays using Blastn with E-value at 1e-10 and identity cutoff at 95% or more.
Identification of other non-coding RNA genes.

The miRNA and snRNA genes were predicted by INFERNAL16 software against the
Rfam database (release 9.1, 1,412 families). To accelerate the speed, a rough
filtering prior to INFERNAL was performed by Blastn against the Rfam sequence
database under E-value at 1. For the miRNA prediction, the assemblies were aligned
to the precursor sequences of Arabidopsis thaliana, Brachypodium distachyon,
Oryza sativa, Sorghum bicolor, Saccharum officinarum, Triticum aestivum, Hordeum
vulgare, and Zea mays, derived from the Rfam sequence database. The extended
11

sequences covering detected loci region and 50 bp franking sequences from both
ends of the region were put into the INFERNAL prediction with cutoff score at 30 or
more. The predicted mature sequences of the bamboo miRNA were aligned to gene
model set to detected miRNA target genes with Blastn under E-value at 1e-10. In
the snRNA predictions, the assemblies were firstly aligned to the snRNA sequences
of Arabidopsis thaliana, Oryza sativa, Sorghum bicolor, Triticum aestivum and Zea
mays from Rfam database. The extended sequences, similar as that in miRNA
prediction, were put into the INFERNAL prediction with cutoff score at 50 or more.
The C/D snoRNA were predicted using snoScan17 with the yeast rRNA 16
methylation sites and yeast rRNA sequences provided by the snoScan distribution.
The minimum cutoff score was based on the settings which yield a false positive
rate of 30 bits. Similarly, H/ACA snoRNAs were detected by snoGPS using the yeast
score tables and target pseudouridines18.
Quantity of all predicted non-coding RNA genes was listed in Supplementary
Table 9.
Reconstruction of phylogeny among 6 fully sequenced grass genomes.

The OrthoMCL clustered a total of 968 single-copy gene families among 6 fully grass
and 2 dicot genomes, which was used to reconstruct the phylogeny. The coding
sequences of the genes were concatenated to a supergene for each species. When
the best substitution model (GTR+gamma+I) were determined by Modeltest19 , the
supergene sequences were subjected to phylogenetic analyses by Mrbayes (main
text ref.54) with the parameter set to 1,000,000 (1 sample / 100 generations) and
the first 250 sample were burned in. Two independent runs reached the same result
using Arabidopsis as an outgroup. Branch-specific dN and dS were estimated with
codeml of PAML20. The output of OrthoMCL and phylogenic tree structure were
subjected to a computational analysis of changes in gene family size with the
software CAFE (Online methods ref. 55).
Estimation of divergence time of paralogous pairs.

12

To estimate the divergence time of the paralogs, we selected the gene families
consisting of exactly 2 members to calculate the Ks of the pairs because the
2-member gene families had a single divergence relationship between two
members. Thus, 3,786 bamboo 2-member gene clusters were put into the
calculation of Ks, together with 2,552 rice, 2,161 sorghum, 1,874 Brachypodium,
3,285 maize, and 2,665 foxtail millet clusters. The Ks was calculated by a model that
averages parameters across 14 candidate models (P-value < 0.001)30 and then
converted to the divergence time using a substitution rate of 6.5 × 10-9 mutations
per site per year.
Estimation of divergence time between orthologous genes.

To estimate the divergence time, the Ks values were calculated between orthologs
of bamboo and other genome from the 968 single-copy gene clusters determined
by the OrthoMCL calculation. The Ks distribution of the one-to-one orthologous
pairs of bamboo-Brachypodium, bamboo-rice, bamboo-foxtail-millet,
bamboo-sorghum, bamboo-maize, and bamboo-wheat suggested the different
divergence time between bamboo and other grass genome, which was consisted
with the phylogenic relationship generated by Mrbayes analysis. The mean Ks was
used to estimated the divergence time between different genomes. The internal
duplication during the WGD was estimated by calculating the Ks of the paralogs in
2-member gene families of bamboo and maize, which was then converted to the
divergence time to indicate the WGD time.
Calling of heterozygous SNPs and small indels.

To detect the heterozygous sequence polymorphism, all of the used PE reads
(around 120× coverage) were firstly mapped to the assembled scaffolds by aligner
SMALT. The SNPs were then called by SSAHA_Pileup (version 0,8) and 6 thresholds
were used to post-filter unreliable SNPs: 1) SSAHA_Pileup SNP score >= 20; 2) ratio
of two alleles between 3:17 to 17:3; 3) the highest sequencing depth of SNP
position <= 240; 4) the lowest sequencing depth for each allele >= 5; 5) the
13

minimum distance for adjacent SNPs >= 10 bp; 6) only one polymorphism detected
at each SNP position. The small indel (length <= 6 bp) were called by the Pindel21
and 4 thresholds were used to remove unreliable small indels: 1) length of indels
<=6 bp; 2) the highest sequencing depth of indel position <= 240; 3) the lowest
sequencing depth for each allele >= 5; 4) ratio of gapped and ungapped reads at the
indel position between 3:17 to 17:3.
14

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Supplementary Figures
Supplementary Figure 1 Cytogenetic analysis of bamboo chromosomes. (a)
25

Fluorescence in situ hybridization of the moso bamboo at mitotic metaphase with
the probe of rice 45S rDNA. The chromosomes were dyed by DAPI. The 45S rDNA
probe was labeled with digoxin. Signals were detected by FITC with a magnification of
microscope at 200 times. Two copies of chromosome sets were displayed. (b) Test
result of Oryza sativa and Phyllostachys heterocycla mixed samples by using flow
cytometry. The term C-value refers to the amount (picograms) of DNA contained
within a haploid nucleus or one half the amount in a diploid somatic cell of a
eukaryotic organism. Blue peak indicated 2 C DNA of Oryza sativa at 16,378. Pink
peak indicated 2 C DNA of Phyllostachys heterocycla at 79,892. Compared with that
of rice (430 Mb), genome size of the moso bamboo was estimated to be 2 075.025 ±
13.08 Mb.
26

Supplementary Figure 2 Phusion-meta pipeline of short read assembly. To complete
assembly of this highly heterozygous genome, we developed an integrated de novo
assembly pipeline for large-sized genomes using short read sequencing data.
Although this pipeline used existing algorithms and assembler, there were three
critical variables introduced into the assembling strategy: i) filtering of the
paired-end (PE) reads by K-mer occurrency to lower sequence error; ii) clustering of
the reads before assembling to reduce assembling errors derived by direct
assembling of the short read; iii) multiple use of reads and contigs in different cycles
to make up for deficiencies of different algorithms. Thus, we generated
comparatively high-quality assemblies by using nearly entire short reads. This
pipeline therefore can be efficiently used in de novo assembly of complex and
large-sized genomes.
27

Supplementary Figure 3 Distribution of Kmer frequency. Distribution of 51-mer
frequency in the reads of short insert size libraries (350 - 400 bp). Values of K-mers
were plotted against the frequency (y-axis) at their occurrency (x-axis). The leftmost
truncated peak at low occurrence (1-2) was mainly due to random base errors in
the raw sequencing reads. The frequency exhibited a bi-modality caused by
heterozygosity.
28

Supplementary Figure 4 Mapping of the full-length cDNA sequences to the moso
bamboo genome. The cDNA sequences were aligned to the assembled scaffolds.
Totally, 8,118 of 8,253 (98.4%) cDNAs were uniquely mapped onto the assemblies
with high identities at 99.1% using the GMAP. The Y axis showed accumulative
frequency of the aligned cDNAs. The X axis exhibited the identity of sequence
alignment.
29

30

31

32

Supplementary Figure 5 Alignment of assembled scaffolds to the BACs sequenced
by Sanger method. Depth of reads in blue was calculated by mapping PE reads onto
the BAC sequences. Repeats in red showed the RepeatMasker-annotated TEs on the
BAC sequences. The blocks in white indicated the unfilled gaps on the scaffolds. The
grey blocks showed aligned region between Sanger BACs and scaffolds. GC contents
were shown in green curves.
33

Supplementary Figure 6 Comparison of detected assembling errors by different
assembling methods.
34

Supplementary Figure 7 Simplified pipeline of gene prediction with the
combination of ab initio gene prediction, mapped RNA-seq reads, and cDNA
sequences. Using both RNA-seq data and 8,253 cDNA sequences, we initially
detected 35,378 transcribed loci in the genome. By applying the stringent criteria to
gene prediction, a total of 31,987 high-confidenced genes were finally identified in
the annotation, which were in the same range as those of other grass families.
35

a b
c d
e f
Supplementary Figure 8 Comparison of gene parameters among fully sequenced

genomes. Gene structure of the Phyllostachys heterocycla (phe) showed highly
consistent with that of other grass speices, including Arabidopsis thaliana (ath),
Brachypodium distachyon (bdi), Oryza sativa ssp. Japonica (osa), Sorghum bicolor
(sbi), and Zea mays (zma), in distribution of gene length, exon number per gene,
coding sequence length, GC content in coding region, exon and intron length.
36

Supplementary Figure 9 Quantitative comparison of single-copy genes and gene
families consisting of 2 to 4 members among foxtail millet, maize, sorghum,
Brachypodium, rice, and bamboo. The gene families and single-copy genes were
categorized by OrthoMCL analysis. For the y axis, number of gene member at 1
indicated the single-copy gene and 2 to 4 meant that the gene families consisted of
2 to 4 member(s). The x axis indicated their proportion (%).
37

a
38

b
Supplementary Figure 10 The bamboo WGD identified by analysis of gene

collinearity between bamboo and rice orthologs. (a) Collinear gene blocks between
bamboo and rice genome. The rice genes are arranged according to their gene order.
Rice gene sets on different chromosomes were exhibited in blue rough lines. The
ordinal number of the genes were measured by the bar in the left. The collinear
gene blocks of bamboo were shown in red blocks, which implicated that moso
bamboo carried nearly two duplicates of rice genome. (b) Estimated divergence
time of bamboo orthologous pairs. Only the orthologous pairs of bamboo sharing
unique rice orthologs in collinear blocks were used to estimate the divergence time.
The 7 to 15 mya was the potential time when two bamboo porgenitors diverged,
and the WGD should occur more recent than it.
39

Supplementary Figure 11 Ks distribution of orthologous genes between bamboo
and grass species. The bin size of Ks value was 0.05. Frequency was quantity of the
one-to-one gene clusters.
40

a
41

b
42

C
Supplementary Figure 12 Phylogenic tree of CesA and Csl gene families among
Arabidopsis, poplar, rice, maize, sorghum, Brachypodium, and bamboo. (a) NJ tree
of CesAs. A, B, C, D, E, F, and G indicated 7 clades where the bamboo genes were
located. (b) NJ tree of Csls. Different subfamilies were shown in different colors. (c)
NJ tree of CCR genes. (d) NJ tree of HCT genes. The bamboo genes were labeled by
red point. The numbers beside the branches were bootstrap percentage.
43

a b
30
Dof
20
RPKM
10
0
S20 S50 RH RT LF P1 P2
200
MADS14
RPKM
100
0
S20 S50 RH RT LF P1 P2
Supplementary Figure 13 A hypothesized pathway in activation of flowering. (a)

Quantified expression levels of bamboo Dof (the homolog of the OsDof12) and
MADS14 (one of homologs of the OsMADS14, involved in the FMI) in different
tissues. The expression is indicated as the normalized quantified transcript levels
(RPKM). (b) A predicted pathway in controlling of flower-time in bamboo. Of the
identified floral genes, the homologs of OsMADS14 (main text ref.30) (bamboo
MADS14s, Identity >70%, FMI genes) were highly expressed in panicles (16- to
84-fold over vegetative tissue, Q-value < 0.001). However, the expressions of the
homologs of its upstream regulatory genes, such as OsSOC123, and Ehd124, were not
detected (Supplementary Table 17) except for a homolog of OsDof1225 (bamboo
Dof, Identity >80%, Supplementary Table 16) with significantly higher expression in
panicles (5- to 26-fold, Q-value < 0.001), implying that the bamboo Dof might also
be functional in regulating MADS14s at the flowering of bamboo. As the previous
studies in rice, the OsDof12 can be induced under long-day conditions25 or drought
stress26. The flowering bamboo were grown in the typical short-day growing area in
Southern China where a severe drought had just occurred, suggesting that the
bamboo Dof was likely induced by drought stress. Taken together, a pathway of
drought-Dof-MADS14-flowering might be active during the flowering.
44

a
Supplementary Figure 14 Distribution of insert sizes in paired-end sequencing

libraries with inserts at around 3 to 18 Kb. (a) Distribution of the library with insert
sizes around 3Kb. (b) Distribution of the library with insert sizes around 7-8 Kb. (c)
Distribution of 16-18 Kb insert library. The insert sizes and their distribution were
estimated by counting the number of read pairs located on existed initial contigs.
45

Supplementary Figure 15 Number of detected non-TE-derived loci by transcriptome
sequences from 7 different tissues, tip of 20cm-high shoot (shoot20), tip of
50cm-high shoot (shoot50), rhizome, root, leaf, panicle at early flowering stage
(panicle_1), and panicle at late flowering stage (panicle_2). The number indicated
quantity of the detected loci in corresponding tissues. Some of the detected loci
were discarded in filtering of gene models, which resulted in the detected number
in some tissues was more than final gene models.
46

Supplementary Figure 16 Transcriptome evidence for gene prediction in moso
bamboo. A potential gene model should be supported by at least 20% coverage of
transcriptome reads in gene coding region. Over 27,000 (87% of 31,987) genes’
coding regions were strongly supported by transcriptome sequences.
47

Supplementary Tables
Supplementary Table 1 Summary of sequence assembly.
Supplementary Table 1a Summary of the BAC-end sequences used in scaffolding

Quantity of BAC-ends 20,654 (10,327 pairs)
Total length of BAC-ends 18.4 Mb
Genome coverage 0.66 ×
Average read length 890 bp
Average distribution density every 103 Kb
Average BAC insert length 140 Kb
Quantity of aligned BAC-ends to the scaffolds 19,069

Total length of aligned BAC-ends to the scaffolds 17.3 MB (94.2%)
Shared identites of BAC-ends in the scaffolds 96.8%
Supplementary Table 1b Summary of sequencing and assembly of the moso

bamboo genome.
Length of
Added paired-end Sequence N50 N80 Total length
max. contig
insert size (bp) coverage (×) (bp) (bp) (bp)
(bp)
Initial contig 11,622 2,338 186,163 1,862,588,005
350 - 400 120
Scaffold 1 13,599 2,876 220,151 1,915,326,230
2,400 - 3,600 13
6,800 - 8,700 12
†
13,500 - 17,500 2
Scaffold 2 328,698 62,052 4,869,017 2,051,719,643
120,000
(10,327 pairs of 0.66
BAC-ends)
†
Final scaffolds with less than 500 bp were excluded.
48

Supplementary Table 1c Comparison of length of contigs and scaffolds assembled
by different methods.
Assemblies by pure Assemblies by
SOAPdenovo Phusion-meta
Length (bp) 5,076 11,882
N50
n 89,573 42,412
Length (bp) 472 3,582
Initial N80
n 412,943 114,186
contigs
Average length (bp) 598 2,088
Maximum length (bp) 99,128 152,833
Total length (bp) 1,837,124,999 1,871,331,085
Length (bp) 81,579 328,698
N50
n 6,285 1,626
Length (bp) 55,746 234,025
N60
n 9,120 2,362
Length (bp) 31,874 149,820
N70
n 13,550 3,450
Length (bp) 13,996 62,052
N80
n 22,289 5,499
Scaffolds
Length (bp) 5,368 1,733
N90
n 43,146 44,100
Length (bp) 500 500
N100
n 172,645 277,278
Average length (bp) 11,215 7,400
Maximum length (bp) 767,478 4,869,017
Total length (bp) 1,936,298,937 2,015,719,643
Genome coverage (%) 92.2 97.7
49

Supplementary Table 2 Comparison of assembled scaffolds and genomic sequences
in Genbank. The known genome sequences with the length at 2 – 40 Kb were
downloaded from GenBank (Accession NO. GQ252841 - 252869). Of the downloaded
sequences, gi|284434746|gb|GQ252834.1| was probably from chloroplastic DNA.
Blast with E-value at less than 1e-05 was used in alignment.
Coverage Coverage
Coverage Coverage
GeneBank Accession Length of single GeneBank Accession Length of single
of all of all
No. (bp) best No. (bp) best
matches matches
match match
gi|284434480|gb|GQ252796.1| 6,939 0.96 0.85 gi|284434609|gb|GQ252853.1| 3,345 0.99 0.99
gi|284434482|gb|GQ252797.1| 31,231 0.99 0.99 gi|284434611|gb|GQ252854.1| 8,050 0.99 0.99
gi|284434487|gb|GQ252799.1| 6,445 0.98 0.94 gi|284434613|gb|GQ252855.1| 4,129 0.90 0.90
gi|284434489|gb|GQ252800.1| 7,811 0.99 0.99 gi|284434615|gb|GQ252856.1| 2,858 0.99 0.99
gi|284434492|gb|GQ252801.1| 6,410 0.99 0.99 gi|284434617|gb|GQ252857.1| 5,290 0.99 0.99
gi|284434494|gb|GQ252802.1| 4,037 0.99 0.99 gi|284434619|gb|GQ252858.1| 26,484 0.99 0.99
gi|284434496|gb|GQ252803.1| 23,256 0.99 0.98 gi|284434622|gb|GQ252859.1| 22,895 0.98 0.95
gi|284434500|gb|GQ252805.1| 24,578 0.99 0.98 gi|284434629|gb|GQ252860.1| 7,028 0.99 0.99
gi|284434507|gb|GQ252806.1| 3,794 0.99 0.99 gi|284434631|gb|GQ252862.1| 15,053 0.99 0.98
gi|284434509|gb|GQ252807.1| 13,227 0.99 0.99 gi|284434635|gb|GQ252863.1| 8,067 0.98 0.98
gi|284434511|gb|GQ252809.1| 6,059 0.99 0.99 gi|284434637|gb|GQ252864.1| 11,009 0.99 0.96
gi|284434513|gb|GQ252810.1| 6,189 0.98 0.88 gi|284434642|gb|GQ252865.1| 8,200 0.96 0.83
gi|284434516|gb|GQ252812.1| 9,531 0.99 0.99 gi|284434644|gb|GQ252866.1| 5,680 0.99 0.99
gi|284434519|gb|GQ252813.1| 5,709 0.99 0.99 gi|284434647|gb|GQ252867.1| 5,306 0.99 0.99
gi|284434522|gb|GQ252814.1| 9,927 0.99 0.99 gi|284434649|gb|GQ252868.1| 25,304 0.96 0.72
gi|284434524|gb|GQ252815.1| 8,244 0.99 0.99 gi|284434653|gb|GQ252869.1| 42,561 0.97 0.50
gi|284434527|gb|GQ252816.1| 18,487 0.99 0.99 gi|284434660|gb|GQ252870.1| 11,864 0.99 0.90
gi|284434533|gb|GQ252818.1| 16,728 0.99 0.95 gi|284434663|gb|GQ252871.1| 9,881 0.96 0.55
gi|284434536|gb|GQ252819.1| 13,505 0.99 0.99 gi|284434666|gb|GQ252872.1| 11,757 0.99 0.99
gi|284434539|gb|GQ252821.1| 3,102 0.94 0.79 gi|284434668|gb|GQ252873.1| 8,127 0.98 0.97
gi|284434541|gb|GQ252822.1| 10,294 0.99 0.99 gi|284434671|gb|GQ252874.1| 20,132 0.96 0.68
gi|284434543|gb|GQ252823.1| 14,582 0.99 0.97 gi|284434676|gb|GQ252875.1| 18,539 0.97 0.53
gi|284434547|gb|GQ252824.1| 7,262 0.98 0.93 gi|284434678|gb|GQ252876.1| 10,060 0.99 0.99
gi|284434549|gb|GQ252825.1| 11,647 0.99 0.99 gi|284434681|gb|GQ252877.1| 7,687 0.99 0.99
gi|284434551|gb|GQ252826.1| 21,041 0.99 0.99 gi|284434684|gb|GQ252879.1| 13,424 0.99 0.86
gi|284434557|gb|GQ252827.1| 21,656 0.99 0.84 gi|284434687|gb|GQ252881.1| 31,459 0.99 0.99
gi|284434561|gb|GQ252828.1| 3,905 0.99 0.99 gi|284434694|gb|GQ252882.1| 5,403 0.99 0.98
gi|284434563|gb|GQ252829.1| 5,314 0.93 0.84 gi|284434697|gb|GQ252884.1| 5,338 0.99 0.97
gi|284434565|gb|GQ252830.1| 6,685 0.99 0.99 gi|284434699|gb|GQ252885.1| 3,379 0.89 0.82
gi|284434568|gb|GQ252831.1| 5,688 0.99 0.99 gi|284434740|gb|GQ252798.1| 3,880 0.98 0.90
gi|284434570|gb|GQ252832.1| 10,633 0.99 0.99 gi|284434741|gb|GQ252804.1| 12,042 0.99 0.99
gi|284434572|gb|GQ252833.1| 10,037 0.99 0.94 gi|284434742|gb|GQ252808.1| 4,347 0.98 0.95
gi|284434574|gb|GQ252836.1| 17,988 0.99 0.98 gi|284434743|gb|GQ252811.1| 4,920 0.99 0.99
50

gi|284434580|gb|GQ252837.1| 3,610 0.99 0.99 gi|284434744|gb|GQ252817.1| 4,026 0.99 0.99
gi|284434582|gb|GQ252838.1| 3,803 0.99 0.97 gi|284434745|gb|GQ252820.1| 3,125 0.99 0.80
gi|284434584|gb|GQ252839.1| 6,741 0.99 0.99 gi|284434746|gb|GQ252834.1| 3,233 0.33 0.23
gi|284434586|gb|GQ252840.1| 9,734 0.94 0.92 gi|284434747|gb|GQ252835.1| 3,415 0.99 0.99
gi|284434589|gb|GQ252841.1| 2,050 0.99 0.99 gi|284434748|gb|GQ252844.1| 4,285 0.99 0.97
gi|284434591|gb|GQ252842.1| 7,689 0.99 0.99 gi|284434749|gb|GQ252846.1| 3,882 0.99 0.98
gi|284434594|gb|GQ252843.1| 7,973 0.99 0.99 gi|284434750|gb|GQ252849.1| 2,512 0.99 0.99
gi|284434596|gb|GQ252845.1| 2,750 0.99 0.86 gi|284434751|gb|GQ252851.1| 6,882 0.99 0.99
gi|284434598|gb|GQ252847.1| 19,143 0.98 0.98 gi|284434752|gb|GQ252861.1| 5,083 0.99 0.99
gi|284434602|gb|GQ252848.1| 3,363 0.99 0.86 gi|284434753|gb|GQ252878.1| 3,917 0.98 0.97
gi|284434604|gb|GQ252850.1| 14,653 0.99 0.99 gi|284434754|gb|GQ252880.1| 2,894 0.99 0.99
gi|284434607|gb|GQ252852.1| 6,356 0.99 0.99 gi|284434755|gb|GQ252883.1| 3,085 0.99 0.99
Sum 429,837 0.98 0.91
51

Supplementary Table 3 Comparison of assembled scaffolds and 18 available genes’
mRNA/coding sequences in the public database. The mRNA and coding sequences
were downloaded from GenBank. Poly(A) sequences at the end of mRNA were
removed anterior to the alignment. Alignment indicated that most of the unmatched
bases were located at the end of the GenBank genes, which were probably
introduced by DNA amplification using homologous genes’ primers of different
species.
Coverage Identities
Coverage
Length of single in
GenBank Accession No. of all Description
(bp) best aligned
matches
match region
gi|145845825|gb|EF549577.1| 1,035 0.960 0.884 0.960 cinnamyl alcohol dehydrogenase
gi|145845829|gb|EF549579.1| 801 0.983 0.983 0.997 caffeoyl-CoA O-methyltransferase
gi|162568699|gb|EU295482.1| 1,130 0.983 0.947 0.998 DRE-binding protein DREB2 (DREB2)
gi|169743367|gb|EU366146.1| 1,060 0.983 0.983 0.993 chloroplast chlorophyll a/b binding protein
gi|169743369|gb|EU366147.1| 1,141 0.976 0.976 0.990 chloroplast chlorophyll a/b binding protein
gi|175050407|gb|EF549578.2| 2,302 0.984 0.984 0.894 phenylalanine ammonia-lyase
gi|190694830|gb|EU780143.1| 554 0.978 0.978 0.994 chloroplast chlorophyll a/b binding protein
gi|195546525|gb|EU860441.1| 1,224 0.984 0.984 0.998 DRE-binding protein DREB1 (DREB1)
gi|222154090|gb|FJ594467.1| 2,171 0.985 0.985 0.949 phenylalanine ammonia-lyase (PAL1)
gi|222154092|gb|FJ594468.1| 2,294 0.985 0.985 0.942 phenylalanine ammonia-lyase (PAL1)
gi|237506882|gb|FJ495287.1| 3,293 0.985 0.985 0.998 cellulose synthase (cesA1)
gi|251766020|gb|FJ475350.1| 3,262 0.985 0.985 1.000 cellulose synthase (CesA2)
gi|251766022|gb|FJ475351.1| 3,306 0.978 0.978 0.986 cellulose synthase (CesA4)
gi|255764546|gb|FJ600727.1| 824 0.983 0.983 0.999 PsbS protein
gi|294818264|gb|GU944762.1| 590 0.981 0.981 0.997 putative pathogenesis protein (WRKY10)
gi|301071262|gb|GU434145.1| 1,245 0.979 0.979 0.997 Actin
gi|312232178|gb|HM747940.1| 1,770 0.985 0.985 0.980 MYB protein
gi|312232180|gb|HM747941.1| 739 0.943 0.943 0.978 VAH protein
Sum 28,741 0.981 0.976 0.981
52

Supplementary Table 4 Comparison of the assembled scaffolds 8 independently
sequenced Sanger BACs. The assemblies were aligned to the BACs using an aligner
MUMmer27 and Blastn with 98% or more identity. The difference of single-base and
insertion/deletion in each aligned block was counted by manual checked. Content of
TE-element were estimate by running RepeatMasker against constructed bamboo
repetitive sequence library.
Coverage Coverage # of Average Rate of

# of
Length of by initial by insertion read single-base
BAC ID TE % single-base
BAC (bp) contigs scaffolds and depth on difference
difference
(%) (%) deletion scaffold (per Kb)
B001E05 69.30 96,839 95.72 100.00 9 13 106 0.09
B001G05 74.11 167,736 75.35 92.43 41 20 132 0.29
B001I05 46.26 126,170 93.64 99.99 2 5 113 0.02
B001I13 49.65 166,343 88.97 100.00 142 18 114 0.85
B015M02 41.36 113,962 99.20 100.00 5 6 127 0.04
B019A14 45.04 126,859 85.49 100.00 16 16 112 0.13
B031C15 43.67 136,024 88.13 100.00 37 9 117 0.27
B035L11 49.83 133,794 90.71 100.00 3 4 105 0.02
Average 52.70 133,466 88.78 98.81 31.9 11.4 116 0.19
53

Supplementary Table 5 Comparison of detected assembling errors by different
methods.
Assemblies by pure Assemblies by

SOAPdenovo Phusion-meta
Rate of single-base difference (# per Kb) 2.27 0.19
Rate of insertion and deletion (# per Kb) 0.83 0.09
Coverage by initial contigs 0.80 0.89
Coverage by supercontigs 0.93 0.99
54

Supplementary Table 6 Statistics of heterozygous polymorphisms. The potential
sites of SNPs and short indels were detected by unique read coverage in genic and
intergenic regions.
Quantity of heterozygous loci

Size of analyzed heterozygous
Source Short
SNP Indel + SNP sequences (bp) rate (×10-3)
indel
gene region 6,818 92,068 98,886 115,641,313 0.85
Intergenic region 44,405 1,917,419 1,961,824 1,936,078,330 1.01
Total 51,223 2,009,487 2,060,710 2,051,719,643 1.00
55

Supplementary Table 7 Overview of gene prediction in some fully sequenced higher plants.
Organism Sorghum Maize Rice Brachypodium Poplar Arabidopsis Foxtail millet Bamboo
Assembly size
730 2,300 382 272 385 125 401 2,051
(Mb)
Transposable
0.62 0.842 0.4 0.281 0.374 0.14 0.4 0.60
element
Gene number 27,640 32,540 34,792 25,532 45,555 25,498 35,472 31,987
Average gene 2,873 2,956 3,350 (without UTR)

3,757 3,039 2,300 2,011 987 (CDS)
length (bp) (without UTR) (without UTR) 1,213 (CDS)
13.1
Gene density
24 (non-repeat 11.0 10.7 8.5 4.5 11.3 64.1
(kb/gene)
region)
Average exon #
4.7 5.3 3.7 5.5 4.3 5.2 4.5 5.3
per gene
Average exon 163

268 304 256 268 254 250 227
len (bp) (median)
Average intron 135

436 516 409 391 379 168 492
length (bp) (median)
Main text Main text Main text

Reference 28 10 14 29 This study
Ref.36 Ref.26 Ref.11
56

Supplementary Table 8 Pathway similarity between bamboo and selected grass
genomes.
P.he vs. O.sa P.he vs. S.bi P.he vs. Z.ma

Entry ID Class of pathway O. P.h Simila S. P.h Simila Z. P.h Simila
sa e rity bi e rity ma e rity
12 10
KO00010 Glycolysis / Gluconeogenesis 91 0.929 66 62 0.818 85 0.840
3 0
KO00020 Citrate cycle (TCA cycle) 48 59 0.895 30 32 0.867 45 34 0.778
KO00030 Pentose phosphate pathway 40 59 0.929 30 27 0.857 42 46 0.929
Fructose and mannose
KO00051 42 50 0.765 26 16 0.600 38 35 0.714
metabolism
KO00052 Galactose metabolism 31 31 0.833 24 13 0.667 24 18 0.857
KO00061 Fatty acid biosynthesis 18 20 1.000 24 10 0.400 24 26 0.800
KO00071 Fatty acid metabolism 31 46 0.700 14 13 0.571 21 25 0.667
KO00100 Steroid biosynthesis 18 24 0.769 36 10 0.467 22 21 0.769
Ubiquinone and other
KO00130 25 15 0.357 19 0 0.000 16 3 0.200
terpenoid-quinone biosynthesis
12 10
KO00190 Oxidative phosphorylation 0.605 89 65 0.413 99 74 0.525
2 9
KO00195 Photosynthesis 71 21 0.259 59 15 0.217 66 18 0.216
10
KO00230 Purine metabolism 96 0.768 96 42 0.406 79 51 0.537
2
KO00240 Pyrimidine metabolism 83 66 0.656 76 29 0.316 70 33 0.447
Alanine, aspartate and glutamate
KO00250 40 36 0.652 25 22 0.450 37 27 0.611
metabolism
Glycine, serine and threonine
KO00260 36 35 0.714 28 17 0.500 26 23 0.765
metabolism
Cysteine and methionine
KO00270 60 72 0.917 33 21 0.500 38 40 0.778
metabolism
Valine, leucine and isoleucine
KO00280 32 39 0.765 20 14 0.500 27 29 0.563
degradation
Valine, leucine and isoleucine
KO00290 29 27 0.600 27 11 0.429 29 16 0.615
biosynthesis
KO00300 Lysine biosynthesis 14 10 0.875 12 2 0.250 12 6 0.625
KO00330 Arginine and proline metabolism 44 64 0.750 29 26 0.478 39 48 0.652
KO00340 Histidine metabolism 19 26 0.500 11 0 0.000 15 14 0.222
KO00350 Tyrosine metabolism 25 31 0.583 17 8 0.222 25 18 0.385
KO00360 Phenylalanine metabolism 47 57 0.667 30 11 0.182 28 22 0.417
KO00380 Tryptophan metabolism 29 40 0.688 15 5 0.222 22 17 0.364
Phenylalanine, tyrosine and
KO00400 33 34 0.611 24 7 0.188 23 20 0.571
tryptophan biosynthesis
KO00410 beta-Alanine metabolism 20 30 0.800 17 8 0.300 20 22 0.667
57

KO00450 Selenoamino acid metabolism 24 25 0.643 15 6 0.250 17 10 0.556
KO00460 Cyanoamino acid metabolism 16 16 0.875 12 5 0.143 10 6 0.500
KO00480 Glutathione metabolism 45 53 0.813 25 16 0.571 31 27 0.667
KO00500 Starch and sucrose metabolism 83 76 0.808 55 23 0.429 54 36 0.684
KO00510 N-Glycan biosynthesis 34 37 0.667 33 15 0.296 32 26 0.560
Amino sugar and nucleotide
KO00520 78 73 0.833 47 20 0.476 49 39 0.722
sugar metabolism
KO00561 Glycerolipid metabolism 32 30 0.471 29 5 0.357 28 18 0.375
KO00562 Inositol phosphate metabolism 29 31 0.769 18 10 0.500 18 12 0.750
KO00564 Glycerophospholipid metabolism 46 38 0.542 34 9 0.389 33 12 0.474
KO00620 Pyruvate metabolism 56 79 0.762 44 24 0.529 49 46 0.650
Glyoxylate and dicarboxylate
KO00630 33 28 0.818 18 15 0.636 19 15 0.700
metabolism
KO00640 Propanoate metabolism 17 31 0.889 18 9 0.364 22 25 0.667
KO00650 Butanoate metabolism 26 22 0.667 18 12 0.556 28 14 0.545
KO00670 One carbon pool by folate 14 15 0.778 18 12 0.571 12 8 0.429
Carbon fixation in photosynthetic
KO00710 71 80 0.773 18 32 0.750 56 58 0.895
organisms
Pantothenate and CoA
KO00770 17 14 0.583 18 7 0.400 15 7 0.444
biosynthesis
Porphyrin and chlorophyll
KO00860 35 31 0.714 18 8 0.240 34 21 0.500
metabolism
KO00900 Terpenoid backbone biosynthesis 38 36 0.750 18 9 0.222 33 20 0.684
KO00906 Carotenoid biosynthesis 17 15 0.615 18 3 0.182 18 5 0.250
KO00910 Nitrogen metabolism 29 42 0.789 18 23 0.500 22 15 0.700
KO00920 Sulfur metabolism 18 14 0.444 18 2 0.400 14 5 0.833
KO00940 Phenylpropanoid biosynthesis 45 52 0.786 18 14 0.375 20 16 0.625
KO00970 Aminoacyl-tRNA biosynthesis 51 47 0.778 18 12 0.375 34 16 0.409
Biosynthesis of unsaturated fatty
KO01040 24 18 0.778 18 14 0.778 26 19 0.889
acids
21 23 22 23
KO03010 Ribosome 0.707 18 0.684 218 0.712
2 6 4 0
KO03018 RNA degradation 50 63 0.643 18 12 0.237 39 20 0.419
KO03020 RNA polymerase 35 22 0.720 18 12 0.400 27 14 0.632
KO03022 Basal transcription factors 26 19 0.550 18 6 0.188 16 9 0.462
KO03030 DNA replication 37 34 0.690 18 4 0.125 23 11 0.368
11
KO03040 Spliceosome 99 0.656 18 37 0.292 93 43 0.443
7
KO03050 Proteasome 61 70 0.829 18 58 0.800 56 54 0.758
KO03060 Protein export 42 37 0.680 18 23 0.524 34 22 0.500
KO03410 Base excision repair 35 21 0.480 18 1 0.059 20 6 0.200
KO03420 Nucleotide excision repair 45 41 0.600 18 7 0.185 26 16 0.421
KO03430 Mismatch repair 26 26 0.650 18 3 0.118 15 7 0.364
KO03440 Homologous recombination 24 21 0.611 18 2 0.083 14 5 0.222
58

Phosphatidylinositol signaling
KO04070 26 52 0.727 18 17 0.556 11 18 0.500
system
KO04120 Ubiquitin mediated proteolysis 81 87 0.653 18 42 0.319 60 53 0.475
SNARE interactions in vesicular
KO04130 26 30 0.824 18 12 0.600 20 17 0.889
transport
Protein processing in 10 11
KO04141 0.632 18 61 0.446 110 78 0.537
endoplasmic reticulum 6 2
KO04144 Endocytosis 54 78 0.793 18 24 0.385 35 37 0.556
KO04145 Phagosome 59 96 0.963 18 66 0.870 43 66 0.952
KO04146 Peroxisome 52 46 0.621 18 15 0.250 43 24 0.458
KO04626 Plant-pathogen interaction 59 42 0.250 18 27 0.231 52 41 0.450
Natural killer cell mediated
KO04650 16 26 0.750 18 15 0.750 16 22 1.000
cytotoxicity
59

Supplementary Table 9 Predicted non-coding RNA genes.
Supplementary Table 9a Summary of tRNA genes identified in maize (Z. ma), rice
(O. sa), sorghum (S. bi), Brachypodium (B. di), bamboo (P. he), and Arabidopsis (A.
th).
Z.ma O.sa S.bi B.di P.he A.th
tRNAs decoding Standard 20 AA 1,413 720 535 593 1,076 685
Selenocysteine tRNAs (TCA) 4 0 1 0 6 0
Possible suppressor tRNAs (CTA,TTA) 7 0 1 0 1 0
tRNAs with undetermined/unknown
14 0 8 7 2 1
isotypes
Predicted pseudogenes 768 26 61 15 82 13
Total tRNAs 2,206 746 606 615 1,167 699
Supplementary Table 9b Conserved non-coding RNA genes in the moso bamboo

genome.
Average length Total length

ncRNA Type Loci # % of genome
(bp) (bp)
tRNA 1,167 75 87,363 0.0043
rRNA 279 714 199,180 0.0097
SnoRNA 321 118 37,985 0.0019
C/D box 277 123 34,025 0.0017
H/ACA 44 90 3,960 0.0002
snRNA 173 140 24,248 0.0019
miRNA 225 114 25,748 0.0013
60

Supplementary Table 9c Prediction of microRNA target genes. The
INFERNAL-predicted miRNAs were aligned to the bamboo gene models by Blastn
with e-value at 1e-10. The microRNAs with were clustered into the different families
according to outputs of the INFERNAL prediction against Rfam database. The
functional domain of each gene was searched by InterproScan against pfam
database.
MicroRNA
Bamboo microRNA ID Target gene Pfam
family
PH01000002G1660 PF03110 SBP
PH01000050G0170 PF03110 SBP
PH01000095G1560 PF03110 SBP
PH01000117G1390 PF03110 SBP
PH01000043m01 PH01000145G0070 Unknown
PH01000118m01 PH01000150G0460 PF03110 SBP
PH01000586m01 PH01000164G0630 PF03110 SBP
PH01000780m01 PH01000176G0670 PF03110 SBP
PH01000906m01 PH01000300G1120 PF04499 SAPS
PH01000906m02 PH01000327G0270 PF02518 HATPase_c; PF00183 HSP90
PH01000906m03 PH01000450G0480 PF03110 SBP

mir156
PH01000906m03 PH01000457G0590 PF00076 RRM_1; PF00398 RrnaAD
PH01001039m01 PH01000548G0580 Unknown
PH01001164m01 PH01000594G0440 Unknown
PH01001488m01 PH01000770G0270 PF03110 SBP
PH01001488m02 PH01000969G0180 PF03110 SBP
PH01001488m03 PH01001337G0400 PF00450 Peptidase_S10
PH01002501m01 PH01002673G0070 PF03110 SBP
PH01002789G0180 PF03110 SBP
PH01003178G0220 PF03110 SBP
PH01003773G0220 PF03110 SBP
PH01007654G0010 PF03110 SBP
PH01000345G0790 PF00072 Response_reg; PF06203 CCT

PH01000564G0790 PF00085 Thioredoxin
PH01000077m01
PH01000630G0430 PF00085 Thioredoxin
PH01000130m01
MIR159 PH01001806G0140 PF06424 PRP1_N
PH01000257m01
PH01003596G0230 Unknown
PH01001252m01
PH01003618G0130 PF00072 Response_reg; PF06203 CCT
PH01005144G0100 PF07690 MFS_1
PH01000093m01 PH01000044G0540 PF02362 B3; PF06507 Auxin_resp
PH01000264m01 PH01000069G1210 PF06507 Auxin_resp

mir160
PH01000290m01 PF04539 Sigma70_r3; PF04542 Sigma70_r2;
PH01000138G0430
PH01000323m01 PF04545 Sigma70_r4
61

PH01000331m01 PF02309 AUX_IAA; PF02362 B3; PF06507
PH01000305G0690
PH01000483m01 Auxin_resp
PH01000702m01 PF00856 SET; PF02182 YDG_SRA; PF05033
PH01000556G0480
PH01001046m03 Pre-SET
PH01002185m01 PF00168 C2; PF01412 ArfGap; PF02362 B3;
PH01000845G0410
PF06507 Auxin_resp
PF02309 AUX_IAA; PF02362 B3; PF06507

PH01001026G0300
Auxin_resp
PH01001175G0060 PF03552 Cellulose_synt
PH01001285G0430 PF02362 B3; PF06507 Auxin_resp
PF02309 AUX_IAA; PF02362 B3; PF06507

PH01002498G0280
Auxin_resp
PF02309 AUX_IAA; PF02362 B3; PF06507

PH01002685G0120
Auxin_resp
PF00892 EamA; PF03151 TPT; PF03188

PH01004610G0130
Cytochrom_B561
PH01000041G2170 PF02365 NAM

PH01000057G1650 PF00642 zf-CCCH; PF00013 KH_1
PH01000093G0340 PF02365 NAM

PH01000110G0680 PF02365 NAM
PH01000183G1320 PF02365 NAM
PH01000210m01
MIR164 PH01000483G1000 PF02365 NAM
PH01000543m01
PH01000501G0450 PF02365 NAM
PH01001122G0430 PF00070 Pyr_redox; PF02852 Pyr_redox_dim

PH01001309G0120 PF02365 NAM
PH01002276G0270 PF02365 NAM
PH01000070G2000 PF05071 NDUFA12
PF00327 Ribosomal_L30; PF08079

PH01000152G1310
Ribosomal_L30_N
PH01000015m01
PF00327 Ribosomal_L30; PF08079
MIR167_1 PH01010914m01 PH01000224G0820
Ribosomal_L30_N
PH01254050m01
PH01001042G0370 PF00664 ABC_membrane; PF00005 ABC_tran
PH01001940G0210 PF00337 Gal-bind_lectin; PF01762 Galactosyl_T

PH01002304G0040 PF00294 PfkB
PH01000280m01 PH01000003G4150 PF04844 DUF623

MIR168
PH01000585m01 PH01000004G2090 PF10369 ALS_ss_C
62

PH01000008G2140 PF01426 BAH; PF00403 HMA; PF05641 Agenet
PH01000009G2100 PF03106 WRKY

PH01000017G1630 PF00225 Kinesin; PF11721 Malectin
PH01000026G0210 PF08417 PaO; PF00355 Rieske

PH01000028G2550 PF07690 MFS_1
PH01000036G1230 PF00069 Pkinase
PH01000069G1200 PF02630 SCO1-SenC
PH01000164G0270 PF01554 MatE

PH01000197G0530 PF00185 OTCace; PF02729 OTCace_N

PH01000223G0540 PF05003 DUF668; PF11961 DUF3475
PH01000224G0730 PF00125 Histone
PH01000352G0040 PF00155 Aminotran_1_2
PH01000356G0540 PF10447 EXOSC1

PH01000358G0390 PF00249 Myb_DNA-binding
PH01000358G0650 PF00612 IQ
PH01000361G0710 PF02576 DUF150
PH01000367G0560 PF01985 CRS1_YhbY
PH01000367G0850 PF04755 PAP_fibrillin
PH01000433G0520 PF00400 WD40

PF00278 Orn_DAP_Arg_deC; PF02784

PH01000439G0060
Orn_Arg_deC_N
PH01000448G0580 PF00010 HLH
PF02134 UBACT; PF00899 ThiF; PF10585

PH01000538G0570
UBA_e1_thiolCys
PH01000542G0140 PF01501 Glyco_transf_8; PF00403 HMA
PH01000603G0510 PF00201 UDPGT

PH01000623G0580 PF03081 Exo70
PH01000666G0100 PF00271 Helicase_C; PF09369 DUF1998
PH01000695G0190 PF03083 MtN3_slv
63

PH01000698G0590 PF01842 ACT
PH01000735G0110 PF03106 WRKY

PH01000780G0490 PF05703 DUF828; PF08458 PH_2
PH01000795G0520 PF01565 FAD_binding_4; PF08031 BBE

PH01000842G0630 PF01535 PPR
PH01000875G0370 PF02836 Glyco_hydro_2_C; PF05282 AAR2
PH01000890G0140 PF00481 PP2C
PH01000895G0460 PF00004 AAA
PH01001004G0250 PF10998 DUF2838

PH01001065G0050 PF10288 DUF2392
PH01001117G0310 PF02701 zf-Dof
PH01001135G0080 PF05770 Ins134_P3_kin

PH01001175G0340 PF00097 zf-C3HC4
PH01001188G0490 PF01486 K-box

PH01001262G0230 PF01501 Glyco_transf_8
PH01001528G0340 PF00226 DnaJ

PH01001760G0230 PF03690 UPF0160
PH01001874G0080 PF00076 RRM_1; PF00098 zf-CCHC

PH01001896G0320 PF00076 RRM_1
PH01001979G0270 PF01106 NifU
PH01002232G0310 PF02540 NAD_synthase
PH01002235G0180 PF01163 RIO1

PH01002316G0200 PF00650 CRAL_TRIO; PF03765 CRAL_TRIO_N
PH01002375G0200 PF00069 Pkinase

PH01002439G0150 PF01535 PPR
PH01002529G0110 PF04570 DUF581
PH01002705G0160 PF01762 Galactosyl_T

PH01003170G0110 PF03106 WRKY
PH01003422G0190 PF01926 MMR_HSR1; PF06071 YchF-GTPase_C
PH01003917G0020 PF01535 PPR
PH01004682G0110 PF02686 Glu-tRNAGln

64

PH01004719G0070 PF04597 Ribophorin_I
PF02309 AUX_IAA; PF02362 B3; PF06507

PH01005322G0010
Auxin_resp
PH01007546G0020 PF07719 TPR_2
PH01262640G0010 PF01171 ATP_bind_3

MIR169_2 PH01000450m01 PH01000148G1100 PF00091 Tubulin; PF12327 FtsZ_C
PH01000117m01 PH01000006G0960 Unknown
PH01000117m02 PH01000235G0700 Unknown

MIR169_5
PH01001476m01 PH01000463G1100 Unknown
PH01002131m01 PH01000752G0210 Unknown
PH01000027G2350 PF00847 AP2
PH01000095G1440 PF00171 Aldedh
PH01000123G0110 PF00171 Aldedh

PH01000170G1390 PF03514 GRAS
PH01000169m01 PH01000229G1370 PF02681 DUF212
PH01000366m01 PH01000498G0680 PF00310 GATase_2; PF01380 SIS
PH01000390m01 PH01000666G0830 PF08389 Xpo1
MIR171_1 PH01001439m01 PH01000770G0710 Unknown

PH01003493m01 PH01000850G0320 Unknown
PH01003786m01 PH01001577G0130 PF03514 GRAS
PH01004538m01 PH01001692G0030 PF03514 GRAS
PH01001780G0280 PF00931 NB-ARC

PH01002325G0040 PF03514 GRAS
PH01002597G0150 PF12214 TPX2_importin
PF08030 NAD_binding_6; PF01794 Ferric_reduct;

PH01000464G0470
PF08414 NADPH_Ox
PF08022 FAD_binding_8; PF08030
PH01004540m01 PH01000596G0230 NAD_binding_6; PF01794 Ferric_reduct; PF08414
MIR171_2 PH01000211m01 NADPH_Ox
PH01000200m01 PH01001043G0440 PF00069 Pkinase
PH01002279G0010 PF03070 TENA_THI-4
PH01003904G0030 PF01535 PPR
PH01000021m01 PH01000052G2050 Unknown

mir172 PH01000466m01 PH01000097G0900 PF00646 F-box
PH01004738m01 PH01000127G0210 Unknown
PH01000213G0510 PF00646 F-box
65

PH01002138G0280 PF00067 p450
PH01002747G0060 PF05450 Nicastrin
PH01003375G0030 PF04859 DUF641
PH01005644G0020 PF00646 F-box

PH01000314G0270 PF00078 RVT_1; PF00789 UBX; PF08284 RVP_2
PH01000607G0360 PF00026 Asp; PF05184 SapB_1; PF10551 MULE
PF03463 eRF1_1; PF03464 eRF1_2; PF03465

PH01000669G0280
eRF1_3
PH01000853G0290 PF03637 Mob1_phocein
PH01000021m01 PH01001115G0420 Unknown

mir395 PH01000466m01 PF00560 LRR_1; PF08263 LRRNT_2; PF00069
PH01001142G0220
PH01004738m01 Pkinase
PF00026 Asp; PF05184 SapB_1; PF03489
PH01001208G0380
SapB_2
PH01001821G0330 PF05703 DUF828
PH01003316G0070 PF03637 Mob1_phocein

PH01000010G1850 PF03016 Exostosin
PH01000157G1010 PF03016 Exostosin


PH01004613m01
PH01001655G0500 PF00566 TBC
PH01000814m01
mir399 PH01002153G0330 Unknown
PH01000429m01
PH01002839G0140 PF04116 FA_hydroxylase; PF12076 Wax2_C
PH01000000m01
PH01004857G0110 PF00566 TBC
PH01006818G0010 PF12076 Wax2_C
PH01000095G1560 PF03110 SBP

PH01000164G0630 PF03110 SBP
PH01001265m01
PH01000176G0670 PF03110 SBP
PH01001265m02
MIR535 PH01000474G0490 PF03005 DUF231
PH01001768m01
PH01004182m01
PH01000740G0630 PF01255 Prenyltransf

PH01001050G0540 PF04577 DUF563
66

PH01001376G0370 PF01490 Aa_trans
PH01001876G0100 PF00190 Cupin_1; PF08700 Vps51

PH01001940G0250 PF03171 2OG-FeII_Oxy
PH01001963G0380 PF00400 WD40
PH01002134G0090 PF00400 WD40
PH01002190G0080 PF00067 p450

PH01003819G0090 PF00139 Lectin_legB; PF00069 Pkinase
PH01004078G0110 PF00069 Pkinase

PH01007654G0010 PF03110 SBP
PH01000753m01 PH01000272G1270 PF00505 HMG_box
PH01000535m01 PH01001058G0400 PF00657 Lipase_GDSL

MIR821
PH01000378m01 PH01001316G0020 PF03110 SBP
PH01003487m01
67

Supplementary Table 10 Statistics of Repetitive sequences.
Supplementary Table 10a Repetitive sequences in the moso bamboo genome.
Length Percentage of
occupied (bp) sequences
Class I elements (Retroelements) 790,027,115 0.385
LTR Retrotransposons 764,632,374 0.373
LTR/Copia 251,526,442 0.123
LTR/Gypsy 505,181,075 0.246
unclassified LTR 7,924,857 0.004
non-LTR Retrotransposons 24,526,904 0.012
LINE 23,701,208 0.012
SINE 825,696 0.000
unclassified retrotransposons 867,837 0.000
Class II elements (DNA Transposons) 194,238,269 0.095
DNA Transposons 176,524,830 0.086
DNA/En-Spm 74,871,248 0.036
DNA/hAT 26,546,823 0.013
DNA/MuDR 73,460,366 0.036
DNA/Harbinger 1,646,393 0.001
MITEs 7,356,902 0.004
DNA/TcMar-Stowaway 3,209,627 0.002
DNA/Tourist 4,147,275 0.002
RC/Helitrons 3,241,423 0.002
unclassified transposons 7,115,114 0.003
Unknown repeats 226,597,546 0.110
Total transposable elements 1,210,862,930 0.590
Low_complexity 1,130,281 0.001
68

Supplementary Table 10b Comparison of TEs with highest copies among moso bamboo, rice, and sorghum.
Bamboo Rice Sorghum
Repeat ID Class of TE-element Copies Repeat ID Class of TE-element Copies Repeat ID Class of TE-element Copies
PH01R6F001124 LTR/Gypsy 20,624 WANDERER_OS DNA/Tourist 8,531 TSB1 Harbinger 20,984
PH01R1F000001 DNA/En-Spm 16,987 STOWAWAY41_OS DNA/TcMar-Stowaway 5,821 Tourist1a_SB Harbinger 7,731
PH01R3F000573 DNA/En-Spm 16,918 Gaijin DNA/Tourist 4,986 Copia-141_SB-LTR Copia 7,430
PH01R1F000000 DNA/En-Spm 15,691 STOWAWAY47_OS DNA/TcMar-Stowaway 4,518 ATHILA-1_SBi-LTR Gypsy 6,810
PH01R6F000783 Unknown 13,094 STOWAWAY1_OS DNA/TcMar-Stowaway 4,445 Gypsy-133_SBi-LTR Gypsy 5,863
PH01R5F002220 LTR/Gypsy 12,658 SEVERIN-2 RC/Helitron 4,260 Gypsy-122_SBi-LTR Gypsy 5,802
PH01R1F000002 LTR/Gypsy 11,637 TREP215 DNA/TcMar-Stowaway 4,142 TSB2 Harbinger 5,720
PH01R5F002786 LTR/Copia 10,725 Explorer DNA 3,854 Gypsy-125_SBi-LTR Gypsy 5,482
PH01R5F002970 LTR/Gypsy 9,602 STOWAWAY2_OS DNA/TcMar-Stowaway 3,671 Gypsy-127_SBi-LTR Gypsy 5,337
PH01R6F002209 LTR/Gypsy 9,446 SINE03_OS SINE 3,507 Gypsy-125_SBi-I Gypsy 5,002
69

Supplementary Table 10c Comparison of TEs occupying most genome size among the moso bamboo, rice, and sorghum.
Bamboo Rice Sorghum
Occupied Occupied Occupied

Class of Class of Class of
Repeat ID Copies genome Repeat ID Copies genome Repeat ID Copies genome
TE-element TE-element TE-element
size (bp) size (bp) size (bp)
PH01R6F001124 LTR/Gypsy 20624 21071416 SPMLIKE DNA/En-Spm 2150 6292696 Gypsy-122_SBi-I Gypsy 4366 27222661
PH01R5F003093 LTR/Gypsy 6366 16535123 RETRO2_I LTR/Gypsy 628 3846962 Gypsy-133_SBi-I Gypsy 4979 17779891
PH01R6F002209 LTR/Gypsy 9446 15516557 RIRE2_I LTR/Gypsy 758 3498738 Gypsy-121_SBi-I Gypsy 3137 14031073
PH01R1F000002 LTR/Gypsy 11637 12906984 RIRE3_LTR LTR/Gypsy 1956 3338048 ATHILA-1_SBi-I Gypsy 4976 11493996
PH01R6F000836 LTR/Copia 7388 12860851 ATLANTYS-I_OS LTR/Gypsy 1086 3215554 Gypsy-136_SBi-I Gypsy 3917 10004929
PH01R5F002786 LTR/Copia 10725 12543585 TRUNCATOR LTR/Gypsy 1755 2952995 ATHILA-1_SBi-LTR Gypsy 6810 8641228
PH01R6F004818 LTR/Gypsy 4337 12059267 RIRE3A_LTR LTR/Gypsy 2301 2796270 Gypsy-125_SBi-I Gypsy 5002 8122387
PH01R6F002298 LTR/Gypsy 6746 11580121 SZ-7_int LTR/Gypsy 693 2394637 Gypsy-128_SBi-LTR Gypsy 2820 7778326
PH01R5F002220 LTR/Gypsy 12658 10774197 TRUNCATOR2_OS LTR/Gypsy 2411 2356738 Gypsy-122B_SBi-I Gypsy 2366 7355980
PH01R1F000015 LTR/Copia 6969 9936341 RIREX_I LTR/Gypsy 967 2179712 ATHILA-3_SBi-I Gypsy 3267 7080252
70

Supplementary Table 11 Mean Ks and divergence time for the bamboo versus grass
species. Mean Ks and divergence time between the bamboo and fully sequenced
grass species were calculated from the Ks distribution of obtainned 968 single-copy
gene families. Calculation of Ks were performed by MA model that averages
parameters across 14 candidate models30. Divergence time were calculted using a
substitution rate of 6.5 × 10-9 mutations per site per year. The Ks of internal
dupliation was estimated by calculating the Ks of the paralogous pair from the
2-member gene clusters, of which the derived divergence time was indicative of the
WGD time.
Divergence
Species Mean Ks
time (mya)
Brachypodium vs.Bamboo 0.610 46.9

1
Wheat vs. Bamboo 0.621 47.8
Rice vs.Bamboo 0.632 48.6
Foxtail millet vs. Bamboo 0.701 53.9
Sorghum vs. Bamboo 0.761 58.5
Maize vs. Bamboo 0.840 64.6
Bamboo internal duplication 0.10 - 0.15 7.7 - 11.5

Maize internal duplication 0.15 - 0.20 11.5 - 15.4
1
The wheat gene models were downloaded at
ftp://ftp.ncbi.nih.gov/repository/UniGene/Triticum_aestivum/.
71

Supplementary Table 12 Change of gene family size in bamboo, with comparison to
different plant genomes. Fields highlighted in green represented the families with
expanding gene number. Fields highlighted in red represented the families with
contracting gene number. The gene families were generated by the OrthoMCL
analysis. The estimation of gene familiy size change was perfromed by a CAFE
calculation with P-value < 0.01.
Family
Description of conserved function domains Phe Bdi Osa Sbi Zma Sit Ath P-value
No.
#4 PF03552 Cellulose_synt,PF01652 IF4E 31 15 23 25 31 27 16 0.005

# 18 PF00931 NB-ARC,PF00560 LRR_1,PF01657 DUF26,PF01419 Jacalin 27 2 39 25 2 30 0 0.000
# 24 PF02364 Glucan_synthase,PF04652 DUF605 18 11 12 12 8 23 12 0.001
# 702 PF00931 NB-ARC 14 0 6 1 0 0 0 0.000
PF00931 NB-ARC,PF00400 WD40,PF02671 PAH,PF03446
# 66 13 0 15 14 8 19 0 0.000
NAD_binding_2
# 43 PF00069 Pkinase 12 9 9 7 11 20 8 0.004
# 451 PF00403 HMA 12 4 3 2 2 1 1 0.009
PF07645 EGF_CA PF02797 Chal_sti_synt_C PF08392
# 82 11 7 12 12 5 15 0 0.000
FAE1_CUT1_RppA PF00069 Pkinase
# 116 PF00931 NB-ARC 11 0 9 13 2 15 0 0.000
# 89 PF00862 Sucrose_synth,PF00534 Glycos_transf_1 9 6 7 3 7 13 6 0.005
# 457 PF00931 NB-ARC 9 1 8 3 0 5 0 0.000
# 98 PF03822 NAF,PF00069 Pkinase 8 5 6 5 6 17 4 0.001
# 125 PF00400 WD40 8 3 3 2 4 12 5 0.001
PF00072 Response_reg,PF02518 HATPase_c,PF00512
# 175 8 3 4 2 7 8 3 0.005
HisKA,PF03924 CHASE
# 285 PF04578 DUF594 8 5 6 5 1 7 0 0.003
# 348 PF00931 NB-ARC 8 2 8 2 1 8 0 0.000
# 109 PF03030 H_PPase 7 4 6 6 8 16 1 0.002
PF04810 zf-Sec23_Sec24,PF04811 Sec23_trunk,PF04815
# 140 7 4 4 4 4 13 5 0.008
Sec23_helical,PF00626 Gelsolin,PF08033 Sec23_BS
# 331 PF00560 LRR_1,PF00931 NB-ARC 7 5 2 9 2 5 0 0.001
# 265 PF02309 AUX_IAA,PF02362 B3,PF06507 Auxin_resp 6 3 3 2 5 9 1 0.009
# 307 PF00560 LRR_1 PF00931 NB-ARC 6 4 8 3 1 9 0 0.001
# 454 PF00931 NB-ARC 6 2 6 8 0 4 0 0.000
# 10664 PF00560 LRR_1 6 0 0 1 0 0 0 0.001
PF01909 NTP_transf_2,PF04926 PAP_RNA-bind,PF04928
# 215 5 3 3 3 3 14 3 0.001
PAP_central
# 243 PF00026 Asp,PF05184 SapB_1,PF03489 SapB_2 5 2 3 1 3 14 3 0.000
# 323 PF00067 p450,PF02298 Cu_bind_like 5 1 3 9 5 7 0 0.004
# 385 PF00560 LRR_1 PF00931 NB-ARC PF00069 Pkinase 5 2 5 3 1 12 0 0.000
# 622 PF01909 NTP_transf_2 4 1 1 1 2 8 1 0.002
72

# 700 PF01428 zf-AN1,PF01754 zf-A20 4 1 2 0 3 6 1 0.003
# 246 PF00067 p450 3 1 2 1 1 10 6 0.002
# 618 PF02896 PEP-utilizers_C PF01326 PPDK_N PF00391 PEP-utilizers 3 1 2 1 2 11 1 0.001
#1 PF00560 LRR_1,PF08263 LRRNT_2,PF00069 Pkinase 30 24 68 44 19 51 5 0.000
#5 PF00139 Lectin_legB,PF00106 adh_short,PF00069 Pkinase 22 28 37 30 23 30 13 0.006
PF00954 S_locus_glycop,PF07714 Pkinase_Tyr,PF01453
#2 19 18 27 28 18 39 26 0.000
B_lectin,PF08276 PAN_2,PF11883
PF00560 LRR_1,PF08263 LRRNT_2,PF00069 Pkinase,PF01280
# 14 15 17 30 21 13 32 5 0.000
Ribosomal_L19e
PF00954 S_locus_glycop,PF01453 B_lectin,PF08276
# 28 15 16 34 15 13 5 1 0.000
PAN_2,PF00069 Pkinase
PF07714 Pkinase_Tyr,PF00202 Aminotran_3,PF11721
# 11 11 6 25 6 8 25 13 0.000
Malectin ,PF00560 LRR_1
PF00954 S_locus_glycop,PF01453 B_lectin,PF08276
# 35 9 11 29 14 5 12 0 0.000
PAN_2,PF00069 Pkinase
# 70 PF00560 LRR_1,PF01464 SLT,PF08263 LRRNT_2 9 9 12 10 4 19 1 0.000
# 74 PF00125 Histone 8 13 10 11 2 1 8 0.000
# 21 PF00271 Helicase_C,PF01535 PPR,PF02365 NAM,PF02466 Tim17 7 7 10 18 7 12 23 0.001
# 126 PF00560 LRR_1,PF00931 NB-ARC 7 16 14 2 0 10 0 0.000
# 96 PF00560 LRR_1,PF00931 NB-ARC 6 14 4 13 3 17 0 0.000
# 122 PF00117 GATase,PF06418 CTP_synth_N 5 5 6 3 5 15 5 0.003
# 108 PF00931 NB-ARC,PF05725 FNIP,PF00560 LRR_1 4 7 12 15 1 14 0 0.000
# 159 PF00128 Alpha-amylase,PF07821 Alpha-amyl_C2 4 3 6 6 4 16 1 0.000
# 197 PF00931 NB-ARC 4 3 12 7 3 9 0 0.000
# 26 PF00560 LRR_1,PF00069 Pkinase 3 12 12 7 3 14 42 0.000
# 71 PF00069 Pkinase 3 4 17 2 8 4 0 0.000
# 131 PF02519 Auxin_inducible 3 1 8 5 3 9 9 0.005
PF00009 GTP_EFTU,PF03143 GTP_EFTU_D3,PF03144
# 138 3 4 4 1 7 16 4 0.000
GTP_EFTU_D2
# 287 PF00931 NB-ARC 3 9 7 4 2 7 0 0.004
# 294 PF07714 Pkinase_Tyr,PF07645 EGF_CA 3 8 7 7 2 5 0 0.002
# 169 PF00931 NB-ARC 2 3 7 6 8 15 0 0.000
# 170 PF07714 Pkinase_Tyr 2 4 12 3 3 3 0 0.010
# 191 PF00232 Glyco_hydro_1 2 2 3 8 4 12 3 0.003
# 205 PF03171 2OG-FeII_Oxy,PF11744 ALMT 2 3 2 3 2 13 5 0.001
# 206 PF04398 DUF538 2 2 9 5 7 13 0 0.000
# 262 PF00854 PTR2 2 3 5 7 3 9 1 0.010
# 313 PF00931 NB-ARC 2 3 5 6 1 12 0 0.000
# 332 PF00931 NB-ARC 2 2 7 5 9 5 0 0.005
# 461 PF02892 zf-BED 2 2 3 6 0 5 1 0.002
# 1316 PF00931 NB-ARC 2 2 7 3 0 3 0 0.004
# 55 PF00560 LRR_1,PF08263 LRRNT_2 1 5 25 6 4 8 18 0.000
PF01107 MP,PF00098 zf-CCHC,PF02160 Peptidase_A3,PF00078
# 68 1 0 12 21 0 3 0 0.000
RVT_1,PF00077 RVP
73

# 106 PF00067 p450 1 10 10 5 3 10 0 0.000
PF00394 Cu-oxidase,PF07731 Cu-oxidase_2,PF07732
# 111 1 10 4 3 4 30 0 0.000
Cu-oxidase_3
# 221 PF00232 Glyco_hydro_1 1 3 5 9 8 2 6 0.007
# 223 PF00891 Methyltransf_2,PF08100 Dimerisation 1 0 7 2 7 3 0 0.000
# 252 PF03330 DPBB_1 1 8 2 5 3 9 0 0.000
# 475 PF00931 NB-ARC 1 1 5 8 2 9 0 0.000
# 556 PF00067 p450 1 1 11 4 2 5 0 0.000
# 678 PF03478 DUF295,PF04493 Endonuclease_5 1 1 2 3 10 3 1 0.001
# 754 PF04578 DUF594 1 2 2 1 0 15 0 0.000
# 755 PF03087 DUF241 1 3 6 4 0 3 0 0.001
# 845 PF02362 B3 1 1 2 12 0 4 0 0.000
# 849 PF04578 DUF594 1 2 3 4 1 9 0 0.001
# 1138 PF00646 F-box 1 2 10 2 0 2 0 0.001
# 1139 PF07714 Pkinase_Tyr,PF07645 EGF_CA,PF08488 WAK 1 3 7 1 1 5 0 0.004
# 1140 PF00646 F-box 1 2 13 1 0 1 0 0.000
# 1536 PF00067 p450 1 3 2 9 1 0 0 0.000
# 2111 PF03088 Str_synth 1 1 3 5 0 4 0 0.001
# 88 PF01593 Amino_oxidase,PF02721 DUF223 0 2 1 2 54 0 0 0.000
# 171 PF05699 hATC 0 0 8 23 0 1 7 0.000
# 222 PF01357 Pollen_allerg_1 0 0 15 6 9 7 0 0.000
# 276 PF03004 Transposase_24 0 2 5 2 19 5 0 0.000
# 295 PF00069 Pkinase 0 8 1 6 8 9 0 0.000
# 333 PF00067 p450 0 2 1 5 1 10 7 0.000
# 335 PF00321 Thionin 0 4 12 1 0 9 4 0.000
# 472 PF00177 Ribosomal_S7 0 5 11 2 3 1 2 0.000
# 473 PF00646 F-box,PF03169 OPT 0 8 5 4 7 2 0 0.000
74

Supplementary Table 13 Gene synteny.
Supplementary Table 13a Statistics of syntenic bamboo loci on the aligned rice
genome
No. of No. of Average gene
Rice syntenic gene syntenic number per
blocks genes block
Chromosome-01 217 2,563 11.8
Chromosome-02 153 1,756 11.5
Chromosome-03 216 2,467 11.4
Chromosome-04 135 1,747 12.9
Chromosome-05 166 1,506 9.1
Chromosome-06 147 1,389 9.4
Chromosome-07 126 1,165 9.2
Chromosome-08 91 812 8.9
Chromosome-12 90 1,586 17.6
sum 1,607 17,735 11.0
Supplementary Table 13b Statistics of syntenic bamboo loci on the aligned sorghum
genome
No. of No. of Average gene
Sorghum syntenic gene syntenic number per
blocks genes block
Chromosome-01 296 3,319 11.2
Chromosome-02 212 1,893 8.9
Chromosome-03 199 2,364 11.9
Chromosome-04 159 1,667 10.5
Chromosome-06 134 1,688 12.6
Chromosome-09 167 1,507 9.0
Chromosome-10 150 1,339 8.9
Sum 1,539 15,746 10.2
Note: A total of 30,379 (94.8% of 31,987) Bamboo loci located on the scaffolds with
length over 50 KB were aligned to the rice and sorghum gene models, respectively.
At least 5 genes are required to call synteny. Within a syntenic gene block, the
maximum number of non-syntenic genes between two adjacent syntenic genes
should be less than 5.
75

Supplementary Table 14 Quantity of cell wall biosynthesis genes in plant genomes.
Supplementary Table 14a Comparison of copy numbers of cellulose synthase (CesA)

and cellulose synthase-like (Csl) genes among grasses, Arabidopsis, and poplar. The
subfamilies CslA, C, D, E, F, G, H, and J were classified by the referenced genes located
on the same clade.
P.he A.th Z.ma B.di S.bi O.sa P.tr
CesA 19 10 20 9 12 11 18
Total 38 29 33 24 37 34 37
CslA 9 8 10 8 8 10 5
CslB 0 6 0 0 0 0 2
CslC 10 5 8 4 6 6 5
CslD 7 6 5 3 5 5 11
Csl
CslE 4 1 2 3 3 3 3
CslF 7 0 7 5 11 8 0
CslG 0 3 0 0 0 0 4
CslH 0 0 0 1 3 2 0
CslJ 1 0 1 0 1 0 2
Supplementary Table 14b Copy number of genes involved in phenylpropanoid and

lignin biosynthetic pathways.
PAL C4H C3H 4CL HCT CCR CCoAOMT CAD F5H COMT
P.he 8 4 3 6 4 3* 2 1 3 1
A.th 4 1 3 4 1 2 1 2 2 1
Z.ma 10 4 2 3 2 1 2 1 2 1
B.di 8 3 1 5 2 2 1 1 2 1
S.bi 9 3 2 5 2 2 1 1 2 1
O.sa 9 4 2 5 2 2 1 1 3 1
P.tr 5 2 3 5 2 7 2 1 4 2
* Two interrupted bamboo CCR genes were not included.
Abbreviation of the encoded proteins: Phenylalanine amonnia lyase (PAL),
Cinnamate-4-hydroxylase (C4H), p-Coumaroyl shikimate 3'-hydroxylase/Coumaroyl
3-hydroxylase (C3H), 4-Coumarate:CoA Ligas (4CL),
Hydroxycinnamoyl-CoA:shikimate/quinate hydroxycinnamoyltransferase (HCT),
Cinnamoyl-CoA reductase (CCR), Trans-caffeoyl-CoA 3-O-methyltransferase
(CCoAOMT), Cinnamyl alcohol dehydrogenase (CAD), Ferulate 5-hydroxylase (F5H),
Caffeic acid 3-O-methyltransferase (COMT).
76

Supplementary Table 15 Expression of cell wall genes in bamboo.
Supplementary Table 15a Gene expression of the CesA subfamilies. The expression
level was shown as the quantified transcript level (RPKM) in the 7 sequenced tissues.
Annotated bamboo Quantified transcript level (RPKM)

loci of CesA
shoot20 shoot50 rhizome root leaf panicle1 panicle2
subfamiy
PH01000018G0380 2 2 16 52 96 46 32
PH01000040G0670 15 13 4 5 2 2 1
PH01000204G0350 39 27 58 115 35 38 15
PH01000357G0340 23 22 9 5 8 6 5
PH01000441G0190 38 33 10 6 4 3 3
PH01000482G0850 27 25 0 3 1 1 0
PH01000536G0710 1 1 2 2 1 2 3
PH01000693G0390 3 1 24 104 125 80 55
PH01000746G0570 3 1 10 43 45 36 19
PH01000905G0290 32 19 17 57 9 10 4
PH01000924G0590 2 0 12 69 64 51 31
PH01001105G0500 23 16 10 22 11 6 2
PH01001146G0100 0 0 0 0 0 1 1
PH01001175G0060 38 28 16 37 8 13 9
PH01001427G0390 47 30 6 8 6 3 2
PH01002002G0290 46 48 46 20 27 26 14
PH01002004G0190 1 1 5 20 28 14 12
PH01002232G0080 8 7 1 3 1 2 0
PH01003000G0020 22 18 16 16 11 9 5
77

Supplementary Table 15b Gene expression of the Csl subfamilies. The expression
level was shown as the quantified transcript level (RPKM) in the 7 sequenced tissues.
Csl Annotated bamboo Quantified transcript level (RPKM)
subfamily loci shoot20 shoot50 rhizome root leaf panicle1 panicle2
PH01000068G1400 18 20 10 5 5 3 2
PH01000135G1390 15 10 15 37 6 5 9
PH01000366G0010 3 2 24 15 4 4 4
PH01000484G0010 9 10 15 6 19 24 16
CslA PH01000926G0020 7 6 2 2 0 0 0
PH01001938G0190 0 0 0 0 0 0 0
PH01002436G0250 124 117 26 17 17 12 5
PH01003149G0030 17 27 8 2 2 4 3
PH01006529G0050 6 6 12 20 13 11 7
PH01000099G1140 5 3 3 4 1 1 0
PH01000155G1560 8 3 0 1 0 0 0
PH01000379G0160 16 13 6 5 10 4 4
PH01000423G0430 7 3 4 9 2 2 2
PH01000523G0700 4 3 4 7 3 2 1
CslC
PH01000883G0140 7 6 6 1 1 1 1
PH01001206G0170 14 13 10 4 21 8 5
PH01001338G0260 22 18 10 1 18 4 1
PH01001674G0100 13 13 6 0 2 0 0
PH01003525G0010 2 3 2 0 1 1 2
PH01000083G1270 24 25 22 14 10 6 5
PH01000246G0240 6 9 5 5 5 4 3
PH01001020G0160 22 24 4 1 1 1 0
CslD PH01001105G0500 23 16 10 22 11 6 2
PH01001695G0020 11 11 3 1 1 1 0
PH01002587G0110 0 0 0 0 0 0 1
PH01002699G0130 0 0 0 0 0 0 0
PH01000699G0390 0 0 1 9 4 4 4
PH01000941G0440 2 2 3 2 13 11 11
CslE
PH01000941G0520 0 0 0 1 87 8 4
PH01001562G0420 2 2 3 7 2 4 3
PH01001344G0180 11 12 16 26 25 13 6
PH01001742G0110 26 16 41 43 31 23 11
PH01001945G0240 0 0 0 0 9 0 0
CslF PH01001945G0320 4 1 49 66 0 0 0
PH01001945G0340 1 0 0 0 0 0 0
PH01002576G0070 0 0 0 0 3 1 1
PH01002576G0110 1 1 3 5 23 7 3
CslJ PH01002763G0260 0 0 0 1 4 9 16
78

Note: The plant cell walls represented the most predominant determinant of overall
form, grow, and development. The younger moso bamboo shoot has fastest growth
speed in the world, which can grow around 4 feet within 24 hours. Our phylogenic
analysis and RNA-seq data revealed gene expansion in CslCs, CslAs, and CesAs and
many duplications involved genes with higher expression in shoot. The CslC has been
identified to encode a xyloglucan glucan synthase to produce β-1-4-glucans
backbone of xyloglucans in primary wall formation31. The CSLA proteins synthesized
β-(1-4)-linked mannan in the cell wall32. The recent study found that some member
of both CslA and CslC subfamily were involved in hemicellulose predominantly in
Golgi membranes33. Correspondingly, the CslA and CslC subfamilies were observed to
have the highest copies among the Csls. So potentially, evolution of CslC and CesA
families were important to formation of bamboo-specific characters in shoot
development.
79

Supplementary Table 16 Gene expression of selected loci with significantly increased transcription level (>2- fold increase, Q-value < 0.001)
in the floral tissues. The involved pathways referenced the function information of the Arabidopsis/rice homologs (TAIR10 and MSU RGAP 6.1)
and conserved domains identified by Interpro. The 7 sequenced tissues were shown as S20 (tip of 20-cm shoot), S50 (tip of 50-cm shoot), RH
(rhizome), RT (root), LF (leaf), P1 (panicle at the early stage), and P2 (panicle at the flowering stage). Only the loci with higher expression in two
or more copies were listed in the table. Table listed the genes carrying clustered conserved function domains (Interpro domains).
Known
Floral genes in
Abbr. homologous Referencing function Interpro domains
bamboo
genes
PH01000032G1740 OsERF334 Drought tolerance
PH01000046G1730
PH01000129G0360
PH01000573G0640 OsAP2-3934 Drought tolerance
PH01000573G0670
PH01001102G0050
PH01001360G0530 IPR001471 Pathogenesis-related
ERF PH01001634G0140 transcriptional factor/ERF, DNA-binding;
PH01001704G0270 IPR016177 DNA-binding, integrase-type
PH01002279G0250
PH01002393G0230
PH01002571G0300
PH01002648G0300
PH01003475G0200
PH01004791G0030
80

PH01000028G1600
PH01000173G1010 OsbZIP2335 Salinity and drought tolerance
PH01000437G0190 OsbZIP2335 Salinity and drought tolerance
IPR004827 Basic-leucine zipper (bZIP)
PH01000682G0190
bZIP transcription factor; IPR011616 bZIP
PH01000811G0380
transcription factor, bZIP-1
PH01001986G0070
PH01000242G0910 OsbZIP4536
PH01000831G0230
CCT/B-box IPR010402 CCT domain
PH01169704G0010
PH01003868G0020
PH01000198G0670 IPR001810 F-box domain, cyclin-like |
F-box
PH01000317G0460 IPR022364 F-box domain, Skp2-like
PH01000610G0210
PH01000383G0320 IPR001005 SANT, DNA-binding;
PH01002069G0200 IPR006447 Myb-like DNA-binding
HTH,
PH01002344G0400 domain, SHAQKYF class; IPR017930
Myb-type
PH01002440G0410 HTH transcriptional regulator, Myb-type,
PH01004165G0090 DNA-binding
PH01000001G0190
PH01000042G1220 IPR001356 Homeobox | IPR003106
homeobox PH01000496G0570 Leucine zipper, homeobox-associated
PH01000922G0150 IPR017970 Homeobox, conserved site
PH01000630G0150
MADS-box PH01001303G0110 IPR002100 Transcription factor,
81

PH01001952G0230 MADS-box
PH01000306G0610 OsMADS14 FMI
PH01002127G0260 OSMADS3 FMI
PH01001188G0490
PH01000053G1650 OsNAC1037
PH01000122G1000 SNAC138 IPR003441 No apical meristem (NAM)
NAC Salinity and drought tolerance
PH01001843G0210 SNAC138 protein
PH01004006G0090 OsNAC1037
PH01000091G0440 SRWD339 Salinity tolerance IPR001680 WD40 repeat | IPR015943
PH01000600G0380 WD40/YVTN repeat-like-containing
WD-40
SRWD539 Salinity tolerance domain | IPR019775 WD40 repeat,
PH01003526G0090
conserved site
YABBY PH01000162G1010 OsYABBY240 FMI IPR006780 YABBY protein
PH01000113G0300 OsDof1223,24 Regulation of FMI
PH01000290G0170
zf-Dof IPR003851 Zinc finger, Dof-type
PH01000323G0330
PH01002061G0210
PH01000015G0220
HSP20 PH01000154G1240 OsHSP17.741 Dought and heat tolerance IPR002068 Heat shock protein Hsp20
PH01000268G0820
82

PH01000543G0160 OsCIPK1542 Defense response
response to heat stress, mechanical
PH01000906G0020 Oshsp18.0-CII43
injury, and salicylic acid
PH01000943G0260
PH01000967G0270 Oshsp2644 Heat and oxidative tolerance
PH01001115G0640 OsHSP17.741 Dought and heat tolerance
PH01001131G0040 Oshsp18.0-CII43
PH01003771G0070 OsHSP17.041 Dought and heat tolerance
PH01004446G0090
PH01172955G0010 Oshsp18.0-CII43
PH01000101G0740
PH01000639G0270 OsHSP71.145
IPR001023 Heat shock protein Hsp70 |
PH01000974G0590 OsHSP71.145
HSP70 Abiotic stress tolerance IPR018181 Heat shock protein 70,
PH01001109G0400 OsHSP71.145
conserved site
PH01001215G0490
PH01001722G0380
PH01000430G0800
PH01001102G0260
IPR001623 Heat shock protein DnaJ,
PH01003393G0080
N-terminal | IPR003095 Heat shock
HSP DnaJ PH01004637G0120
protein DnaJ | IPR018253 Heat shock
PH01035373G0010
protein DnaJ, conserved site
PH01000298G0920
PH01000667G0420
83

PH01000000G3800
PH01000081G0140 OsHSF746
PH01000174G0590 OsHSF746
IPR000232 Heat shock factor (HSF)-type,
PH01000194G0800 OsHsfA2c47
DNA-binding | IPR011991 Winged
HSF PH01000208G0690 OsHSF746 Heat and oxidative tolerance
helix-turn-helix transcription repressor
PH01000314G0470 OsHsfB2b47
DNA-binding
PH01000546G0840 OsHsfA2c47
PH01003169G0070
PH01002606G0040
PH01000207G0510 IPR000823 Plant peroxidase | IPR019793
AT1G30870,
peroxidase PH01004839G0040 Oxidative tolerance Peroxidases heam-ligand binding site |
AT1G4497048
PH01017692G0010 IPR019794 Peroxidase, active site
PH01000279G0080
Dehydrin AT3G5098049 Drought tolerance IPR000167 Dehydrin
PH01001299G0140
PH01001035G0130 IPR001938 Thaumatin,
Thaumatin pathogenesis-related | IPR017949
PH01001519G0090
Thaumatin, conserved site
PH01000010G3140
IPR006121 Heavy metal
HM PH01000689G0270 AT4G1638050 Drought tolerance
transport/detoxification protein
PH01002103G0360
PH01001117G0170
PH01004749G0070 IPR000347 Plant metallothionein, family
MT AT5G0238051 Defense response
PH01001892G0210 15
PH01001967G0220
84

PH01003107G0020
PH01000333G0270
PH01000435G0330
BURP AT5G2561052 Drought tolerance IPR004873 BURP
PH01001626G0090
PH01001648G0010
PH01000021G0560
MIP PH01001074G0010 AT1G0162053 Drought tolerance IPR000425 Major intrinsic protein
PH01001117G0550
Note: description of the abbreviation was listed at the follows: ERF, ethylene-responsive transcriptional factor ; bZIP, Basic-leucine zipper (bZIP)
transcription factor; CCT/B-box, CCT/B-box zinc finger protein; F-box, F-box domain containing protein; HTH myb-type, Helix-turn-helix
transcriptional regulator, Myb-type; Homeobox, Homeobox domain containing protein; MADS-box, Transcription factor, MADS-box; NAC, NAC
domain transcription factor; WD-40, WD-40 repeat family protein; YABBY, YABBY domain containing protein; zf-Dof, dof zinc finger domain
containing protein. HSP20, Heat shock protein Hsp20; HSP70, Heat shock protein Hsp70; HSP DnaJ, Heat shock protein DnaJ; HSF, Heat shock
factor (HSF)-type; Peroxidase, Plant peroxidase; Dehydrin, Dehydrin domain containing proteins; Thaumatin, Thaumatin domain containing
proteins; HM, Heavy metal transport/detoxification protein); MT, Plant metallothionein, family 15; BURP, BURP domain containing proteins; MIP,
Major intrinsic protein.
85

Supplementary Table 17 Insertion of TEs in homologs of CO and FPI genes.
Known floral genes Homologous loci in moso bamboo Insertion of the repeats
in rice and Expression at
Function
Scaffold Position TE type Position‡ flowering
Arabidopsis†
3'-UTR, 390 bp
Transcription PH01000682 157487 - 159283 LINE/L1 very low¶
54 from stop-codon
factor CO (At5g15840) &
PH01005551 14180 - 15803 not detected
CONSTANS Hd-1
intron,
(up-regulation (LOC_Os06g16370)55
PH01002508 56985 - 62300 LTR/Gypsy insertion >4,000 not detected
of FPIs)
bp
promoter, 578 bp
PH01000216 339337 - 340520 LINE/L1 very low
from start-codon
3'-UTR, 456 bp
PH01002091 17501 - 18413 LINE/L1 not detected
from stop-codon
PH01001461 145851 - 156173 LTR/Copia coding region not detected
FT (At1g65480), TSF
intron,
(At4g20370), TFL1
FPIs (floral PH01000257 828385 - 839445 LTR/Gypsy & DNA/En-Spm insertion >8,000 not detected
(At5g03840)56, RCN2
pathway bp
(LOC_Os02g32950)57
integrators) 5'-UTR, 187 bp
& Hd3a PH01002149 213193 - 215000 DNA/TcMar-Stowaway not detected
from start-codon
(LOC_Os06g06320)
promter, 661 bp
PH01000020 1187666 - 1189438 Unclassified TE very low
form start-codon
PH01000089 982699 - 984616 Unclassified TE coding region not detected
near 3'-UTR, 920
PH01000128 233584 - 235378 LTR/Gypsy not detected
bp from
86

stop-codon
promoter, <400
PH01000255 718847 - 720785 Unclassified TE bp from very low
start-codon
intron,
PH01000191 326436 - 332802 DNA/hAT-Tag1 & unclassified TE insertion >5,000 not detected
bp
intron,
PH01000063 1107445 - 1113586 DNA/hAT-Tag1 & DNA/En-Spm insertion >5,000 not detected
bp
promoter, 240 bp
PH01000253 791493 - 793545 Unclassified TE very low
from start-codon
PH01002961 177515 - 178039 LTR/Copia coding region not detected
promter, 457 bp
PH01001126 132864 - 133880 Unclassified TE not detected
form start-codon
PH01002288 8168 - 9361 DNA/TcMar-Stowaway coding region not detected
3'-UTR, 395 bp
PH01001134 281529 - 282416 DNA/MuDR not detected
from stop-codon
PH01003363 146371 - 147247 very low
5'-UTR, 140 bp
from start-codon
promoter, 400 bp
PH01004268 53808 - 55349 DNA/MuDR not detected
from start-codon
PH01003270 154451 - 153545 not detected
PH01001769 121285 - 125158 LTR/Gypsy & DNA/En-Spm coding region not detected
PH01001953 255266 - 256989 LINE/L1 promoter, 500 bp very low
87

from start-codon
promoter, 500 bp
PH01000265 193381 - 195152 LINE/L1 not detected
from start-codon
PH01000019 26402 - 27560 LINE/L1 coding region not detected
ATC (At2g27550)56 &
3'-UTR, 500 bp
BFT (At5g62040)58 PH01000354 535405 - 536549 DNA/MuDR very low
from stop-codon
promoter, 600 bp
from start-codon
MFT (At1g18090)59 No homologs found
TFL2 (At5g17690)60 No homologs found
Ehd1
No homologs found
(LOC_Os10g32600)22
coding region,
PH01000596 810562 - 811503 DNA/hAT-Ac higher in leaf
lost 2 exon
5'-UTR, 20 bp
OsSOC1 PH01000107 455178 - 459374 DNA/hAT-Ac higher in shoot
from start-codon
(LOC_Os03g03070)21
coding region,
PH01000759 371677 - 372787 LTR/Copia very low
lost 2 exon
PH01002152 94108 - 96884 LTR/Gypsy 1st intron higher in shoot and leaf
RFL PH01001425 66798 - 69307 very low
(LOC_Os04g51000)61 PH01000386 696552 - 703389 DNA/hAT-Ac coding region not detected
†
Abbreviations of gene description: CONSTANS (CO), Heading date 1 (Hd-1), FLOWERING LOCUS T (FT), TWIN SISTER OF FT (TSF), BROTHER OF
FT AND TFL2 (TFL1), Reduced Culm Number 2 (RCN2), Heading date-3a (Hd3a), Arabidopsis thaliana CENTRORADIALIS (ATC), BROTHER OF FT
AND TFL1 (BFT), MOTHER OF FT AND TFL1 (MFT), BROTHER OF FT AND TFL2 (TFL2), Early heading date 1 (End1), rice LFY homolog (RFL), and
SUPPRESSOR OF OVEREXPRESSION OF CO 1 (OsSOC1).
88

‡
For the position of repeat insertion, the 3’-UTR (3’-untranslated region), 5’-UTR, and promoter regions were estimated according to the
analysis of the bamboo full-length cDNAs when the end of the gene model was not supported by the full-length cDNA. The estimated 3-UTR
length was set at less than 500 bp from stop-codon, 5’-UTR less 250 bp from start-codon, and promoter region at over 250bp upstream of
start-codon.
¶ Very low meant RPKM less than 5.
89

Supplementary Table 18 Quantified transcription levels of bamboo genes with homologs of Arabidopsis floral genes.
Identified RPKM
Homologs in
genes in Abbreviation† Function
bamboo S20 S50 RH RT LF P1 P2
Arabidopsis
AT4G24540, PH01000038G1550 9 9 4 21 2 3 2
AGL24, SVP Regulator of FPI/FMI
AT2G2254062 PH01000437G0930 72 71 52 36 26 11 10
AT2G2755063, PH01001134G0390 0 0 0 0 0 0 0
AT5G6204058, ATC, BFT, TFL1 FPI PH01002570G0010 4 2 0 0 0 0 0
AT5G0384064 PH01003363G0220 0 1 0 0 0 0 0
PH01000029G1950 2 1 1 0 1 0 1
AT5G0610065 ATMYB33 Regulator of FPI/FMI
PH01000009G0060 2 2 1 1 2 1 7
PH01000263G1210 6 4 1 2 5 3 1
AT4G0892066, PH01000968G0540 8 6 3 2 4 4 4
CRY1, CRY2 Photoperiod pathway
AT1G0440067 PH01002304G0120 4 3 4 4 3 1 1
PH01002373G0140 3 2 1 1 3 2 1
PH01001266G0500 20 32 19 7 7 8 6
AT4G2214068 EBS Regulator of FPI/FMI PH01001406G0500 12 14 3 1 1 6 5
PH01002328G0250 9 12 0 0 0 0 0
PH01000364G0790 2 3 2 1 2 1 1
Autonomous
AT4G1588069 ESD4 PH01000526G0230 8 12 9 7 7 5 7
pathway
PH01001219G0240 6 7 10 5 7 4 6
PH01002213G0250 9 9 2 2 3 3 5
AT1G6805070 FKF1 Photoperiod pathway PH01002958G0010 11 9 6 16 7 10 22
PH01007024G0030 15 15 6 6 9 6 7
90

PH01000114G1110 11 12 6 4 6 5 5
PH01000836G0340 9 7 3 9 6 12 16
PH01000025G1210 11 10 9 9 3 7 8
Autonomous PH01000171G0620 158 175 157 133 76 76 75
AT3G0461071 FLK
pathway PH01000280G1350 3 1 5 2 4 3 6
PH01001197G0230 3 4 4 3 1 1 1
PH01000002G4150 2 1 6 2 9 15 18
AT5G2486072 FPF1 Gibberellin pathway PH01001317G0310 0 0 0 2 5 1 2
PH01002809G0210 13 10 10 16 0 18 47
Autonomous
AT4G0065073 FRI PH01000371G0250 2 1 3 1 2 2 4
pathway
AT1G6548074, PH01002288G0050 0 0 0 0 1 0 0
FT,TSF FPI
AT4G2037075 PH01000020G1780 0 0 0 0 1 1 1
Autonomous PH01000048G0850 42 35 37 17 21 14 10
AT2G1952076 FVE
pathway PH01000241G0710 56 52 93 38 57 39 28
AT4G0278077 GA1 Gibberellin pathway PH01000557G0660 4 3 2 2 3 6 4
PH01004823G0070 3 1 2 1 1 1 2
AT1G14920,
PH01143550G0010 0 0 0 0 0 0 0
AT2G01570,
GAI,RGA,RGL78-80 Gibberellin pathway PH01190367G0010 25 33 9 10 3 4 9
AT1G66350,
PH01000142G0910 27 40 92 60 19 33 65
AT3G03450
PH01000254G0530 0 0 0 0 0 0 0
PH01001316G0350 4 3 3 2 6 8 10
AT3G05120, PH01002734G0310 3 3 1 0 3 2 4
Gar81 Gibberellin pathway
AT5G27320 PH01000068G0090 8 6 65 6 2 2 4
PH01000068G0120 0 0 3 1 0 0 1
91

AT2G3981082 HOS1 Gibberellin pathway PH01000750G0240 22 20 12 11 9 7 6
Autonomous
AT4G0256083 LD PH01006816G0010 6 7 6 7 9 7 5
pathway
PH01001819G0320 24 26 19 17 14 13 8
AT1G2554084 PFT1 Photoperiod pathway
PH01002482G0220 22 24 22 25 19 16 15
AT1G09570, PH01000013G2230 11 11 4 1 3 1 2
AT2G18790, PH01000013G2240 8 11 9 3 2 3 2
PHY85 Light-quality pathway
AT4G16250, PH01000222G1330 11 13 4 3 3 3 3
AT4G18130 PH01000606G0390 17 20 2 1 1 2 1
Autonomous PH01000672G0430 11 12 4 4 4 4 2
AT3G1281086 PIE1
pathway PH01001540G0210 7 6 2 1 1 1 1
AT4G2421087 SLY1 Gibberellin pathway PH01000146G1260 11 10 9 5 7 5 7
PH01000616G0020 1 1 0 1 2 1 1
PH01000759G0450 1 0 2 2 3 1 1
AT2G4566088 SOC1 FPI
PH01002152G0120 22 27 5 54 210 9 12
PH01000059G1270 0 1 0 1 5 1 0
PH01000299G0650 24 23 25 12 14 18 15
AT3G1154089 SPY Gibberellin pathway
PH01003018G0160 11 10 9 3 8 7 6
PH01000836G0140 20 18 17 16 22 23 24
PH01001556G0190 4 5 1 0 1 1 0
AT5G5738090, Ambient-temperature
VIN3,VIN3-L PH01000006G3670 4 4 1 1 1 1 1
AT3G2444091 pathway
PH01000258G0590 5 5 6 3 6 4 3
PH01000674G0720 7 7 1 1 0 2 1
92

† Abbreviations of the genes: AGAMOUS-LIKE 24 (AGL24), SHORT VEGETATIVE PHASE (SVP), Arabidopsis thaliana CENTRORADIALIS (ATC),
BROTHER OF FT AND TFL1 (BFT), TERMINAL FLOWER 1 (TFL1), MYB DOMAIN PROTEIN 33 (ATMYB33), CRYPTOCHROME 1 (CRY1),
CRYPTOCHROME 2 (CRY2), EARLY BOLTING IN SHORT DAYS (EBS), EARLY IN SHORT DAYS 4 (ESD4), FLAVIN-BINDING KELCH DOMAIN F BOX
PROTEIN 1 (FKF1), FLOWERING LOCUS KH DOMAIN (FLK), FLOWERING PROMOTING FACTOR 1 (FPF1), FRIGIDA (FRI), FLOWERING LOCUS T (FT),
FVE (FVE), GA REQUIRING 1 (GA1), GA INSENSITIVE (GAI), REPRESSOR OF GA1-3 (RGA), RGA-LIKE (RGL), GAI AN REVERTANT (Gar), HIGH
EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1 (HOS1), LUMINIDEPENDENS (LD), PHYTOCHROME AND FLOWERING TIME 1 (PFT1),
PHYTOCHROME (PHY), PHOTOPERIOD-INDEPENDENT EARLY FLOWERING (PIE), SLEEPY 1 (SLY1), SUPPRESSOR OF OVEREXPRESSION OF
CONSTANS 1 (SOC1), SPINDLY (SPY), VERNALIZATION INSENSITIVE 3 (VIN3), and VERNALIZATION INSENSITIVE 3-LIKE 1 (VIN3-L).
93

Supplementary Table 19 Bamboo floral genes sharing high identities (> 50%) with known rice genes.
Identities
Homologous rice Description of rice Involved
Bamboo gene ID of amino Function
gene gene pathway†
acids
PH01000015G0220 LOC_Os01g04380 OsHSP17.045 0.90 Stress tolerance ABA
PH01000032G1740 LOC_Os01g58420 OsERF44 0.66 Drought tolerance ETH
PH01000053G1650 LOC_Os11g03300 OsNAC1037 0.64 Drought tolerance ABA
PH01000058G1180 LOC_Os01g72530 OsCML3192 0.75 Signal transduction Ca2+ sensor
PH01000068G0660 LOC_Os07g44330 OsPDK193 0.92 Signal transduction GA
PH01000074G0590 LOC_Os02g44235 OsTPP194 0.51 Stress tolerance ABA
PH01000081G0140 LOC_Os03g06630 OsHSF746 0.82 Stress tolerance
PH01000091G0440 LOC_Os03g26870 SRWD339 0.80 Salinity tolerance
PH01000099G1710 LOC_Os01g42860 OCPI195 0.66 Drought tolerance
PH01000111G0850 LOC_Os01g66120 OsNAC6 ; SNAC296 0.82 Stress tolerance ABA
PH01000113G0300 LOC_Os03g07360 OsDof12 23,24 0.80 Regulator of FMI Flowering
PH01000122G1000 LOC_Os03g60080 SNAC138 0.70 Drought tolerance
PH01000154G1240 LOC_Os03g16040 OsHSP17.741 0.54 Drought and heat stress tolerance
PH01000162G1010 LOC_Os03g44710 OsYABBY2; OsYAB240 0.71 FMI
PH01000173G1010 LOC_Os02g52780 OsbZIP2335 0.59 Drought and salinity tolerance ABA
PH01000174G0590 LOC_Os07g08140 OsHsfA2b97 0.62 Heat stress tolerance
PH01000192G1330 LOC_Os04g41540 OsCML2292 0.54 Signal transduction Ca2+ sensor
PH01000194G0800 LOC_Os10g28340 OsHsfA2c47 0.80 Heat and oxidative stress tolerance
PH01000208G0690 LOC_Os03g06630 OsHSF746 0.78 Heat stress tolerance
PH01000222G1190 LOC_Os03g54160 OsMADS14 0.69 FMI Flowering
PH01000242G0910 LOC_Os05g49420 OsbZIP4536 0.78 Reproductive development and stress ABA
94

tolerance
98
PH01000280G1220 LOC_Os02g34560 SRT-5 0.61 Hydrolysis of sucrose
OsClpB-cyt;
PH01000284G0720 LOC_Os05g44340 0.87 Heat stress tolerance
HSP10047
Lignin
PH01000286G0770 LOC_Os02g56460 OsCCR199 0.57 Defense and cell wall biosynthesis
biosynthesis
PH01000298G0570 LOC_Os05g48930 OsGRX17100 0.57 Glutaredoxin
PH01000309G1110 LOC_Os10g36650 OsActin101 0.93 Salinity tolerance ABA
PH01000314G0470 LOC_Os08g43334 OsHsfB2b97 0.54 Heat and oxidative stress tolerance
PH01000344G0730 LOC_Os03g04680 OsCYP96B4102 0.74 Cytochrome P450 Lipid metabolism
PH01000356G0210 LOC_Os10g33250 Wda1103 0.53 Pollen Development
Sugar
PH01000416G0840 LOC_Os03g22120 SUS4104 0.95 Sucrose synthase
metabolism
PH01000437G0190 LOC_Os02g52780 OsbZIP2335 0.59 Salinity and drought tolerance ABA
PH01000491G0570 LOC_Os01g09620 OsDOS105 0.72 Delaying Leaf Senescence
PH01000534G0160 LOC_Os11g02240 OsCIPK1542 0.51 Signal transduction Ca2+ sensor
PH01000546G0830 LOC_Os10g28340 OsHsfA2c47 0.83 Heat stress tolerance
PH01000548G0440 LOC_Os11g35710 OsOSC11; OsIAS1 0.78 Isoarborinol synthase and defense
PH01000573G0640 LOC_Os04g52090 OsAP2-3944 0.53 Drought tolerance ABA/GA
PH01000595G0160 LOC_Os05g04700 OsLti6b106 0.54 Low temperature stress tolerance ABA
PH01000654G0080 LOC_Os03g31300 OsClpB-c107 0.73 Stress tolerance
PH01000664G0490 LOC_Os03g50885 OsActin108 0.88 Drought tolerance ABA
95

PH01000794G0630 LOC_Os01g66120 OsNAC6 ; SNAC296 0.73 Stress tolerance ABA
PH01000845G0420 LOC_Os04g59440 psbS2109 0.67 Absorbed Light Energy PHOTOSYSTEM
PH01000877G0160 LOC_Os08g01330 OsSWN3110 0.52 Secondary Wall Biosynthesis
PH01000906G0020 LOC_Os01g08860 Oshsp18.0-CII43 0.67 Stress tolerance
PH01000967G0270 LOC_Os03g14180 Oshsp2644 0.51 Heat and oxidative stress tolerance
PH01001038G0420 LOC_Os03g60560 ZFP182111 0.65 Salinity and drought tolerance
PH01001115G0640 LOC_Os03g16040 OsHSP17.741 0.80 Drought and heat stress tolerance
PH01001298G0250 LOC_Os07g08840 OsTrx23,OsTRXh1112 0.64 Oxidative stress tolerance ABA
heat stress tolerance and seed
PH01001464G0430 LOC_Os02g28980 rFKBP75113 0.79
development
PH01001546G0030 LOC_Os07g08840 OsTrx23,OsTRXh1112 0.74 Oxidative stress tolerance ABA
OsClpB-cyt;
PH01001726G0230 LOC_Os05g44340 0.92 Heat stress tolerance
HSP10047
PH01001843G0210 LOC_Os03g60080 SNAC138 0.50 Drought tolerance
PH01001888G0390 LOC_Os01g71670 OsGLN2114 0.53 Rice endo-1,3-β-glucanase ABA/GA
OsMADS1115; LHS1;
PH01001952G0190 LOC_Os03g11614 0.54 FMI Flowering
AFO
PH01002127G0260 LOC_Os01g10504 OSMADS3116 0.79 FMI Flowering
heat stress tolerance and seed
PH01002642G0160 LOC_Os02g28980 rFKBP75113 0.55
development
PH01003526G0090 LOC_Os03g26870 SRWD539 0.73 Salinity tolerance
Sugar
PH01003638G0080 LOC_Os04g59550 OsUGT1117 0.83 Sugar transporters
metabolism
96

PH01003771G0070 LOC_Os01g04380 OsHSP17.041 0.89 Drought and heat stress tolerance ABA
PH01004006G0090 LOC_Os11g03300 OsNAC1037 0.53 Drought tolerance ABA
PH01005579G0050 LOC_Os03g49380 OsLOX1118 0.55 Stress tolerance JA
PH01005903G0030 LOC_Os02g08230 OsGL1-2119 0.82 Drought tolerance
PH01006818G0010 LOC_Os10g33250 Wda1103 0.64 Pollen development
† Abbreviation of the pathways: Floral pathways of FMI or FPI (Flowering), abscisic acid pathway (ABA), Gibberellin pathway (GA),
ethylene-responsive pathway (ETH), jasmonic acid pathway (JA).
97

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The draft genome of the fast growing non-timber forest species Moso

Bamboo (Phyllostachys heterocycla)

Nature Genetics: doi:10.1038/ng.2569

Bamboo and the individual subjected to genome sequencing.

Nature Genetics: doi:10.1038/ng.2569

The tissues for the transcriptome sequencing.

Cytogenetic analysis of moso bamboo chromosomes.

Nature Genetics: doi:10.1038/ng.2569

Estimation of genome size of the moso bamboo by the flow cytometry.

Estimation of genome size of the moso bamboo by the frequency of k-mer

BAC and BAC-end sequencing.

Nature Genetics: doi:10.1038/ng.2569

Prediction of protein-coding genes.

Nature Genetics: doi:10.1038/ng.2569

Comparison of parameters of gene models among plant genomes.

Nature Genetics: doi:10.1038/ng.2569

Comparison of the assembled scaffolds to the available moso bamboo sequences

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Identification of gene synteny and whole-genome duplication.

Nature Genetics: doi:10.1038/ng.2569

Annotation of gene function and comparison of fundamental pathways.

Nature Genetics: doi:10.1038/ng.2569

Annotation of conserved non-coding RNA (ncRNA) genes.

Identification of rRNA genes.

Identification of other non-coding RNA genes.

Nature Genetics: doi:10.1038/ng.2569

Reconstruction of phylogeny among 6 fully sequenced grass genomes.

Estimation of divergence time of paralogous pairs.

Nature Genetics: doi:10.1038/ng.2569

Estimation of divergence time between orthologous genes.

Calling of heterozygous SNPs and small indels.

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Supplementary Figure 1 Cytogenetic analysis of bamboo chromosomes. (a)

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569

Supplementary Figure 8 Comparison of gene parameters among fully sequenced

Nature Genetics: doi:10.1038/ng.2569

Nature Genetics: doi:10.1038/ng.2569