New Mitogenomes of the Harnischia Generic Complex (Diptera: Chironomidae) and Their Implication in Phylogenetics
<p>The mitogenome map delineates the distinct mitochondrial genome characteristics of various representative species across three genera within the <span class="html-italic">Harnischia</span> generic complex. The map uses arrows to denote gene transcription direction and employs standard abbreviations for PCGs and rRNAs, along with simplified tRNA notations, for clarity. The second circle displays GC content, revealing nucleotide composition, while the third circle shows GC-skew, highlighting structural asymmetry. The innermost circle summarizes mitogenome length, offering a holistic view of its attributes.</p> "> Figure 2
<p>Evolution rate of 13 PCGs of the subfamily Chironominae in mitogenomes, (<b>a</b>): <span class="html-italic">Harnischia</span> generic complex, (<b>b</b>): other genera within Chironominae. Ka and Ks represent non-synonymous and synonymous nucleotide substitutions, respectively, with their ratio, Ka/Ks, indicating the selection pressure on protein-coding genes (PCGs). The plot’s x-axis shows 13 PCGs, and the y-axis shows Ka/Ks values.</p> "> Figure 3
<p>The assessment of the heterogeneity among the mitogenomes of 29 species belonging to the Chironomidae. This figure highlights the sequence similarities among Protein-Coding Genes (PCGs), amino acid sequences, and ribosomal RNAs (rRNAs) through a visually striking color-coded block representation. Utilizing the AliGROOVE scoring system, we assigned colors from −1 (red, denoting high heterogeneity) to +1 (blue, denoting low heterogeneity). The color scheme is such that lighter shades represent increased genetic variability, and deeper tones suggest reduced heterogeneity.</p> "> Figure 4
<p>Phylogenetic tree of Chironominae, ML tree based on analysis cds_rRNA in Partition.</p> ">
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling and Sequencing
2.2. Assembly, Annotation and Composition Analyses
2.3. Phylogenetic Analyses
Subfamily | Species | GenBank Accession Number | Reference |
---|---|---|---|
Chironominae | Parachironomus demissum | Pending | This study |
Robackia demeijerei | Pending | This study | |
Saetheria tamanipparai | Pending | This study | |
Cladopelma edwardsi | PQ014460 | [5] | |
Cladopelma virescens | PQ014464 | [5] | |
Cryptochironomus maculus | PQ014454 | [5] | |
Cryptochironomus rostratus | PQ014455 | [5] | |
Demicryptochironomus minus | PQ014456 | [5] | |
Demicryptochironomus spatulatus | PQ014457 | [5] | |
Harnischia angularis | PQ014458 | [5] | |
Harnischia turgidula | PQ014459 | [5] | |
Chironomus anthracinus | ON975026 | [47] | |
Chironomus nipponensis | ON975028 | [47] | |
Microchironomus tener | ON975027 | [47] | |
Microchironomus tabarui | MZ261913 | [48] | |
Stenochironomus okialbus | OL753645 | [49] | |
Stenochironomus tobaduodecimus | OL753648 | [49] | |
Endochironomus albipennis | OP950227 | [7] | |
Endochironomus pekanus | OP950219 | [7] | |
Polypedilum yongsanensis | OP950222 | [7] | |
Polypedilum masudai | OK513041 | [7] | |
Stictochironomus akizukii | OP950218 | [7] | |
Stictochironomus juncaii | OP950226 | [7] | |
Microtendipes bimaculatus | PP966953 | NCBI | |
Microtendipes tuberosus | PP966949 | NCBI | |
Orthocladiinae | Cricotopus bicinctus | OP006251 | [29] |
Cricotopus dentatus | OP006255 | [29] | |
Tanypodinae | Tanypus chinensis | PQ014462 | [31] |
Tanypus kraatti | PQ014453 | [31] |
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene Type | Length (bp) | Base Composition (%) | Skew | ||||||
---|---|---|---|---|---|---|---|---|---|
A | T | C | G | A + T | G + C | AT-Skew | GC-Skew | ||
Whole genome | 16,266 | 39.61 | 36.27 | 14.55 | 9.57 | 75.88 | 24.12 | 0.044 | −0.206 |
PCG | 11,216 | 31.28 | 42.73 | 13.45 | 12.54 | 74.00 | 26.00 | −0.155 | −0.035 |
PCG 1st codon position | 3740 | 31.96 | 36.47 | 12.22 | 19.35 | 68.43 | 31.57 | −0.066 | 0.226 |
PCG 2nd codon position | 3738 | 20.99 | 45.57 | 19.93 | 13.51 | 66.56 | 33.44 | −0.369 | −0.192 |
PCG 3rd codon position | 3738 | 40.87 | 46.15 | 8.21 | 4.77 | 87.03 | 12.98 | −0.061 | −0.265 |
ATP6 | 678 | 32.45 | 41.00 | 15.63 | 10.91 | 73.45 | 26.54 | −0.116 | −0.178 |
ATP8 | 168 | 42.86 | 39.88 | 12.50 | 4.76 | 82.74 | 17.26 | 0.036 | −0.448 |
COX1 | 1534 | 28.68 | 37.87 | 17.67 | 15.78 | 66.55 | 33.45 | −0.138 | −0.057 |
COX2 | 688 | 35.03 | 37.79 | 15.12 | 12.06 | 72.82 | 27.18 | −0.038 | −0.113 |
COX3 | 789 | 30.54 | 36.88 | 17.74 | 14.83 | 67.42 | 32.57 | −0.094 | −0.089 |
CYTB | 1137 | 32.63 | 37.03 | 17.77 | 12.58 | 69.66 | 30.35 | −0.063 | −0.171 |
ND1 | 948 | 24.58 | 49.05 | 9.07 | 17.30 | 73.63 | 26.37 | −0.332 | 0.312 |
ND2 | 1026 | 32.46 | 45.42 | 12.87 | 9.26 | 77.88 | 22.13 | −0.166 | −0.163 |
ND3 | 354 | 31.07 | 41.81 | 16.38 | 10.73 | 72.88 | 27.11 | −0.147 | −0.208 |
ND4 | 1341 | 28.34 | 47.35 | 8.58 | 15.73 | 75.69 | 24.31 | −0.251 | 0.294 |
ND4L | 294 | 27.55 | 52.04 | 6.80 | 13.61 | 79.59 | 20.41 | −0.308 | 0.334 |
ND5 | 1734 | 28.43 | 45.50 | 9.69 | 16.38 | 73.93 | 26.07 | −0.231 | 0.257 |
ND6 | 525 | 34.48 | 46.48 | 12.19 | 6.86 | 80.96 | 19.05 | −0.148 | −0.280 |
All rRNA | 2202 | 37.30 | 42.91 | 6.73 | 13.07 | 80.21 | 19.79 | −0.070 | 0.320 |
12S | 807 | 36.68 | 42.38 | 7.43 | 13.51 | 79.06 | 20.94 | −0.072 | 0.290 |
16S | 1395 | 37.92 | 43.44 | 6.02 | 12.62 | 81.36 | 18.64 | −0.068 | 0.354 |
CR | 952 | 47.16 | 43.59 | 7.14 | 2.10 | 90.75 | 9.24 | 0.039 | −0.545 |
Gene Type | Length (bp) | Base Composition (%) | Skew | ||||||
---|---|---|---|---|---|---|---|---|---|
A | T | C | G | A + T | G + C | AT-Skew | GC-Skew | ||
Whole genome | 16,218 | 41.61 | 39.25 | 7.96 | 11.18 | 80.86 | 19.14 | 0.03 | −0.17 |
PCG | 11,220 | 33.22 | 46.16 | 9.90 | 10.72 | 79.38 | 20.62 | −0.16 | −0.04 |
PCG 1st codon position | 3740 | 34.48 | 39.10 | 15.62 | 10.80 | 73.59 | 26.41 | −0.06 | 0.18 |
PCG 2nd codon position | 3740 | 21.61 | 49.13 | 11.69 | 17.57 | 70.74 | 29.26 | −0.39 | −0.20 |
PCG 3rd codon position | 3740 | 43.57 | 50.23 | 2.40 | 3.80 | 93.80 | 6.20 | −0.07 | −0.23 |
ATP6 | 678 | 34.81 | 42.63 | 8.85 | 13.72 | 77.44 | 22.57 | −0.10 | −0.22 |
ATP8 | 168 | 42.86 | 44.64 | 4.17 | 8.33 | 87.50 | 12.50 | −0.02 | −0.33 |
COX1 | 1536 | 32.10 | 37.96 | 14.26 | 15.69 | 70.06 | 29.95 | −0.08 | −0.05 |
COX2 | 684 | 36.11 | 40.50 | 10.38 | 13.01 | 76.61 | 23.39 | −0.06 | −0.11 |
COX3 | 789 | 30.54 | 39.04 | 13.94 | 16.48 | 69.58 | 30.42 | −0.12 | −0.08 |
CYTB | 1137 | 32.81 | 41.07 | 11.17 | 14.95 | 73.88 | 26.12 | −0.11 | −0.14 |
ND1 | 942 | 27.71 | 49.68 | 14.33 | 8.28 | 77.39 | 22.61 | −0.28 | 0.27 |
ND2 | 1029 | 35.28 | 49.17 | 6.22 | 9.33 | 84.45 | 15.55 | −0.16 | −0.20 |
ND3 | 354 | 35.03 | 47.74 | 7.91 | 9.32 | 82.77 | 17.23 | −0.15 | −0.08 |
ND4 | 1338 | 30.64 | 50.07 | 12.33 | 6.95 | 80.71 | 19.28 | −0.24 | 0.28 |
ND4L | 294 | 25.17 | 59.18 | 9.18 | 6.46 | 84.35 | 15.64 | −0.40 | 0.17 |
ND5 | 1737 | 30.63 | 49.45 | 11.46 | 8.46 | 80.08 | 19.92 | −0.24 | 0.15 |
ND6 | 534 | 38.20 | 48.88 | 4.49 | 8.43 | 87.08 | 12.92 | −0.12 | −0.30 |
All rRNA | 2248 | 43.11 | 43.03 | 9.24 | 4.64 | 86.13 | 13.88 | 0.00 | 0.33 |
12S | 854 | 44.03 | 41.57 | 9.37 | 5.04 | 85.60 | 14.41 | 0.03 | 0.30 |
16S | 1394 | 42.18 | 44.48 | 9.11 | 4.23 | 86.66 | 13.34 | −0.03 | 0.37 |
CR | 481 | 48.23 | 48.65 | 1.87 | 1.25 | 96.88 | 3.12 | 0.00 | 0.20 |
Gene Type | Length (bp) | Base Composition (%) | Skew | ||||||
---|---|---|---|---|---|---|---|---|---|
A | T | C | G | A + T | G + C | AT-Skew | GC-Skew | ||
Whole genome | 15,899 | 39.91 | 39.20 | 8.40 | 12.50 | 79.11 | 20.90 | 0.01 | −0.20 |
PCG | 11,220 | 31.60 | 45.80 | 10.44 | 12.16 | 77.40 | 22.60 | −0.18 | −0.08 |
PCG 1st codon position | 3740 | 32.93 | 39.61 | 16.36 | 11.10 | 72.54 | 27.46 | −0.09 | 0.19 |
PCG 2nd codon position | 3740 | 21.07 | 48.39 | 11.91 | 18.63 | 69.46 | 30.54 | −0.39 | −0.22 |
PCG 3rd codon position | 3740 | 40.80 | 49.38 | 3.05 | 6.77 | 90.18 | 9.82 | −0.10 | −0.38 |
ATP6 | 678 | 31.27 | 44.69 | 8.26 | 15.78 | 75.96 | 24.04 | −0.18 | −0.31 |
ATP8 | 168 | 36.90 | 47.02 | 2.98 | 13.10 | 83.92 | 16.08 | −0.12 | −0.63 |
COX1 | 1536 | 30.60 | 38.41 | 14.71 | 16.28 | 69.01 | 30.99 | −0.11 | −0.05 |
COX2 | 684 | 33.48 | 38.89 | 11.99 | 15.64 | 72.37 | 27.63 | −0.07 | −0.13 |
COX3 | 789 | 30.80 | 38.15 | 13.81 | 17.24 | 68.95 | 31.05 | −0.11 | −0.11 |
CYTB | 1137 | 32.10 | 39.58 | 11.70 | 16.62 | 71.68 | 28.32 | −0.10 | −0.17 |
ND1 | 942 | 27.49 | 49.79 | 14.12 | 8.60 | 77.28 | 22.72 | −0.29 | 0.24 |
ND2 | 1029 | 33.53 | 49.37 | 7.00 | 10.11 | 82.90 | 17.11 | −0.19 | −0.18 |
ND3 | 354 | 32.49 | 45.48 | 8.47 | 13.56 | 77.97 | 22.03 | −0.17 | −0.23 |
ND4 | 1338 | 28.48 | 49.25 | 14.72 | 7.55 | 77.73 | 22.27 | −0.27 | 0.32 |
ND4L | 294 | 25.51 | 58.84 | 9.86 | 5.78 | 84.35 | 15.64 | −0.40 | 0.26 |
ND5 | 1737 | 30.69 | 47.55 | 13.07 | 8.69 | 78.24 | 21.76 | −0.22 | 0.20 |
ND6 | 534 | 37.45 | 48.31 | 5.06 | 9.18 | 85.76 | 14.24 | −0.13 | −0.29 |
All rRNA | 2195 | 43.35 | 42.36 | 9.66 | 4.65 | 85.70 | 14.31 | 0.01 | 0.35 |
12S | 785 | 43.57 | 41.66 | 9.81 | 4.97 | 85.23 | 14.78 | 0.02 | 0.33 |
16S | 1410 | 43.12 | 43.05 | 9.50 | 4.33 | 86.17 | 13.83 | 0.00 | 0.37 |
CR | 700 | 40.14 | 55.86 | 1.29 | 2.71 | 96.00 | 4.00 | −0.16 | −0.36 |
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Liu, W.; Tang, Y.; Nie, J.; Yan, H.; Liang, W.; Zhang, Y.; Yan, C. New Mitogenomes of the Harnischia Generic Complex (Diptera: Chironomidae) and Their Implication in Phylogenetics. Diversity 2025, 17, 96. https://doi.org/10.3390/d17020096
Liu W, Tang Y, Nie J, Yan H, Liang W, Zhang Y, Yan C. New Mitogenomes of the Harnischia Generic Complex (Diptera: Chironomidae) and Their Implication in Phylogenetics. Diversity. 2025; 17(2):96. https://doi.org/10.3390/d17020096
Chicago/Turabian StyleLiu, Wenbin, Yaning Tang, Jiaxin Nie, Haoran Yan, Wentao Liang, Yanfei Zhang, and Chuncai Yan. 2025. "New Mitogenomes of the Harnischia Generic Complex (Diptera: Chironomidae) and Their Implication in Phylogenetics" Diversity 17, no. 2: 96. https://doi.org/10.3390/d17020096
APA StyleLiu, W., Tang, Y., Nie, J., Yan, H., Liang, W., Zhang, Y., & Yan, C. (2025). New Mitogenomes of the Harnischia Generic Complex (Diptera: Chironomidae) and Their Implication in Phylogenetics. Diversity, 17(2), 96. https://doi.org/10.3390/d17020096