Phylogenetic and Comparative Analysis of Cryptochironomus, Demicryptochironomus and Harnischia Inferred from Mitogenomes (Diptera: Chironomidae)
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Taxon Sampling and Sequencing
2.2. Assembly, Annotation and Composition Analyses
2.3. Phylogenetic Analyses
3. Results and Discussion
3.1. Mitogenomic Organization
3.2. Protein-Coding Genes, Codon Usage, and Evolutionary Rates
3.3. Phylogenetic Relationships
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | Sample ID | Location | Longitude and Latitude | Data | Collector |
---|---|---|---|---|---|
Cryptochironomus defectus | KTM004 | Tianmu Mountain, Zhejiang, China | 30°31′23″ N; 119°44′59″ E | 29.VII.2011 | Shu-Li Li |
Cryptochironomus sp. | KKH002 | Kaihua, Zhejiang, China | 29°25′00″ N; 118°09′25″ E | 8.VII.2017 | Wei Cao |
Cryptochironomus maculus | WGL002 | Zunyi, Guizhou, China | 28°94′48″ N; 107°88′80″ E | 29.VII.2021 | Wei Cao |
Cryptochironomus rostratus | 2BW005 | Bawangling National Forest Park, Hainan, China | 19°08′86″ N; 109°12′92″ E | 3.IV.2008 | Qian Wang |
Demicryptochironomus minus | WTS110 | Tongren, Guizhou, China | 28°31′73″ N; 109°19′95″ E | 29.VII.2021 | ChunCai Yan |
Demicryptochironomus spatulatus | KJL001 | Kowloon National Wetland Park, Zhejiang, China | 28°39′48″ N; 118°84′58″ E | 5.VIII.2011 | Xiao-Long Lin |
Harnischia angularis | DTH95 | Yueyang, Hunan, China | 28°99′21″ N; 112°89′07″ E | 30.XII.2021 | Fei-Xiang He |
Harnischia turgidula | KTD484 | Taizhou, Zhejiang, China | 28°48′67″ N; 121°89′96″ E | 20.V.2011 | Xing Qi |
Cladopelma edwardsi | KHZ175 | Hangzhou, Zhejiang, China | 30°25′51″ N; 120°14′15″ E | 23.IV.2011 | Xiao-Long Lin |
Cladopelma virescens | XTC002 | Tengchong, Yunnan, China | 25°00′67″N; 98°45′82″E | 23.IV.2018 | Wei Cao |
Species | Whole Genome | PCG | tRNA | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Length (bp) | AT% | AT-Skew | GC% | GC-Skew | Length (bp) | AT% | AT-Skew | GC% | GC-Skew | Length (bp) | AT% | AT-Skew | GC% | GC-Skew | |
Cladopelma edwardsi | 15,662 | 77.55 | 0.036 | 22.45 | −0.211 | 11,220 | 76.36 | −0.186 | 23.64 | −0.049 | 1493 | 79.10 | 0.016 | 20.90 | 14.10 |
Cladopelma virescens | 15,997 | 77.97 | 0.036 | 22.03 | −0.219 | 11,220 | 76.50 | −0.184 | 23.50 | −0.070 | 1483 | 79.16 | 0.014 | 20.84 | 13.92 |
Cryptochironomus defectus | 15,820 | 78.35 | 0.022 | 21.65 | −0.185 | 11,229 | 77.15 | −0.187 | 22.85 | −0.024 | 1495 | 80.27 | 0.023 | 19.73 | 15.25 |
Cryptochironomus sp. | 17,331 | 79.85 | 0.025 | 20.1 | −0.199 | 11,223 | 76.90 | −0.175 | 23.10 | −0.037 | 1491 | 79.54 | 0.037 | 20.46 | 9.51 |
Cryptochironomus maculus | 16,243 | 78.77 | 0.035 | 21.23 | −0.192 | 11,220 | 76.92 | −0.173 | 23.08 | −0.050 | 1494 | 80.19 | 0.030 | 19.81 | 11.49 |
Cryptochironomus rostratus | 17,642 | 80.34 | 0.032 | 19.66 | −0.202 | 11,229 | 77.54 | −0.174 | 22.46 | −0.058 | 1492 | 80.63 | 0.013 | 19.37 | 14.88 |
Demicryptochironomus minus | 15,903 | 79.05 | 0.013 | 20.95 | −0.169 | 11,223 | 77.57 | −0.177 | 22.43 | −0.037 | 1498 | 80.77 | 0.008 | 19.23 | 15.28 |
Demicryptochironomus spatulatus | 16,858 | 78.85 | 0.016 | 21.14 | −0.235 | 11,220 | 76.16 | −0.168 | 23.84 | −0.100 | 1491 | 81.09 | 0.049 | 18.91 | 12.77 |
Harnischia angularis | 15,901 | 78.42 | 0.021 | 21.57 | −0.182 | 11,220 | 76.66 | −0.183 | 23.33 | −0.041 | 1494 | 80.12 | 0.014 | 19.88 | 14.48 |
Harnischia turgidula | 15,942 | 78.34 | 0.028 | 21.66 | −0.195 | 11,220 | 76.73 | −0.183 | 23.27 | −0.053 | 1493 | 80.04 | 0.011 | 19.96 | 13.42 |
Microchironomus tabarui | 15,667 | 76.31 | 0.042 | 23.69 | −0.203 | 11,220 | 74.72 | −0.182 | 25.27 | −0.067 | 1496 | 78.81 | 0.030 | 21.19 | 11.67 |
Microchironomus tener | 15,791 | 77.73 | 0.027 | 22.28 | −0.206 | 11,222 | 75.64 | −0.182 | 24.36 | −0.073 | 1494 | 79.92 | 0.020 | 20.08 | 17.33 |
Endochironomus albipennis | 15,916 | 79.80 | 0.028 | 20.20 | −0.198 | 11,229 | 76.93 | −0.170 | 23.07 | −0.230 | 1497 | 81.56 | 0.030 | 18.44 | 14.49 |
Polypedilum yongsanensis | 16,226 | 77.01 | 0.050 | 22.99 | −0.240 | 11,232 | 73.86 | −0.200 | 26.14 | −0.035 | 1510 | 80.00 | 0.030 | 20.00 | 14.57 |
Species | rRNA | CR | GenBank Accession | Reference | |||||||||||
Length (bp) | AT% | AT-Skew | GC% | GC-Skew | Length (bp) | AT% | AT-Skew | GC% | GC-Skew | ||||||
Cladopelma edwardsi | 2171 | 83.99 | −0.028 | 16.02 | 0.380 | 521 | 94.24 | −0.027 | 5.76 | −0.33 | PQ014460 | This Study | |||
Cladopelma virescens | 2171 | 83.81 | −0.027 | 16.20 | 0.393 | 799 | 94.75 | −0.044 | 5.13 | −0.22 | PQ014464 | This Study | |||
Cryptochironomus defectus | 2200 | 84.21 | −0.003 | 15.79 | 0.386 | 612 | 95.59 | −0.046 | 4.41 | −0.48 | PQ014461 | This Study | |||
Cryptochironomus sp. | 2224 | 84.74 | −0.001 | 15.27 | 0.369 | 2031 | 94.98 | −0.039 | 4.73 | −0.50 | PQ014463 | This Study | |||
Cryptochironomus maculus | 2224 | 84.43 | 0.013 | 15.57 | 0.386 | 893 | 94.85 | 0.020 | 5.16 | −0.43 | PQ014454 | This Study | |||
Cryptochironomus rostratus | 2208 | 84.68 | 0.005 | 15.34 | 0.369 | 2450 | 94.86 | 0.034 | 5.10 | −0.20 | PQ014455 | This Study | |||
Demicryptochironomus minus | 2210 | 84.89 | −0.009 | 15.11 | 0.325 | 656 | 96.34 | −0.089 | 3.66 | −0.08 | PQ014456 | This Study | |||
Demicryptochironomus spatulatus | 2252 | 84.09 | −0.009 | 15.92 | 0.412 | 1334 | 93.25 | −0.122 | 6.60 | −0.36 | PQ014457 | This Study | |||
Harnischia angularis | 2208 | 84.57 | 0.005 | 15.44 | 0.362 | 741 | 96.09 | −0.048 | 3.91 | −0.17 | PQ014458 | This Study | |||
Harnischia turgidula | 2213 | 84.21 | −0.006 | 15.79 | 0.368 | 739 | 94.99 | −0.046 | 5.00 | −0.24 | PQ014459 | This Study | |||
Microchironomus tabarui | 2182 | 84.51 | −0.020 | 15.50 | 0.377 | 548 | 94.71 | −0.044 | 5.29 | −0.38 | MZ261913 | [21] | |||
Microchironomus tener | 2193 | 84.25 | −0.002 | 15.76 | 0.375 | 674 | 95.11 | −0.020 | 4.90 | −0.45 | ON975027 | [20] | |||
Endochironomus albipennis | 2252 | 86.01 | −0.01 | 14.00 | 0.340 | 110 | 98.18 | −0.100 | 1.82 | 1.00 | OP950227 | [19] | |||
Polypedilum yongsanensis | 2288 | 84.88 | −0.02 | 15.12 | 0.353 | 312 | 95.51 | −0.100 | 4.49 | −0.43 | OP950222 | [19] |
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Liu, W.; Wang, C.; Wang, J.; Tang, Y.; Pei, W.; Ge, X.; Yan, C. Phylogenetic and Comparative Analysis of Cryptochironomus, Demicryptochironomus and Harnischia Inferred from Mitogenomes (Diptera: Chironomidae). Insects 2024, 15, 642. https://doi.org/10.3390/insects15090642
Liu W, Wang C, Wang J, Tang Y, Pei W, Ge X, Yan C. Phylogenetic and Comparative Analysis of Cryptochironomus, Demicryptochironomus and Harnischia Inferred from Mitogenomes (Diptera: Chironomidae). Insects. 2024; 15(9):642. https://doi.org/10.3390/insects15090642
Chicago/Turabian StyleLiu, Wenbin, Chengyan Wang, Jingyuan Wang, Yaning Tang, Wenxuan Pei, Xinyu Ge, and Chuncai Yan. 2024. "Phylogenetic and Comparative Analysis of Cryptochironomus, Demicryptochironomus and Harnischia Inferred from Mitogenomes (Diptera: Chironomidae)" Insects 15, no. 9: 642. https://doi.org/10.3390/insects15090642