Characteristics and Comparative Analysis of Six Mitogenomes of Genus Kiefferulus Goetghebuer, 1922 (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 Relationship
3. Results and Discussions
3.1. Mitogenomic Structure
3.2. Protein-Coding Genes, Codon Usage, and Evolutionary Rates
3.3. Phylogenetic Relationships
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | Location | Longitude and Latitude | Elevation (m) | Life Stage | Date | Collector | Accession Number | References |
---|---|---|---|---|---|---|---|---|
Kiefferulus sp.1XL | Namibia, Otjozondjupa | 16.745° E, −22.111° N | 1220 | Adult | 4 December 2018 | Xiaolong Lin | PP884096 | This study |
Kiefferulus brevipalpis | Namibia, Otjozondjupa | 16.745° E, −22.111° N | 1220 | Adult | 4 December 2018 | Xiaolong Lin | PP884099 | This study |
Kiefferulus glauciventris | China, Xishuangbanna | 99.989° E, 22.055° N | 700 | Adult | 6 May 2013 | Xiaolong Lin | PP884098 | This study |
Kiefferulus intertinctus | New Caledonia, Tontouta | 166.206° E, −22.008° N | 10 | Pupa | 11 May 2018 | Nathalie Mary | PP884097 | This study |
Kiefferulus tainanus | China, Guangzhou | 113.959° E, 23.339° N | 149 | Adult | 12 April 2018 | Xiaolong Lin | PP972215 | This study |
Kiefferulus trigonum | China, Huanggang | 115.738° E, 31.095° N | 552 | Adult | 11 July 2021 | Shuang Qiu | PP884095 | This study |
Species | Regions | Length (bp) | A | T | C | G | AT | GC | AT-Skew | GC-Skew |
---|---|---|---|---|---|---|---|---|---|---|
Kiefferulus brevipalpis | Whole genome | 15,767 | 40.21 | 37.12 | 13.64 | 9.02 | 77.33 | 22.66 | 0.040 | −0.204 |
PCGs | 11,619 | 31.22 | 44.50 | 12.85 | 11.43 | 75.72 | 24.27 | −0.175 | −0.059 | |
Site 1 | 4141 | 31.93 | 38.64 | 12.07 | 17.35 | 70.57 | 29.43 | −0.090 | 0.155 | |
Site 2 | 3739 | 21.47 | 48.55 | 18.01 | 11.95 | 70.02 | 29.96 | −0.385 | −0.203 | |
Site 3 | 3739 | 40.26 | 46.30 | 8.46 | 4.98 | 86.56 | 13.44 | −0.069 | −0.233 | |
tRNA | 1488 | 41.06 | 38.64 | 8.67 | 11.63 | 79.70 | 20.30 | 0.030 | 0.146 | |
l-rRNA | 1381 | 41.20 | 43.95 | 4.71 | 10.14 | 85.16 | 14.84 | −0.032 | 0.366 | |
s-rRNA | 815 | 42.82 | 40.61 | 5.40 | 11.17 | 83.44 | 16.56 | 0.026 | 0.348 | |
CR | 674 | 46.44 | 49.11 | 2.67 | 1.78 | 95.55 | 4.45 | −0.028 | −0.200 | |
Kiefferulus glauciventris | Whole genome | 15,644 | 39.24 | 37.77 | 13.84 | 9.15 | 77.01 | 22.99 | 0.019 | −0.204 |
PCGs | 11,619 | 30.48 | 44.62 | 13.10 | 11.80 | 75.10 | 24.90 | −0.188 | −0.052 | |
Site 1 | 4141 | 31.41 | 37.34 | 13.13 | 18.12 | 68.75 | 31.25 | −0.080 | 0.161 | |
Site 2 | 3739 | 21.45 | 48.57 | 18.04 | 11.93 | 70.02 | 29.98 | −0.385 | −0.206 | |
Site 3 | 3739 | 38.59 | 47.94 | 8.12 | 5.34 | 86.53 | 13.47 | −0.108 | −0.200 | |
tRNA | 1487 | 41.29 | 38.53 | 8.88 | 11.30 | 79.83 | 20.17 | 0.035 | 0.120 | |
l-rRNA | 1368 | 43.64 | 41.08 | 4.68 | 10.60 | 84.72 | 15.28 | 0.030 | 0.388 | |
s-rRNA | 810 | 42.10 | 41.23 | 5.43 | 11.23 | 83.33 | 16.67 | 0.010 | 0.348 | |
CR | 568 | 49.47 | 45.77 | 2.64 | 2.11 | 95.25 | 4.75 | 0.039 | −0.111 | |
Kiefferulus intertinctus | Whole genome | 15,644 | 39.87 | 38.24 | 13.05 | 8.84 | 78.11 | 21.89 | 0.021 | −0.192 |
PCGs | 11,619 | 31.13 | 45.34 | 12.33 | 11.20 | 76.47 | 23.53 | −0.186 | −0.048 | |
Site 1 | 4141 | 31.76 | 38.38 | 12.10 | 17.75 | 70.14 | 29.86 | −0.088 | 0.185 | |
Site 2 | 3739 | 21.48 | 48.09 | 18.44 | 11.98 | 69.58 | 30.42 | −0.379 | −0.213 | |
Site 3 | 3739 | 40.16 | 49.54 | 6.44 | 3.86 | 89.70 | 10.30 | −0.104 | −0.235 | |
Kiefferulus intertinctus | tRNA | 1490 | 41.07 | 39.13 | 8.46 | 11.34 | 80.20 | 19.80 | 0.024 | 0.146 |
l-rRNA | 1376 | 42.08 | 43.31 | 4.65 | 9.96 | 85.39 | 14.61 | −0.014 | 0.363 | |
s-rRNA | 815 | 42.58 | 41.23 | 5.40 | 10.80 | 83.80 | 16.20 | 0.016 | 0.333 | |
CR | 533 | 43.71 | 51.78 | 1.88 | 2.63 | 95.50 | 4.50 | −0.085 | 0.167 | |
Kiefferulus sp.1XL | Whole genome | 15,588 | 38.42 | 36.70 | 15.03 | 9.85 | 75.12 | 24.88 | 0.023 | −0.208 |
PCGs | 11,619 | 29.94 | 43.16 | 14.58 | 12.32 | 73.10 | 26.90 | −0.181 | −0.084 | |
Site 1 | 4141 | 31.84 | 36.34 | 13.80 | 18.02 | 68.18 | 31.82 | −0.062 | 0.115 | |
Site 2 | 3739 | 21.19 | 48.13 | 18.61 | 12.06 | 69.33 | 30.67 | −0.385 | −0.214 | |
Site 3 | 3739 | 36.79 | 45.00 | 11.32 | 6.89 | 81.79 | 18.21 | −0.100 | −0.256 | |
tRNA | 1488 | 40.39 | 38.98 | 9.07 | 11.56 | 79.37 | 20.63 | 0.018 | 0.121 | |
l-rRNA | 1369 | 43.83 | 40.32 | 5.26 | 10.59 | 84.15 | 15.85 | 0.042 | 0.336 | |
s-rRNA | 811 | 40.57 | 41.43 | 5.67 | 12.33 | 82.00 | 18.00 | −0.010 | 0.370 | |
CR | 546 | 48.17 | 46.34 | 3.48 | 2.01 | 94.51 | 5.49 | 0.019 | −0.267 | |
Kiefferulus trigonum | Whole genome | 15,657 | 40.47 | 38.97 | 12.19 | 8.37 | 79.44 | 20.56 | 0.019 | −0.186 |
PCGs | 11,621 | 31.82 | 46.42 | 11.21 | 10.54 | 78.24 | 21.76 | −0.187 | −0.031 | |
Site 1 | 4141 | 32.52 | 39.19 | 11.40 | 16.88 | 71.72 | 28.28 | −0.090 | 0.163 | |
Site 2 | 3740 | 21.28 | 49.01 | 17.84 | 11.87 | 70.29 | 29.71 | −0.392 | −0.205 | |
Site 3 | 3740 | 41.67 | 51.05 | 4.40 | 2.87 | 92.72 | 7.28 | −0.101 | −0.180 | |
tRNA | 1484 | 41.98 | 38.88 | 8.09 | 11.05 | 80.86 | 19.14 | 0.038 | 0.155 | |
l-rRNA | 1378 | 41.36 | 43.90 | 4.57 | 10.16 | 85.27 | 14.73 | −0.030 | 0.379 | |
s-rRNA | 812 | 44.09 | 40.76 | 5.30 | 9.85 | 84.85 | 15.15 | 0.039 | 0.301 | |
CR | 518 | 44.98 | 51.16 | 2.70 | 1.16 | 96.14 | 3.86 | −0.064 | −0.400 | |
Kiefferulus tainanus | Whole genome | 15,748 | 40.15 | 38.67 | 12.56 | 8.62 | 78.82 | 21.18 | 0.018 | −18.620 |
PCGs | 11,220 | 30.77 | 45.41 | 11.75 | 12.08 | 76.18 | 23.82 | −0.192 | 1.380 | |
Site 1 | 3740 | 31.34 | 38.05 | 11.9 | 18.72 | 69.39 | 30.61 | −0.096 | 22.27 | |
Site 2 | 3740 | 20.43 | 47.51 | 18.96 | 13.10 | 67.94 | 32.06 | −0.398 | −18.27 | |
Site 3 | 3740 | 40.53 | 50.67 | 4.39 | 4.41 | 91.20 | 8.80 | −0.111 | 0.300 | |
tRNA | 1494 | 41.5 | 38.76 | 8.43 | 11.31 | 80.25 | 19.75 | 0.034 | 14.580 | |
l-rRNA | 1388 | 43.23 | 42.51 | 4.54 | 9.73 | 85.73 | 14.27 | 0.008 | 36.360 | |
s-rRNA | 814 | 43.24 | 41.28 | 5.16 | 10.32 | 84.52 | 15.48 | 0.023 | 33.330 | |
CR | 554 | 45.67 | 49.28 | 3.43 | 1.62 | 94.95 | 5.05 | −0.038 | −35.710 |
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Zhang, D.; Jin, W.-D.; Xu, H.-F.; Li, X.-B.; Jiang, Y.-W.; Li, D.-Q.; Lin, X.-L. Characteristics and Comparative Analysis of Six Mitogenomes of Genus Kiefferulus Goetghebuer, 1922 (Diptera: Chironomidae). Insects 2024, 15, 646. https://doi.org/10.3390/insects15090646
Zhang D, Jin W-D, Xu H-F, Li X-B, Jiang Y-W, Li D-Q, Lin X-L. Characteristics and Comparative Analysis of Six Mitogenomes of Genus Kiefferulus Goetghebuer, 1922 (Diptera: Chironomidae). Insects. 2024; 15(9):646. https://doi.org/10.3390/insects15090646
Chicago/Turabian StyleZhang, Dan, Wei-Dong Jin, Hai-Feng Xu, Xue-Bo Li, Yong-Wei Jiang, Dai-Qing Li, and Xiao-Long Lin. 2024. "Characteristics and Comparative Analysis of Six Mitogenomes of Genus Kiefferulus Goetghebuer, 1922 (Diptera: Chironomidae)" Insects 15, no. 9: 646. https://doi.org/10.3390/insects15090646