A Comparative Analysis of Selection Pressures Suffered by Mitochondrial Genomes in Two Planthopper Species with Divergent Climate Distributions
Mitochondrial DNA (mtDNA) has been widely used as a valuable tool in studies related to evolution and population genetics, under the implicit assumption of neutral evolution. However, recent studies suggest that natural selection also plays a significant role in shaping mitochondrial genome evolutio...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-11-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/24/23/16847 |
| _version_ | 1797400058846511104 |
|---|---|
| author | Kang-Kang Sun Yi Ding Lei Chen Jing-Tao Sun |
| author_facet | Kang-Kang Sun Yi Ding Lei Chen Jing-Tao Sun |
| author_sort | Kang-Kang Sun |
| collection | DOAJ |
| description | Mitochondrial DNA (mtDNA) has been widely used as a valuable tool in studies related to evolution and population genetics, under the implicit assumption of neutral evolution. However, recent studies suggest that natural selection also plays a significant role in shaping mitochondrial genome evolution, although the specific driving forces remain elusive. In this study, we aimed to investigate whether and how climate influences mitochondrial genome evolution by comparing the selection pressures acting on mitochondrial genomes between two rice planthoppers, <i>Sogatella furcifera</i> (Horváth) and <i>Laodelphax striatellus</i> (Fallén), which have different climate distributions. We employed the dN/dS method, MK test and Tajima’s D tests for our analysis. Our results showed that the mitochondrial genomes of the two species appear to undergo predominantly purifying selection, consistent with the nearly neutral evolution model. However, we observed varied degrees of purifying selection among the 13 protein-coding genes. Notably, <i>ND1</i>, <i>ND2</i>, <i>ND6</i>, <i>COIII</i>, and <i>ATP8</i> exhibited significantly stronger purifying selection and greater divergence between the two species compared to the other genes. Additionally, we observed relatively stronger purifying selection in the mitochondrial genomes of <i>S. furcifera</i> compared to <i>L. striatellus</i>. This difference could be attributed to varying metabolic requirements arising from distinct habitats or other factors that are unclear here. Furthermore, we speculate that mito-nuclear epistatic interactions may play a role in maintaining nonsynonymous polymorphisms, particularly for <i>COI</i> and <i>COII</i>. Overall, our results shed some light on the influence of climate on mitochondrial genome evolution. |
| first_indexed | 2024-03-09T01:50:03Z |
| format | Article |
| id | doaj.art-94c1e72acc9d4012b0087103b05eca82 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T01:50:03Z |
| publishDate | 2023-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-94c1e72acc9d4012b0087103b05eca822023-12-08T15:17:23ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-11-0124231684710.3390/ijms242316847A Comparative Analysis of Selection Pressures Suffered by Mitochondrial Genomes in Two Planthopper Species with Divergent Climate DistributionsKang-Kang Sun0Yi Ding1Lei Chen2Jing-Tao Sun3Department of Entomology, Nanjing Agricultural University, Nanjing 210095, ChinaDepartment of Entomology, Nanjing Agricultural University, Nanjing 210095, ChinaDepartment of Entomology, Nanjing Agricultural University, Nanjing 210095, ChinaDepartment of Entomology, Nanjing Agricultural University, Nanjing 210095, ChinaMitochondrial DNA (mtDNA) has been widely used as a valuable tool in studies related to evolution and population genetics, under the implicit assumption of neutral evolution. However, recent studies suggest that natural selection also plays a significant role in shaping mitochondrial genome evolution, although the specific driving forces remain elusive. In this study, we aimed to investigate whether and how climate influences mitochondrial genome evolution by comparing the selection pressures acting on mitochondrial genomes between two rice planthoppers, <i>Sogatella furcifera</i> (Horváth) and <i>Laodelphax striatellus</i> (Fallén), which have different climate distributions. We employed the dN/dS method, MK test and Tajima’s D tests for our analysis. Our results showed that the mitochondrial genomes of the two species appear to undergo predominantly purifying selection, consistent with the nearly neutral evolution model. However, we observed varied degrees of purifying selection among the 13 protein-coding genes. Notably, <i>ND1</i>, <i>ND2</i>, <i>ND6</i>, <i>COIII</i>, and <i>ATP8</i> exhibited significantly stronger purifying selection and greater divergence between the two species compared to the other genes. Additionally, we observed relatively stronger purifying selection in the mitochondrial genomes of <i>S. furcifera</i> compared to <i>L. striatellus</i>. This difference could be attributed to varying metabolic requirements arising from distinct habitats or other factors that are unclear here. Furthermore, we speculate that mito-nuclear epistatic interactions may play a role in maintaining nonsynonymous polymorphisms, particularly for <i>COI</i> and <i>COII</i>. Overall, our results shed some light on the influence of climate on mitochondrial genome evolution.https://www.mdpi.com/1422-0067/24/23/16847mitochondrial genomeenvironmental adaptationselection pressure |
| spellingShingle | Kang-Kang Sun Yi Ding Lei Chen Jing-Tao Sun A Comparative Analysis of Selection Pressures Suffered by Mitochondrial Genomes in Two Planthopper Species with Divergent Climate Distributions International Journal of Molecular Sciences mitochondrial genome environmental adaptation selection pressure |
| title | A Comparative Analysis of Selection Pressures Suffered by Mitochondrial Genomes in Two Planthopper Species with Divergent Climate Distributions |
| title_full | A Comparative Analysis of Selection Pressures Suffered by Mitochondrial Genomes in Two Planthopper Species with Divergent Climate Distributions |
| title_fullStr | A Comparative Analysis of Selection Pressures Suffered by Mitochondrial Genomes in Two Planthopper Species with Divergent Climate Distributions |
| title_full_unstemmed | A Comparative Analysis of Selection Pressures Suffered by Mitochondrial Genomes in Two Planthopper Species with Divergent Climate Distributions |
| title_short | A Comparative Analysis of Selection Pressures Suffered by Mitochondrial Genomes in Two Planthopper Species with Divergent Climate Distributions |
| title_sort | comparative analysis of selection pressures suffered by mitochondrial genomes in two planthopper species with divergent climate distributions |
| topic | mitochondrial genome environmental adaptation selection pressure |
| url | https://www.mdpi.com/1422-0067/24/23/16847 |
| work_keys_str_mv | AT kangkangsun acomparativeanalysisofselectionpressuressufferedbymitochondrialgenomesintwoplanthopperspecieswithdivergentclimatedistributions AT yiding acomparativeanalysisofselectionpressuressufferedbymitochondrialgenomesintwoplanthopperspecieswithdivergentclimatedistributions AT leichen acomparativeanalysisofselectionpressuressufferedbymitochondrialgenomesintwoplanthopperspecieswithdivergentclimatedistributions AT jingtaosun acomparativeanalysisofselectionpressuressufferedbymitochondrialgenomesintwoplanthopperspecieswithdivergentclimatedistributions AT kangkangsun comparativeanalysisofselectionpressuressufferedbymitochondrialgenomesintwoplanthopperspecieswithdivergentclimatedistributions AT yiding comparativeanalysisofselectionpressuressufferedbymitochondrialgenomesintwoplanthopperspecieswithdivergentclimatedistributions AT leichen comparativeanalysisofselectionpressuressufferedbymitochondrialgenomesintwoplanthopperspecieswithdivergentclimatedistributions AT jingtaosun comparativeanalysisofselectionpressuressufferedbymitochondrialgenomesintwoplanthopperspecieswithdivergentclimatedistributions |