Comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily Cobitinae
Abstract Background Loaches of Cobitinae, widely distributed in Eurasian continent, have high economic, ornamental and scientific value. However, the phylogeny of Cobitinae fishes within genera or family level remains complex and controversial. Up to now, about 60 Cobitinae mitogenomes had been depo...
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| Format: | Article |
| Language: | English |
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BMC
2021-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-020-07360-w |
| _version_ | 1819052079293923328 |
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| author | Peng Yu Li Zhou Wen-Tao Yang Li-jun Miao Zhi Li Xiao-Juan Zhang Yang Wang Jian-Fang Gui |
| author_facet | Peng Yu Li Zhou Wen-Tao Yang Li-jun Miao Zhi Li Xiao-Juan Zhang Yang Wang Jian-Fang Gui |
| author_sort | Peng Yu |
| collection | DOAJ |
| description | Abstract Background Loaches of Cobitinae, widely distributed in Eurasian continent, have high economic, ornamental and scientific value. However, the phylogeny of Cobitinae fishes within genera or family level remains complex and controversial. Up to now, about 60 Cobitinae mitogenomes had been deposited in GenBank, but their integrated characteristics were not elaborated. Results In this study, we sequenced and analyzed the complete mitogenomes of a female Cobits macrostigma. Then we conducted a comparative mitogenome analysis and revealed the conserved and unique characteristics of 58 Cobitinae mitogenomes, including C. macrostigma. Cobitinae mitogenomes display highly conserved tRNA secondary structure, overlaps and non-coding intergenic spacers. In addition, distinct base compositions were observed among different genus and significantly negative linear correlation between AT% and AT-skew were found among Cobitinae, genus Cobitis and Pangio mitogenomes, respectively. A specific 3 bp insertion (GCA) in the atp8-atp6 overlap was identified as a unique feature of loaches, compared to other Cypriniformes fish. Additionally, all protein coding genes underwent a strong purifying selection. Phylogenetic analysis strongly supported the paraphyly of Cobitis and polyphyly of Misgurnus. The strict molecular clock predicted that Cobitinae might have split into northern and southern lineages in the late Eocene (42.11 Ma), furthermore, mtDNA introgression might occur (14.40 Ma) between ancestral species of Cobitis and ancestral species of Misgurnus. Conclusions The current study represents the first comparative mitogenomic and phylogenetic analyses within Cobitinae and provides new insights into the mitogenome features and evolution of fishes belonging to the cobitinae family. |
| first_indexed | 2024-12-21T12:14:08Z |
| format | Article |
| id | doaj.art-43c4a9908aac4332a11ee4c40f699d02 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-21T12:14:08Z |
| publishDate | 2021-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-43c4a9908aac4332a11ee4c40f699d022022-12-21T19:04:29ZengBMCBMC Genomics1471-21642021-01-0122111910.1186/s12864-020-07360-wComparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily CobitinaePeng Yu0Li Zhou1Wen-Tao Yang2Li-jun Miao3Zhi Li4Xiao-Juan Zhang5Yang Wang6Jian-Fang Gui7State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of SciencesState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of SciencesState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of SciencesState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of SciencesState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of SciencesState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of SciencesState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of SciencesState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of SciencesAbstract Background Loaches of Cobitinae, widely distributed in Eurasian continent, have high economic, ornamental and scientific value. However, the phylogeny of Cobitinae fishes within genera or family level remains complex and controversial. Up to now, about 60 Cobitinae mitogenomes had been deposited in GenBank, but their integrated characteristics were not elaborated. Results In this study, we sequenced and analyzed the complete mitogenomes of a female Cobits macrostigma. Then we conducted a comparative mitogenome analysis and revealed the conserved and unique characteristics of 58 Cobitinae mitogenomes, including C. macrostigma. Cobitinae mitogenomes display highly conserved tRNA secondary structure, overlaps and non-coding intergenic spacers. In addition, distinct base compositions were observed among different genus and significantly negative linear correlation between AT% and AT-skew were found among Cobitinae, genus Cobitis and Pangio mitogenomes, respectively. A specific 3 bp insertion (GCA) in the atp8-atp6 overlap was identified as a unique feature of loaches, compared to other Cypriniformes fish. Additionally, all protein coding genes underwent a strong purifying selection. Phylogenetic analysis strongly supported the paraphyly of Cobitis and polyphyly of Misgurnus. The strict molecular clock predicted that Cobitinae might have split into northern and southern lineages in the late Eocene (42.11 Ma), furthermore, mtDNA introgression might occur (14.40 Ma) between ancestral species of Cobitis and ancestral species of Misgurnus. Conclusions The current study represents the first comparative mitogenomic and phylogenetic analyses within Cobitinae and provides new insights into the mitogenome features and evolution of fishes belonging to the cobitinae family.https://doi.org/10.1186/s12864-020-07360-wCobitinaeLoachMitochondrial genomemtDNA introgressionPhylogenyDivergence time |
| spellingShingle | Peng Yu Li Zhou Wen-Tao Yang Li-jun Miao Zhi Li Xiao-Juan Zhang Yang Wang Jian-Fang Gui Comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily Cobitinae BMC Genomics Cobitinae Loach Mitochondrial genome mtDNA introgression Phylogeny Divergence time |
| title | Comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily Cobitinae |
| title_full | Comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily Cobitinae |
| title_fullStr | Comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily Cobitinae |
| title_full_unstemmed | Comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily Cobitinae |
| title_short | Comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily Cobitinae |
| title_sort | comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily cobitinae |
| topic | Cobitinae Loach Mitochondrial genome mtDNA introgression Phylogeny Divergence time |
| url | https://doi.org/10.1186/s12864-020-07360-w |
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