Phylogenetic Relationships of the Pseudogobionini Group (Teleostei: Cyprinidae) with Selection Pressure Analyses to Genes of Mitochondrial Genome
We newly sequenced complete mitochondrial genomes (mitogenome) of two gudgeon species <i>Saurogobio dabryi</i> and <i>S. punctatus</i>, and we downloaded 49 gudgeon mitogenomes from GenBank to investigate the phylogeny of the Pseudogobionini group and analyze selection pressu...
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| Format: | Article |
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MDPI AG
2023-04-01
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| Series: | Fishes |
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| Online Access: | https://www.mdpi.com/2410-3888/8/4/201 |
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| author | Lin Chen Xiaoyu Zhang Huanzhang Liu |
| author_facet | Lin Chen Xiaoyu Zhang Huanzhang Liu |
| author_sort | Lin Chen |
| collection | DOAJ |
| description | We newly sequenced complete mitochondrial genomes (mitogenome) of two gudgeon species <i>Saurogobio dabryi</i> and <i>S. punctatus</i>, and we downloaded 49 gudgeon mitogenomes from GenBank to investigate the phylogeny of the Pseudogobionini group and analyze selection pressure of the genes. With genera <i>Gobio</i>, <i>Acanthogobio</i>, and <i>Romanogobio</i> as outgroups, the phylogeny of the Pseudogobionini group was revealed as ((<i>Xenophysogobio</i> + <i>Gobiobotia</i>) + (<i>Saurogobio</i> + (<i>Abbottina</i> + (<i>Pseudogobio</i> + <i>Biwia</i> complex)))) based on the concatenated nucleotide sequences of 13 protein-coding genes (PCGs). Based on the molecular phylogeny and morphological or osteological characters, we proposed a classification system of the Pseudogobionini group. Moreover, five pairs of sister taxa were selected for gene selection pressure analyses to explore the link of mitochondrial gene evolution to group differentiation and adaptations. We detected significantly different dN/dS values in 11 out of 13 (excluding <i>ND3</i> and <i>ND4L</i>) PCGs in five pairs of clades, significantly different mean dN/dS, dN, and/or dS values in 8 out of 13 PCGs (excluding <i>ND2</i>, <i>ATP8</i>, <i>ND3</i>, <i>ND4L</i>, and <i>ND6</i>) in three pairs of sub-clades and seven positively selected sites in another three pairs of sub-clades. These results indicated that mitochondrial gene evolution might have contributed to group differentiation and adaptations especially for river or lake environments. |
| first_indexed | 2024-03-11T05:02:15Z |
| format | Article |
| id | doaj.art-91c6ec1428314e49aaf78db2c3374b32 |
| institution | Directory Open Access Journal |
| issn | 2410-3888 |
| language | English |
| last_indexed | 2024-03-11T05:02:15Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Fishes |
| spelling | doaj.art-91c6ec1428314e49aaf78db2c3374b322023-11-17T19:12:40ZengMDPI AGFishes2410-38882023-04-018420110.3390/fishes8040201Phylogenetic Relationships of the Pseudogobionini Group (Teleostei: Cyprinidae) with Selection Pressure Analyses to Genes of Mitochondrial GenomeLin Chen0Xiaoyu Zhang1Huanzhang Liu2The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, ChinaCollege of Fisheries, Henan Normal University, Xinxiang 453007, ChinaThe Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, ChinaWe newly sequenced complete mitochondrial genomes (mitogenome) of two gudgeon species <i>Saurogobio dabryi</i> and <i>S. punctatus</i>, and we downloaded 49 gudgeon mitogenomes from GenBank to investigate the phylogeny of the Pseudogobionini group and analyze selection pressure of the genes. With genera <i>Gobio</i>, <i>Acanthogobio</i>, and <i>Romanogobio</i> as outgroups, the phylogeny of the Pseudogobionini group was revealed as ((<i>Xenophysogobio</i> + <i>Gobiobotia</i>) + (<i>Saurogobio</i> + (<i>Abbottina</i> + (<i>Pseudogobio</i> + <i>Biwia</i> complex)))) based on the concatenated nucleotide sequences of 13 protein-coding genes (PCGs). Based on the molecular phylogeny and morphological or osteological characters, we proposed a classification system of the Pseudogobionini group. Moreover, five pairs of sister taxa were selected for gene selection pressure analyses to explore the link of mitochondrial gene evolution to group differentiation and adaptations. We detected significantly different dN/dS values in 11 out of 13 (excluding <i>ND3</i> and <i>ND4L</i>) PCGs in five pairs of clades, significantly different mean dN/dS, dN, and/or dS values in 8 out of 13 PCGs (excluding <i>ND2</i>, <i>ATP8</i>, <i>ND3</i>, <i>ND4L</i>, and <i>ND6</i>) in three pairs of sub-clades and seven positively selected sites in another three pairs of sub-clades. These results indicated that mitochondrial gene evolution might have contributed to group differentiation and adaptations especially for river or lake environments.https://www.mdpi.com/2410-3888/8/4/201Gobioninae<i>Pseudogobio esocinus</i>amino acid substitutionadaptive evolution |
| spellingShingle | Lin Chen Xiaoyu Zhang Huanzhang Liu Phylogenetic Relationships of the Pseudogobionini Group (Teleostei: Cyprinidae) with Selection Pressure Analyses to Genes of Mitochondrial Genome Fishes Gobioninae <i>Pseudogobio esocinus</i> amino acid substitution adaptive evolution |
| title | Phylogenetic Relationships of the Pseudogobionini Group (Teleostei: Cyprinidae) with Selection Pressure Analyses to Genes of Mitochondrial Genome |
| title_full | Phylogenetic Relationships of the Pseudogobionini Group (Teleostei: Cyprinidae) with Selection Pressure Analyses to Genes of Mitochondrial Genome |
| title_fullStr | Phylogenetic Relationships of the Pseudogobionini Group (Teleostei: Cyprinidae) with Selection Pressure Analyses to Genes of Mitochondrial Genome |
| title_full_unstemmed | Phylogenetic Relationships of the Pseudogobionini Group (Teleostei: Cyprinidae) with Selection Pressure Analyses to Genes of Mitochondrial Genome |
| title_short | Phylogenetic Relationships of the Pseudogobionini Group (Teleostei: Cyprinidae) with Selection Pressure Analyses to Genes of Mitochondrial Genome |
| title_sort | phylogenetic relationships of the pseudogobionini group teleostei cyprinidae with selection pressure analyses to genes of mitochondrial genome |
| topic | Gobioninae <i>Pseudogobio esocinus</i> amino acid substitution adaptive evolution |
| url | https://www.mdpi.com/2410-3888/8/4/201 |
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