Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications
The superfamily Certhioidea currently comprises five families. Due to the rapid diversification, the phylogeny of Certhioidea is still controversial. The advent of next generation sequencing provides a unique opportunity for a mitogenome-wide study. Here, we first provided six new complete mitogenom...
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MDPI AG
2022-12-01
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| author | Hengwu Ding De Bi Shiyun Han Ran Yi Sijia Zhang Yuanxin Ye Jinming Gao Jianke Yang Xianzhao Kan |
| author_facet | Hengwu Ding De Bi Shiyun Han Ran Yi Sijia Zhang Yuanxin Ye Jinming Gao Jianke Yang Xianzhao Kan |
| author_sort | Hengwu Ding |
| collection | DOAJ |
| description | The superfamily Certhioidea currently comprises five families. Due to the rapid diversification, the phylogeny of Certhioidea is still controversial. The advent of next generation sequencing provides a unique opportunity for a mitogenome-wide study. Here, we first provided six new complete mitogenomes of Certhioidea (<i>Certhia americana</i>, <i>C. familiaris</i>, <i>Salpornis spilonota</i>, <i>Cantorchilus leucotis</i>, <i>Pheugopedius coraya</i>, and <i>Pheugopedius genibarbis</i>). We further paid attention to the genomic characteristics, codon usages, evolutionary rates, and phylogeny of the Certhioidea mitogenomes. All mitogenomes we analyzed displayed typical ancestral avian gene order with 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and one control region (CR). Our study indicated the strand-biased compositional asymmetry might shape codon usage preferences in mitochondrial genes. In addition, natural selection might be the main factor in shaping the codon usages of genes. Additionally, evolutionary rate analyses indicated all mitochondrial genes were under purifying selection. Moreover, <i>MT-ATP8</i> and <i>MT-CO1</i> were the most rapidly evolving gene and conserved genes, respectively. According to our mitophylogenetic analyses, the monophylies of Troglodytidae and Sittidae were strongly supported. Importantly, we suggest that <i>Salpornis</i> should be separated from Certhiidae and put into Salpornithidae to maintain the monophyly of Certhiidae. Our findings are useful for further evolutionary studies within Certhioidea. |
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| spelling | doaj.art-8529c64e9b1046b1bab2d4d97181a8cf2023-11-16T14:19:00ZengMDPI AGAnimals2076-26152022-12-011319610.3390/ani13010096Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic ImplicationsHengwu Ding0De Bi1Shiyun Han2Ran Yi3Sijia Zhang4Yuanxin Ye5Jinming Gao6Jianke Yang7Xianzhao Kan8Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, ChinaCollege of Landscape Engineering, Suzhou Polytechnic Institute of Agriculture, Suzhou 215000, ChinaAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, ChinaAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, ChinaAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, ChinaAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, ChinaAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, ChinaAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, ChinaAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, ChinaThe superfamily Certhioidea currently comprises five families. Due to the rapid diversification, the phylogeny of Certhioidea is still controversial. The advent of next generation sequencing provides a unique opportunity for a mitogenome-wide study. Here, we first provided six new complete mitogenomes of Certhioidea (<i>Certhia americana</i>, <i>C. familiaris</i>, <i>Salpornis spilonota</i>, <i>Cantorchilus leucotis</i>, <i>Pheugopedius coraya</i>, and <i>Pheugopedius genibarbis</i>). We further paid attention to the genomic characteristics, codon usages, evolutionary rates, and phylogeny of the Certhioidea mitogenomes. All mitogenomes we analyzed displayed typical ancestral avian gene order with 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and one control region (CR). Our study indicated the strand-biased compositional asymmetry might shape codon usage preferences in mitochondrial genes. In addition, natural selection might be the main factor in shaping the codon usages of genes. Additionally, evolutionary rate analyses indicated all mitochondrial genes were under purifying selection. Moreover, <i>MT-ATP8</i> and <i>MT-CO1</i> were the most rapidly evolving gene and conserved genes, respectively. According to our mitophylogenetic analyses, the monophylies of Troglodytidae and Sittidae were strongly supported. Importantly, we suggest that <i>Salpornis</i> should be separated from Certhiidae and put into Salpornithidae to maintain the monophyly of Certhiidae. Our findings are useful for further evolutionary studies within Certhioidea.https://www.mdpi.com/2076-2615/13/1/96mitogenomesuperfamily certhioideaphylogenycodon usage pattern |
| spellingShingle | Hengwu Ding De Bi Shiyun Han Ran Yi Sijia Zhang Yuanxin Ye Jinming Gao Jianke Yang Xianzhao Kan Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications Animals mitogenome superfamily certhioidea phylogeny codon usage pattern |
| title | Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications |
| title_full | Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications |
| title_fullStr | Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications |
| title_full_unstemmed | Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications |
| title_short | Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications |
| title_sort | mitogenomic codon usage patterns of superfamily certhioidea aves passeriformes insights into asymmetrical bias and phylogenetic implications |
| topic | mitogenome superfamily certhioidea phylogeny codon usage pattern |
| url | https://www.mdpi.com/2076-2615/13/1/96 |
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