The mitochondrial genome and phylogenetic analysis of Rhacophorus rhodopus
Abstract Classification of the genus Rhacophorus has been problematic. In particular there has been considerable controversy surrounding the phylogenetic relationships among Rhacophorus rhodopus, R. bipunctatus, and R. reinwardtii. To examine the relationship among these Rhacophorus species, we asse...
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Nature Portfolio
2022-08-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-17814-8 |
| _version_ | 1798042483427377152 |
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| author | Wei Chen Haifen Qin Zhenkun Zhao Jiahong Liao Hongzhou Chen Lichun Jiang Buddhi Dayananda |
| author_facet | Wei Chen Haifen Qin Zhenkun Zhao Jiahong Liao Hongzhou Chen Lichun Jiang Buddhi Dayananda |
| author_sort | Wei Chen |
| collection | DOAJ |
| description | Abstract Classification of the genus Rhacophorus has been problematic. In particular there has been considerable controversy surrounding the phylogenetic relationships among Rhacophorus rhodopus, R. bipunctatus, and R. reinwardtii. To examine the relationship among these Rhacophorus species, we assembled the complete mitochondrial genome sequence of R. rhodopus. The R. rhodopus genome is 15,789 bp in length with 12 protein-coding genes (PCGs) (losing ND5), two ribosomal genes, 22 transfer RNA genes, and a control region (D-loop). Base composition of the overall sequence was 60.86% for A + T content and 39.14% for C + G content. Most of the PCGs used ATG as a start codon, except for the COX I gene, which used the ATA start codon. COX I and ND6 used AGG and ATP8 stop codons respectively, while ND3 and ND4L used the TAA stop codon. For the remaining seven genes, the stop codons was incomplete. In addition, both 5' and 3' of the control areas had distinct repeating regions. Based on three datasets and two methods (Bayesian inference (BI) and maximum likelihood (ML)), we reconstructed three phylogenetic trees to explore the taxonomic status of the species and the phylogenetic relationship among R. rhodopus, R. bipunctatus and R. reinwardtii. Our results indicated that these three species are non-monophyletic; thus, the phylogenetic relationship among them is complex and difficult to determine. Further, R. rhodopus is divided into three lineages from different parts of China. The two Rhacophorus samples showed very close phylogenetic relationship with R. rhodopus. Our results add to the mitochondrial genome database of amphibians and will help to disentangle the phylogenetic relationships within the Rhacophoridae. |
| first_indexed | 2024-04-11T22:36:08Z |
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| language | English |
| last_indexed | 2024-04-11T22:36:08Z |
| publishDate | 2022-08-01 |
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| spelling | doaj.art-d2dbb2fdf20842f2b90717671d83a8392022-12-22T03:59:13ZengNature PortfolioScientific Reports2045-23222022-08-0112111010.1038/s41598-022-17814-8The mitochondrial genome and phylogenetic analysis of Rhacophorus rhodopusWei Chen0Haifen Qin1Zhenkun Zhao2Jiahong Liao3Hongzhou Chen4Lichun Jiang5Buddhi Dayananda6School of Resources and Environmental Engineering, Anhui UniversityKey Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal UniversityKey Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal UniversityKey Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal UniversityKey Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal UniversityKey Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal UniversitySchool of Agriculture and Food Sciences, The University of QueenslandAbstract Classification of the genus Rhacophorus has been problematic. In particular there has been considerable controversy surrounding the phylogenetic relationships among Rhacophorus rhodopus, R. bipunctatus, and R. reinwardtii. To examine the relationship among these Rhacophorus species, we assembled the complete mitochondrial genome sequence of R. rhodopus. The R. rhodopus genome is 15,789 bp in length with 12 protein-coding genes (PCGs) (losing ND5), two ribosomal genes, 22 transfer RNA genes, and a control region (D-loop). Base composition of the overall sequence was 60.86% for A + T content and 39.14% for C + G content. Most of the PCGs used ATG as a start codon, except for the COX I gene, which used the ATA start codon. COX I and ND6 used AGG and ATP8 stop codons respectively, while ND3 and ND4L used the TAA stop codon. For the remaining seven genes, the stop codons was incomplete. In addition, both 5' and 3' of the control areas had distinct repeating regions. Based on three datasets and two methods (Bayesian inference (BI) and maximum likelihood (ML)), we reconstructed three phylogenetic trees to explore the taxonomic status of the species and the phylogenetic relationship among R. rhodopus, R. bipunctatus and R. reinwardtii. Our results indicated that these three species are non-monophyletic; thus, the phylogenetic relationship among them is complex and difficult to determine. Further, R. rhodopus is divided into three lineages from different parts of China. The two Rhacophorus samples showed very close phylogenetic relationship with R. rhodopus. Our results add to the mitochondrial genome database of amphibians and will help to disentangle the phylogenetic relationships within the Rhacophoridae.https://doi.org/10.1038/s41598-022-17814-8 |
| spellingShingle | Wei Chen Haifen Qin Zhenkun Zhao Jiahong Liao Hongzhou Chen Lichun Jiang Buddhi Dayananda The mitochondrial genome and phylogenetic analysis of Rhacophorus rhodopus Scientific Reports |
| title | The mitochondrial genome and phylogenetic analysis of Rhacophorus rhodopus |
| title_full | The mitochondrial genome and phylogenetic analysis of Rhacophorus rhodopus |
| title_fullStr | The mitochondrial genome and phylogenetic analysis of Rhacophorus rhodopus |
| title_full_unstemmed | The mitochondrial genome and phylogenetic analysis of Rhacophorus rhodopus |
| title_short | The mitochondrial genome and phylogenetic analysis of Rhacophorus rhodopus |
| title_sort | mitochondrial genome and phylogenetic analysis of rhacophorus rhodopus |
| url | https://doi.org/10.1038/s41598-022-17814-8 |
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