The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysis
The mitochondrial genome (mitogenome) sequence of the tree frog Polypedates megacephalus (16,473 bp) was previously reported as having the unusual characteristic of lacking the ND5 gene. In this study, a new mitogenome of P. megacephalus (19,952 bp) was resequenced using the next-generation sequenci...
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doaj-f0c6cdac66da41aaac61c41396972bfb2020-11-24T22:18:03ZengPeerJ Inc.PeerJ2167-83592019-08-017e741510.7717/peerj.7415The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysisAn Huang0Shuo Liu1Haijun Li2Hongdi Luo3Qingyong Ni4Yongfang Yao5Huailiang Xu6Bo Zeng7Ying Li8Zhimin Wei9Song Li10Mingwang Zhang11College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, ChinaKunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, ChinaCollege of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, ChinaCollege of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, ChinaCollege of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, ChinaCollege of Life Science, Sichuan Agricultural University, Yaan, ChinaCollege of Life Science, Sichuan Agricultural University, Yaan, ChinaCollege of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, ChinaCollege of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, ChinaInstitute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, ChinaKunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, ChinaCollege of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, ChinaThe mitochondrial genome (mitogenome) sequence of the tree frog Polypedates megacephalus (16,473 bp) was previously reported as having the unusual characteristic of lacking the ND5 gene. In this study, a new mitogenome of P. megacephalus (19,952 bp) was resequenced using the next-generation sequencing (NGS) and standard Sanger sequencing technologies. It was discovered that the ND5 gene was not lost but translocated to the control region (CR) from its canonical location between the ND4 and ND6 genes. In addition, a duplicated control region was found in the new mitogenome of this species. Conservative region identification of the ND5 gene and phylogenetic analysis confirmed that the ND5 gene was located between two control regions. The phylogenetic relationship among 20 related species of anura revealed a rearrangement of the ND5 gene during the evolutionary process. These results also highlighted the advantages of next-generation sequencing. It will not only decrease the time and cost of sequencing, but also will eliminate the errors in published mitogenome databases.https://peerj.com/articles/7415.pdfMitochondrial gene rearrangementND5Phylogenetic relationshipsPolypedates megacephalus |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
An Huang Shuo Liu Haijun Li Hongdi Luo Qingyong Ni Yongfang Yao Huailiang Xu Bo Zeng Ying Li Zhimin Wei Song Li Mingwang Zhang |
spellingShingle |
An Huang Shuo Liu Haijun Li Hongdi Luo Qingyong Ni Yongfang Yao Huailiang Xu Bo Zeng Ying Li Zhimin Wei Song Li Mingwang Zhang The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysis PeerJ Mitochondrial gene rearrangement ND5 Phylogenetic relationships Polypedates megacephalus |
author_facet |
An Huang Shuo Liu Haijun Li Hongdi Luo Qingyong Ni Yongfang Yao Huailiang Xu Bo Zeng Ying Li Zhimin Wei Song Li Mingwang Zhang |
author_sort |
An Huang |
title |
The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysis |
title_short |
The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysis |
title_full |
The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysis |
title_fullStr |
The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysis |
title_full_unstemmed |
The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysis |
title_sort |
revised complete mitogenome sequence of the tree frog polypedatesmegacephalus (anura, rhacophoridae) by next-generation sequencing and phylogenetic analysis |
publisher |
PeerJ Inc. |
series |
PeerJ |
issn |
2167-8359 |
publishDate |
2019-08-01 |
description |
The mitochondrial genome (mitogenome) sequence of the tree frog Polypedates megacephalus (16,473 bp) was previously reported as having the unusual characteristic of lacking the ND5 gene. In this study, a new mitogenome of P. megacephalus (19,952 bp) was resequenced using the next-generation sequencing (NGS) and standard Sanger sequencing technologies. It was discovered that the ND5 gene was not lost but translocated to the control region (CR) from its canonical location between the ND4 and ND6 genes. In addition, a duplicated control region was found in the new mitogenome of this species. Conservative region identification of the ND5 gene and phylogenetic analysis confirmed that the ND5 gene was located between two control regions. The phylogenetic relationship among 20 related species of anura revealed a rearrangement of the ND5 gene during the evolutionary process. These results also highlighted the advantages of next-generation sequencing. It will not only decrease the time and cost of sequencing, but also will eliminate the errors in published mitogenome databases. |
topic |
Mitochondrial gene rearrangement ND5 Phylogenetic relationships Polypedates megacephalus |
url |
https://peerj.com/articles/7415.pdf |
work_keys_str_mv |
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