The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysis

An Huang; Shuo Liu; Haijun Li; Hongdi Luo; Qingyong Ni; Yongfang Yao; Huailiang Xu; Bo Zeng; Ying Li; Zhimin Wei; Song Li; Mingwang Zhang

doi:10.7717/peerj.7415

The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysis

PeerJ. 2019 Aug 1:7:e7415. doi: 10.7717/peerj.7415. eCollection 2019.

Authors

An Huang^#^{1

2}, Shuo Liu^#³, Haijun Li^{1

2}, Hongdi Luo^{1

2}, Qingyong Ni^{1

2}, Yongfang Yao⁴, Huailiang Xu⁴, Bo Zeng^{1

2}, Ying Li^{1

2}, Zhimin Wei⁵, Song Li³, Mingwang Zhang^{1

2}

Affiliations

¹ College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.
² Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.
³ Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, China.
⁴ College of Life Science, Sichuan Agricultural University, Yaan, China.
⁵ Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.

^# Contributed equally.

Abstract

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.

Keywords: Mitochondrial gene rearrangement; ND5; Phylogenetic relationships; Polypedates megacephalus.

Associated data

figshare/10.6084/m9.figshare.7935194.v1

Grants and funding

This work was supported by the National Natural Science Foundation of China (NSFC) to MingWang Zhang (No. 31470444) and the Innovative Research Team in University of Sichuan Bureau of Education (No. 14TD0002). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.