Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes in Amolops chunganensis and Quasipaa boulengeri

Siqi Yuan; Yun Xia; Yuchi Zheng; Xiaomao Zeng

doi:10.7717/peerj.2786

Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes in Amolops chunganensis and Quasipaa boulengeri

PeerJ. 2016 Dec 15:4:e2786. doi: 10.7717/peerj.2786. eCollection 2016.

Authors

Siqi Yuan¹, Yun Xia², Yuchi Zheng², Xiaomao Zeng²

Affiliations

¹ Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China; University of Chinese Academy of Sciences, Beijing, China.
² Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , Sichuan , China.

Abstract

Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order, Amolops chunganensis and Quasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome of A. chunganensis and Q. boulengeri are typical neobatrachian pattern except for rearrangements at the position of "WANCY" tRNA genes cluster. Further, the mitogenome of Q. boulengeri is characterized with a tandem duplication of trnM. Moreover, we utilize 13 protein-coding genes of A. chunganensis, Q. boulengeri and other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity of A. chunganensis and Q. boulengeri. In this work, we provide nearly complete mitochondrial genomes of A. chunganensis and Q. boulengeri.

Keywords: Gene rearrangement; Illumina sequencing; Mitogenome; Neobatrachian; WANCY.

Grants and funding

This study was funded by National Natural Science Foundation of China (NSFC–31272282; 31372181; 31401960; 31572243), and the China Postdoctoral Science Foundation (2014M552386), and West Light Foundation of the Chinese Academy of Sciences. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.