title: Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes inAmolops chunganensisandQuasipaa boulengeri.
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 chunganensisandQuasipaa 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 ofA. chunganensisandQ. boulengeriare typical neobatrachian pattern except for rearrangements at the position of "WANCY" tRNA genes cluster. Further, the mitogenome ofQ. boulengeriis characterized with a tandem duplication oftrnM. Moreover, we utilize 13 protein-coding genes ofA. chunganensis,Q. boulengeriand other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity ofA. chunganensisandQ. boulengeri. In this work, we provide nearly complete mitochondrial genomes ofA. chunganensisandQ. boulengeri.
authors.affiliation: Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China; University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Siqi
authors.initials: S
authors.lastname: Yuan
authors.affiliation: Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , Sichuan , China.
authors.forename: Yun
authors.initials: Y
authors.lastname: Xia
authors.affiliation: Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , Sichuan , China.
authors.forename: Yuchi
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , Sichuan , China.
authors.forename: Xiaomao
authors.initials: X
authors.lastname: Zeng
keywords: Gene rearrangement; Illumina sequencing; Mitogenome; Neobatrachian; WANCY