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

Abstract

Recent improvements in next-generation sequencing (NGS) technologies can facilitatethe obtainment of mitochondrial genomes. However, it is not clear whether NGS couldbe effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly andalignment errors. Here, we choose two frogs with rearranged gene order, Amolopschunganensis and Quasipaa boulengeri, to test whether gene rearrangements affectthe mitogenome assembly and alignment by using NGS. The mitogenomes withgene rearrangements are sequenced through Illumina MiSeq genomic sequencing andassembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents inthe mitogenome of A. chunganensis and Q. boulengeri are typical neobatrachian patternexcept 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 andother neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrialsequence authenticity of A. chunganensis and Q. boulengeri. In this work, we providenearly complete mitochondrial genomes of A. chunganensis and Q. boulengeri.