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.
Highlights
In metazoan mitochondrial genomes, the organization is usually conserved (Boore, 1999)
A total of 15.29 million raw PE reads were produced on Illumina MiSeq (PE300) systems (4.9 Gb and 4.2 Gb raw data for Q. boulengeri and A. chunganensis, respectively)
It implies that Trinity is better than SOAPdenovo2 to recover mitogenome for low coverage metagenomic skimming data
Summary
The organization is usually conserved (Boore, 1999). Because of maternal inheritance features and other characteristics of mitogenome (i.e., relatively conserved gene content and organization, rapid mutation rate, and limited recombination), mitochondrial DNA (mtDNA) is a valuable and popular molecular marker (Xia et al, 2014; Hahn, Bachmann & Chevreux, 2013; Zhang et al, 2013). It has been extensively applied in population genetics, evolutionary biology, phylogeography, as well as phylogenetic relationships. The rearrangements would cause amplification, assembly and alignment errors or failure
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