The complete mitogenome of Amolops loloensis and related phylogenetic relationship among Ranidae

Abstract

Rufous-spotted Torrent Frog (Amolops loloensis) is a vulnerable species, which belongs to the family Ranidae and is distributed in high-gradient streams of Sichuan and Yunnan, China. In this study, we first determined the complete mitochondrial DNA sequence of A. loloensis (GenBank accession no. KT750963). The mitogenome sequence of A. loloensis was 18 926 bp in size. It contained 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs, and a D-loop region. Amolops loloensis shared the same gene arrangement pattern with A. mantzorum. The O structures of A. loloensis and A. mantzorum were both located at the upstream of trnA-trnN, while the O structures of A. ricketti and A. wuyiensis were both located at the downstream of trnA-trnN. It is of great interest to discuss the gene rearrangement mechanisms in the following study.

Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes inAmolops chunganensisandQuasipaa boulengeri

“…Compared with reported ranid frogs, the location of replication origin (O L ) in A. chunganensis mitogenome was rearranged. This gene order was consistent with other reported Amolops species (Zhang, Xia & Zeng, 2016; Xue et al, 2015; Xia et al, 2014). The O L is located in the tRNA genes cluster “WANCY”.…”

“…It is similar to A. mantzorum and A. loloensis gene arrangement pattern (Shan et al, 2016; Xue et al, 2015). Interestingly, a trnK pseudogene was located between cox2 and atp8 genes (Fig.…”

“…In the D-loop region, different repeated units, repetitive sequence and repetitions resulted in different sequence length (length polymorphism). For example, in Amolops species, the D-loop region ranged from 2,211 bp ( A. mantzorum ) to 3,391 bp ( A. loloensis ) (Zhang, Xia & Zeng, 2016; Shan et al, 2014; Xue et al, 2015). Actually, even if long tandem repeat regions can be successfully amplified by long PCR, they also represent a problem for Sanger sequencing (Xia et al, 2014).…”

“…Gene order reorganization was reported in the “WANCY” gene cluster of some Amolops mitogenomes (Xia et al, 2014; Xue et al, 2015; Zhang, Xia & Zeng, 2016; Shan et al, 2016). The “WANCY” gene cluster was also rearranged in the spiny-bellied frog, Quasipaa boulengeri (Shan et al, 2014).…”

The complete mitogenome of the granular torrent frog, Amolops granulosus (Anura: Ranidae)

“…The genus Amolops is distributed across Nepal, northern India, western and southern China to Malaya and contains 58 species (Frost 2019). Recently, some mitochondrial genomes of genus Amolops have been reported that the tRNA gene cluster, 'WANCY', as a hotspot of mtDNA rearrangement, and it has provided evidence of rearrangements between species within the genus (Huang et al 2014;Shan et al 2016;Xue et al 2016;Zhang et al 2016). But the phylogenetic relationship of these species still remains controversial.…”