The complete mitochondrial genome of Pyxicephalus adspersus: high gene rearrangement and phylogenetics of one of the world's largest frogs.

Yin-Yin Cai,Li-Xu Lu,Dan-Na Yu,Kenneth B Storey,Shi-Qi Shen,Jia-Yong Zhang

doi:10.7717/peerj.7532

Abstract

The family Pyxicephalidae including two subfamilies (Cacosterninae and Pyxicephalinae) is an ecologically important group of frogs distributed in sub-Saharan Africa. However, its phylogenetic position among the Anura has remained uncertain. The present study determined the complete mitochondrial genome sequence of Pyxicephalus adspersus, the first representative mitochondrial genome from the Pyxicephalinae, and reconstructed the phylogenetic relationships within Ranoidae using 10 mitochondrial protein-coding genes of 59 frog species. The P. adspersus mitochondrial genome showed major gene rearrangement and an exceptionally long length that is not shared with other Ranoidae species. The genome is 24,317 bp in length, and contains 15 protein-coding genes (including extra COX3 and Cyt b genes), four rRNA genes (including extra 12S rRNA and 16S rRNA genes), 29 tRNA genes (including extra tRNALeu (UAG), tRNALeu (UUR), tRNAThr, tRNAPro, tRNAPhe, tRNAVal, tRNAGln genes) and two control regions (CRs). The Dimer-Mitogenome and Tandem duplication and random loss models were used to explain these gene arrangements. Finally, both Bayesian inference and maximum likelihood analyses supported the conclusion that Pyxicephalidae was monophyletic and that Pyxicephalidae was the sister clade of (Petropedetidae + Ptychadenidae).

Highlights

Anuran mitochondrial genomes are closed double-stranded DNA molecules with the lengths varying from 15 to 23 kb (Kakehashi et al, 2013; Zhang et al, 2018a) and typically encode 37 genes: two ribosomal RNAs (12S and 16S rRNAs), 22 transfer RNAs, 13 protein-coding genes (PCGs), and the control region (CR) or D-loop region (Boore, 1999, 2000)
All PCGs excluding the ND6 gene and four rRNA genes as well as all transfer RNAs (tRNAs) genes excluding tRNAAla, tRNAAsn, tRNACys, tRNAGln, tRNAGlu, tRNAPro, tRNASer, tRNATyr genes were encoded on the major strand
The length of the Pyxicephalus adspersus mitogenome was the largest size among all known anuran mitogenomes

Summary

Introduction

Anuran mitochondrial (mt) genomes are closed double-stranded DNA molecules with the lengths varying from 15 to 23 kb (Kakehashi et al, 2013; Zhang et al, 2018a) and typically encode 37 genes: two ribosomal RNAs (12S and 16S rRNAs), 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and the control region (CR) or D-loop region (Boore, 1999, 2000). The complete mitochondrial genome of Pyxicephalus adspersus: high gene rearrangement and phylogenetics of one of the world’s largest frogs. By increasing the number of sequenced frog mt genomes, we can gain valuable information about mt genome arrangements and improve our understanding of mt genomic phylogenetics and evolution, population genetics (Cai et al, 2018; Cheng et al, 2018; Lin et al, 2014; Ni et al, 2015; Ye et al, 2016) and mt genome expression (Zhang et al, 2019)

Methods

Results

Conclusion