The complete mitochondrial genome ofPyxicephalus adspersus: high gene rearrangement and phylogenetics of one of the world’s largest frogs

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).

Conversion of the names Pyxicephaloidea, Pyxicephalidae and Pyxicephalinae (Anura, Ranoidea) into phylogenetic nomenclature

“…They recognized both PYXICEPHALINAE and CACOSTERNINAE and used the old name PYXICEPHALIDAE from Bonaparte (1850) as the name of the large clade encompassing both subfamilies. This topology was supported with subsequent analyses of Bossuyt et al (2006), Pyron & Wiens (2011) and Van der Meijden et al (2011), and more recent studies still find a close relationship between the two clades (Bittencourt-Silva et al, 2016;Feng et al 2017;Jetz & Pyron 2018;Cai et al 2019). The recent work of Dubois et al (2021) also corroborated this relationship, but considered the two clades as two families, PYXICEPHALIDAE and CACOSTERNIDAE, grouped in an epifamily PYXICEPHALOIDAE.…”

Two-Fold ND5 Genes, Three-Fold Control Regions, lncRNA, and the “Missing” ATP8 Found in the Mitogenomes of Polypedates megacephalus (Rhacophridae: Polypedates)

“…We amplified 10 overlapping genes via normal PCR and long-accurate PCR methods slightly modified from Zhang et al [ 45 ]. Additionally, the ND5 fragments were successfully obtained using primers designed by Cai et al [ 46 ]. After obtaining the ND5 gene fragment, four sets of primers were designed to sequence adjacent gene fragments, including the region from ND5 (1) to ND5 (2) genes, the region from Cytb to ND5 (1) genes, and the region from ND5 (2) to tRNA Pro genes ( Figure 1 ).…”

Characterization of Two Mitogenomes of Hyla sanchiangensis (Anura: Hylidae), with Phylogenetic Relationships and Selection Pressure Analyses of Hylidae

“…The reaction volume for PCR amplification was 50 µL. PCR amplification used standard methods as in Cai et al [33]. The PCR products were identified by 1% agarose gel electrophoresis, and all PCR-purified products were sequenced at Sangon Biotech Company (Shanghai, China).…”