Complete Mitogenomes of Polypedates Tree Frogs Unveil Gene Rearrangement and Concerted Evolution within Rhacophoridae

Abstract

New developments in sequencing technology and nucleotide analysis have allowed us to make great advances in reconstructing anuran phylogeny. As a clade of representative amphibians that have radiated from aquatic to arboreal habitats, our understanding of the systematic status and molecular biology of rhacophorid tree frogs is still limited. We determined two new mitogenomes for the genus Polypedates (Rhacophoridae): P. impresus and P. mutus. We conducted comparative and phylogenetic analyses using our data and seven other rhacophorid mitogenomes. The mitogenomes of the genera Polypedates, Buergeria, and Zhangixalus were almost identical, except that the ATP8 gene in Polypedates had become a non-coding region; Buergeria maintained the legacy “LTPF” tRNA gene cluster compared to the novel “TLPF” order in the other two genera; and B. buergeri and Z. dennysi had no control region (CR) duplication. The resulting phylogenetic relationship supporting the above gene rearrangement pathway suggested parallel evolution of ATP8 gene loss of function (LoF) in Polypedates and CR duplication with concerted evolution of paralogous CRs in rhacophorids. Finally, conflicting topologies in the phylograms of 185 species reflected the advantages of phylogenetic analyses using multiple loci.

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

“…In the current study, the phylogenetic tree showed the pairs of P. mutus and P. braueri versus P. megacephalus and P. impresus formed separate decisive sister groups. This topology was consistent with that published previously in other studies [ 21 , 86 , 87 ]. Past studies revealed that the P. leucomystax complex was considered to be composed of seven highly supported clades [ 2 , 87 , 88 ].…”

“…Gene rearrangement is a frequent phenomenon in tree frogs and can be explained by the tandem duplication–random loss (TDRL) model [ 16 ] and the slipped-strand mispairing model [ 17 ]. Among the known species of tree frogs, mitochondrial ND5 gene rearrangements are classified into the following two types: (1) those in which the ND5 gene is shifted from between ND4 and ND6 genes to between the CR and LTPF gene cluster ( Buergeria buergeri [ 18 ], Zhangixalus dennysi [ 19 ]), and (2) those in which the ND5 gene is translocated between the two CRs ( Zhangixalus schlegelii [ 20 ], P. impresus [ 21 ], Polypedates mutus [ 21 ], Polypedates braueri [ 22 ]). The mitogenome of P. megacephalus was initially sequenced by Zhang et al, revealing a 16,473 bp genome lacking the ND5 gene and the ATP8 gene [ 23 ].…”

“…Despite this, due to its short length and highly divergent nature even within a genus, the ATP8 gene is not conserved in flatworms [ 44 ]. Gene loss is rare among vertebrates compared to gene rearrangement, but it has been reported that the ATP8 gene is missing only in the genus Polypedates [ 21 , 23 , 24 ]. Whether the ATP8 gene was actually “missing” in Polypedates has become a concern for researchers.…”

Two-fold ND5 genes, three-fold control regions, lnc RNA, and the “missing” ATP8 were surprisingly found in the mitogenomes of Polypedates megacephalus (Rhacophridae: Polypedates)

“…Gene rearrangement is a frequent phenomenon in tree frogs and can be explained by the tandem duplication-random loss (TDRL) model [16] and the slipped-strand mispairing model [17]. Among the known species of tree frogs, mitochondrial ND5 gene rearrangements are classified into the following two types: (1) those in which the ND5 gene is shifted from between ND4 and ND6 genes to between the CR and LTPF gene cluster (Buergeria buergeri [18], Zhangixalus dennysi [19]), and (2) those in which the ND5 gene is translocated between the two CRs (Zhangixalus schlegelii [20], P. impresus [21], Polypedates mutus [21], Polypedates braueri [22]). The mitogenome of P. megacephalus was initially sequenced by Zhang et al, revealing a 16,473 bp genome lacking the ND5 gene and the ATP8 gene [23].…”