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

Lin Cui; An Huang; Zhi He; Lisha Ao; Fei Ge; Xiaolan Fan; Bo Zeng; Mingyao Yang; Deying Yang; Qingyong Ni; Yan Li; Yongfang Yao; Huailiang Xu; Jiandong Yang; Zhimin Wei; Tongqing Li; Taiming Yan; Mingwang Zhang

doi:10.3390/ani12182449

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

Animals (Basel). 2022 Sep 16;12(18):2449. doi: 10.3390/ani12182449.

Authors

Lin Cui^{1

2}, An Huang^{1

2}, Zhi He^{1

2}, Lisha Ao^{1

2}, Fei Ge^{1

2}, Xiaolan Fan^{1

2}, Bo Zeng^{1

2}, Mingyao Yang^{1

2}, Deying Yang^{1

2}, Qingyong Ni^{1

2}, Yan Li^{1

2}, Yongfang Yao³, Huailiang Xu³, Jiandong Yang^{1

2}, Zhimin Wei⁴, Tongqing Li⁵, Taiming Yan^{1

2}, Mingwang Zhang^{1

2}

Affiliations

¹ Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
² Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
³ College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
⁴ Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China.
⁵ Hebei Fisheries Technology Extension Center, Shijiazhuang 050051, China.

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.

Keywords: Polypedates; Rhacophoridae; gene rearrangement; mitogenome; phylogenetic analysis.

Grants and funding

No. 31470444/National Natural Science Foundation of China (NSFC) to MWZ