Complete Mitogenomes of <i>Polypedates</i> 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

Animals (Sep 2022)

Complete Mitogenomes of <i>Polypedates</i> 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

Affiliations

Lin Cui: 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
An Huang: 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
Zhi He: 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
Lisha Ao: 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
Fei Ge: 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
Xiaolan Fan: 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
Bo Zeng: 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
Mingyao Yang: 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
Deying Yang: 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
Qingyong Ni: 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
Yan Li: 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
Yongfang Yao: College of Life Science, Sichuan Agricultural University, Ya’an 625014, China
Huailiang Xu: College of Life Science, Sichuan Agricultural University, Ya’an 625014, China
Jiandong Yang: 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
Zhimin Wei: Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
Tongqing Li: Hebei Fisheries Technology Extension Center, Shijiazhuang 050051, China
Taiming Yan: 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
Mingwang Zhang: 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

DOI: https://doi.org/10.3390/ani12182449
Journal volume & issue: Vol. 12, no. 18
p. 2449

Abstract

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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.

Published in Animals

ISSN: 2076-2615 (Online)
Publisher: MDPI AG
Country of publisher: Switzerland
LCC subjects: Agriculture: Animal culture: Veterinary medicine; Science: Zoology
Website: http://www.mdpi.com/journal/animals/

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