A chromosomal level genome sequence for Quasipaa spinosa (Dicroglossidae) reveals chromosomal evolution and population diversity

Xiaoxiao Hu, Zeyuan Jiang, Yao Ming, Jianbo Jian, Sanjie Jiang, Dandan Zhang, Jiayong Zhang, Shanjian Zheng, Xiaodong Fang, Yulan Yang, Rongquan Zheng*

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

Abstract

Quasipaa spinosa, an Asian commercial Dicroglossidae species, is noted for the spiny chest of adult male individuals. Here, we report the first chromosomal level Q. spinosa genome employing PacBio long read sequencing and High-through Chromosome Conformation Capture (Hi-C) technology. The total length of the final assembled genome was 2,839,292,578 bp, with contig N50 of 3.79 Mb and scaffold N50 of 327.44 Mb. Approximately 99.30% of the length of the assembled genome sequences were anchored to 13 chromosomes with the assistance of Hi-C reads. A total of 26,173 protein-coding genes were predicted, and 95.98% of the genes were functionally annotated. The annotated genes covered a total of 92.10% of the complete vertebrate core gene set according to the BUSCO pipeline evaluation. Approximately 41 million years ago, Q. spinosa began to diverge from its dicroglossid sister taxon Nanorana parkeri. The Q. spinosa genome revealed obvious chromosomal fissions compared with Xenopus tropicalis, which likely represented a specific chromosome evolutionary history within frogs. Population analysis showed that Chinese Q. spinosa could be divided into eastern and western genetic clusters, with the western population showing higher diversity than the eastern population. The effective population size of Q. spinosa showed a continuously decreasing trend from one million years ago to 10,000 years ago. In summary, this study sheds light on Q. spinosa evolution and population differentiation, providing a valuable genomic resource for further biological and genetic studies on this species, and other closely related frog taxa.
Original languageEnglish
JournalMolecular Ecology Resources
ISSN1755-098X
DOIs
Publication statusAccepted/In press - 2022

Keywords

  • Quasipaa spinosa
  • Diversity
  • Genome
  • Population
  • Synteny

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