TY - JOUR
T1 - A chromosomal level genome sequence for Quasipaa spinosa (Dicroglossidae) reveals chromosomal evolution and population diversity
AU - Hu, Xiaoxiao
AU - Jiang, Zeyuan
AU - Ming, Yao
AU - Jian, Jianbo
AU - Jiang, Sanjie
AU - Zhang, Dandan
AU - Zhang, Jiayong
AU - Zheng, Shanjian
AU - Fang, Xiaodong
AU - Yang, Yulan
AU - Zheng, Rongquan
PY - 2022
Y1 - 2022
N2 - 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.
AB - 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.
KW - Quasipaa spinosa
KW - Diversity
KW - Genome
KW - Population
KW - Synteny
U2 - 10.1111/1755-0998.13560
DO - 10.1111/1755-0998.13560
M3 - Journal article
C2 - 34837460
VL - 22
SP - 1545
EP - 1558
JO - Molecular Ecology Resources
JF - Molecular Ecology Resources
SN - 1755-098X
IS - 4
ER -