Open AccessArticle
Genome Insights and Identification of Sex Determination Region and Sex Markers in Argyrosomus japonicus
by
Yike Liu, Wanbo Li, Dinaer Yekefenhazi, Xianfeng Yang, Qihui Zhu, Kun Ye, Fang Han and Dongdong Xu
Genes 2024, 15(12), 1493; https://doi.org/10.3390/genes15121493 (registering DOI) - 21 Nov 2024
Abstract
Background:
Argyrosomus japonicus, a member of the Sciaenidae family, is widely distributed across the sea areas near China, Japan, Australia, and South Africa. The aim of this study is to provide a high-quality genome with new technology and to understand the sex
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Background:
Argyrosomus japonicus, a member of the Sciaenidae family, is widely distributed across the sea areas near China, Japan, Australia, and South Africa. The aim of this study is to provide a high-quality genome with new technology and to understand the sex determination mechanism of this species. Methods: We generated a high-quality chromosome-level genome for
Argyrosomus japonicus using PacBio HiFi and Hi-C sequencing technologies. To map the sex determination region, we employed re-sequencing data from 38
A. japonicus and conducted genome-wide association studies (GWASs) on sex phenotypes. Results: Utilizing Hifiasm, we assembled a 708.8 Mb genome with a contig N50 length of 30 Mb. Based on Hi-C data, these contigs were organized into 24 chromosomes. The completeness of the assembly was assessed to be 99% using BUSCO, and over 98% according to Merqury. We identified a total of 174.57 Mb of repetitive elements and annotated 24,726 protein-coding genes in the genome. We mapped a 2.8 Mb sex determination region on chromosome 9, within which we found two sex-linked markers. Furthermore, we confirmed that the XX-XY sex determination system is adopted in
A. japonicus. Conclusions: The findings of this study provide significant insights into genetic breeding, genome evolution research, and sex control breeding in
A. japonicus.
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