Whole‐genome sequencing of brown‐marbled grouper (Epinephelus fuscoguttatus) provides insights into adaptive evolution and growth differences. (14th September 2021)

• Record Type: Journal Article
• Authors: Yang, Yang; Wang, Tong; Chen, Jingfang; Wu, Lina; Wu, Xi; Zhang, Weiwei; Luo, Jian; Xia, Junhong; Meng, Zining; Liu, Xiaochun
• Is Part Of: Molecular ecology resources. Volume 22:Number 2(2022)
• Page Start: 711
• Page End: 723
• Publication Date: 2021-09-14
• Subjects: brown‐marbled grouper -- disease resistance -- genome -- growth traits -- quantitative trait loci; Molecular ecology -- Periodicals; 572.8
• DOI: 10.1111/1755-0998.13494
• Languages: English
• ISSNs: 1755-098X

Abstract

Abstract: The brown‐marbled grouper ( Epinephelus fuscoguttatus ) is an important species of fish in the coral reef ecosystem and marine aquaculture industry. In this study, a high‐quality chromosome‐level genome of brown‐marbled grouper was assembled using Oxford Nanopore technology and Hi‐C technology. The GC content and heterozygosity were approximately 42% and 0.35%, respectively. A total of 230 contigs with a total length of 1047 Mb and contig N50 of 13.8 Mb were assembled, and 228 contigs (99.13%) were anchored into 24 chromosomes. A total of 24, 005 protein‐coding genes were predicted, among which 23, 862 (99.4%) predicted genes were annotated. Phylogenetic analysis showed that brown‐marbled grouper and humpback grouper were clustered into one clade that separated approximately 11–23 million years ago. Collinearity analyses showed that there was no obvious duplication of large fragments between chromosomes in the brown‐marbled grouper. Genomes of the humpback grouper and giant grouper showed a high collinearity with that of the brown‐marbled grouper. A total of 305 expanded gene families were detected in the brown‐marbled grouper genome, which is mainly involved in disease resistance. In addition, a genetic linkage map with 3061.88 cM was constructed. Based on the physical and genetic map, one growth‐related quantitative trait loci was detected in 32, 332, 447 bp of chromosome 20, and meox1 and etv4 were considered candidate growth‐related genes. This study provides pivotal genetic resources for further evolutionary analyses and artificial breeding of groupers.