Whole-Genome Resequencing Reveals Signatures of Adaptive Evolution in Acanthopagrus latus and Rhabdosargus sarba

Author:

Yang Jingyu1,Cai Zizi12,Fang Yan13,Shan Binbin4,Zhang Ran1,Lin Longshan13,Li Yuan15,Zhang Jing135

Affiliation:

1. Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China

2. School of Life Science, Central China Normal University, Wuhan 430079, China

3. Fisheries College, Jimei University, Xiamen 361021, China

4. South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China

5. Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Xiamen 361021, China

Abstract

Acanthopagrus latus and Rhabdosargus sarba are economically important marine species along the coast of China, with similar external morphological characteristics and living habits, with wide distribution and strong adaptability. To investigate the molecular mechanisms underlying the adaptive evolution of these two species, we conducted whole-genome resequencing of 10 individuals of both species from the coastal waters of Wuyu Island, Fujian, China, using high-throughput sequencing technology. We obtained SNP, InDel, CNV, and SV variation information and annotated these variations, constructing a genomic variation database for both species. By comparing the resequencing data with reference genomes, we identified 9,829,511 SNP loci in the population of A. latus and 34,051,056 SNP loci in the population of R. sarba. Using whole-genome SNP data, we employed Fst and ROD methods to identify candidate genomic regions under selection. Functional annotation and enrichment analysis using GO and KEGG databases revealed potential adaptive evolution in R. sarba associated with immune response, feeding, growth and development, and locomotion, while A. latus showed potential adaptive evolution associated with immune response, nervous system, growth and development, and metabolism.

Funder

National Natural Science Foundation of China

Scientific Research Foundation of Third Institute of Oceanography, MNR

Open Research Fund Program of Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment

Publisher

MDPI AG

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