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. 2024 Aug 14;14(16):2339.
doi: 10.3390/ani14162339.

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

Jingyu Yang  1 , Zizi Cai  1   2 , Yan Fang  1   3 , Binbin Shan  4 , Ran Zhang  1 , Longshan Lin  1   3 , Yuan Li  1   5 , Jing Zhang  1   3   5
Affiliations

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

Jingyu Yang et al. Animals (Basel). .

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.

Keywords: Acanthopagrus latus; Rhabdosargus sarba; adaptive evolution; selection signatures; whole-genome resequencing.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
The geographic map of sample sources for yellowfin seabream (a) and goldlined seabream (b) in this study.
Figure 2
Figure 2
PCA plot (PC1, PC2 and PC3) showing the genetic structure of the 10 yellowfin seabream individuals (WA) and 10 goldlined seabream individuals (WY). The degrees of explained variance are given in parentheses.
Figure 3
Figure 3
Enrichment analysis of GO (a) and KEGG (b) of selected genes.
Figure 4
Figure 4
The Manhattan plot of the ROD values along chromosomes. The yellow/blue dots represent the ROD value of all SNPs, and the red dashed line represents the threshold line of the top 5% of ROD.
Figure 5
Figure 5
(A) The value of FST, πθ and Tajima’s D near gene NCOR2. (B) The value of FST, πθ and Tajima’s D near gene FOXO3B. (C) The value of FST, πθ and Tajima’s D near gene CAPN. (D) The value of FST, πθ and Tajima’s D near gene NF1A. (E) The value of FST, πθ and Tajima’s D near gene TCF7L2. The yellow highlight indicates gene regions with strong selective signals.
See this image and copyright information in PMC

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