Whole Genome Resequencing Reveals High Genetic Homogeneity and Localized Candidate Differentiation Signals in Saxidomus purpuratus Along the Yellow and Bohai Sea
- 1Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Yantai 265800, China
- 2Island and Reef Fishery Research Center, Chinese Academy of Fishery Sciences, Yantai 265800, China
- 3Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
Abstract
Saxidomus purpuratus (S. purpuratus) is an economically important bivalve along the northern coast of China, where intensifying fishing pressure threatens its wild stocks. Its genome-wide population genetic variation remains poorly characterized. We resequenced 75 wild individuals from five populations spanning the northern Yellow Sea (Donggang, DDDG; Ganjingzi, DLGJ; Huancui, WHHC) and the Bohai Sea (Changdao, YTCD; Laizhou, YTLZ). The sampled populations exhibited relatively low genetic diversity (He = 0.1301–0.1324), weak among-population differentiation (Fst = 0.0035–0.0040), and heterozygosity deficiency (Fis = 0.0480–0.0831). PCA, NJ, and ADMIXTURE detected no geographic structure. PSMC revealed concordant demographic histories, with a sustained decline following a Middle Pleistocene expansion, consistent with historical allele exchange. Selection scans (DDDG as the target population; WHHC and YTCD as references) identified 1268 candidate genes, of which 197 were shared across the two comparisons. After masking a tandem histone gene cluster, the remaining 155 non-histone genes fell into five functional categories: receptor and signal transduction, membrane transport and ion channels, innate immunity and defense, extracellular matrix and adhesion, and detoxification and metabolism. These signals recurred in both comparisons, identifying DDDG as a candidate population for genotype–environment association testing. Together, these results indicate that the five populations constitute a single genetically connected unit, while pinpointing a small set of candidate loci that may underpin local adaptation and should inform stock-enhancement programmes.
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BibTeX
@article{xu2026whole,
title = {{Whole Genome Resequencing Reveals High Genetic Homogeneity and Localized Candidate Differentiation Signals in Saxidomus purpuratus Along the Yellow and Bohai Sea}},
author = {Shuai Xu and Chunnuan Zhao and Haiying Han and Yuping Wu and Liqun Ren and Biao Wu and Chaoyi Xie and Junjie Li and Tao Yu},
journal = {International Journal of Molecular Sciences},
year = {2026},
month = oct,
doi = {10.3390/ijms27219627},
url = {https://www.mdpi.com/1422-0067/27/21/9627},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Whole Genome Resequencing Reveals High Genetic Homogeneity and Localized Candidate Differentiation Signals in Saxidomus purpuratus Along the Yellow and Bohai Sea
AU - Shuai Xu
AU - Chunnuan Zhao
AU - Haiying Han
AU - Yuping Wu
AU - Liqun Ren
AU - Biao Wu
AU - Chaoyi Xie
AU - Junjie Li
AU - Tao Yu
PY - 2026
DA - 2026/10/27
JO - International Journal of Molecular Sciences
DO - 10.3390/ijms27219627
UR - https://www.mdpi.com/1422-0067/27/21/9627
AB - Saxidomus purpuratus (S. purpuratus) is an economically important bivalve along the northern coast of China, where intensifying fishing pressure threatens its wild stocks. Its genome-wide population genetic variation remains poorly characterized. We resequenced 75 wild individuals from five populations spanning the northern Yellow Sea (Donggang, DDDG; Ganjingzi, DLGJ; Huancui, WHHC) and the Bohai Sea (Changdao, YTCD; Laizhou, YTLZ). The sampled populations exhibited relatively low genetic diversity (He = 0.1301–0.1324), weak among-population differentiation (Fst = 0.0035–0.0040), and heterozygosity deficiency (Fis = 0.0480–0.0831). PCA, NJ, and ADMIXTURE detected no geographic structure. PSMC revealed concordant demographic histories, with a sustained decline following a Middle Pleistocene expansion, consistent with historical allele exchange. Selection scans (DDDG as the target population; WHHC and YTCD as references) identified 1268 candidate genes, of which 197 were shared across the two comparisons. After masking a tandem histone gene cluster, the remaining 155 non-histone genes fell into five functional categories: receptor and signal transduction, membrane transport and ion channels, innate immunity and defense, extracellular matrix and adhesion, and detoxification and metabolism. These signals recurred in both comparisons, identifying DDDG as a candidate population for genotype–environment association testing. Together, these results indicate that the five populations constitute a single genetically connected unit, while pinpointing a small set of candidate loci that may underpin local adaptation and should inform stock-enhancement programmes.
SN - 1422-0067
ER -