Differentiation and decreased genetic diversity in field contaminated oysters Crassostrea hongkongensis: Identification of selection signatures

The extent to which chemical contamination affects the population structure and genetic diversity of natural populations remains elusive. Here, we used the whole-genome resequencing and transcriptome to diagnose the effects of long-term exposure to multiple elevated chemical pollutants on the population differentiation and genetic diversity in oysters Crassostrea hongkongensis in a typically polluted Pearl River Estuary (PRE) of Southern China. Population structure revealed an obvious differentiation between the PRE oysters and those collected from a nearby clean Beihai (BH) individuals, while no significant differentiation was observed among individuals collected from the three pollution sites within PRE due to the high gene flow. The decreased genetic diversity in the PRE oysters reflected the long-term effects of chemical pollutants. Selective sweeps between BH and PRE oysters revealed that chemical defensome genes, including glutathione S-transferase, zinc transporter, were responsible for their differentiation, sharing common metabolic process of other pollutants. Combined with the genome-wide association analysis, 25 regions containing 77 genes were identified to be responsible for the direct selection regions of metals. Linkage disequilibrium blocks and haplotypes within these regions provided the biomarkers of permanent effects. Our results provide important insights to the genetic mechanisms underlying the rapid evolution under chemical contamination in marine bivalves. © 2023 Elsevier Ltd.