Genome of the estuarine oyster reveals climate impact and adaptive plasticity

Understanding genomic bases of environmental adaptation is central to evolutionary biology and important for assessing adaptive potential of organisms under rapid climate change. Climate change is causing profound changes in world’s ocean, and genomic studies on keystone marine species such as the estuarine oyster (Crassostrea ariakensis) may inform how marine ecosystems respond to environmental shifts. We constructed a chromosome-level assembly of the estuarine oyster genome that spans 613.89 Mb and encodes 29,631 proteins. Resequencing of 264 wild individuals across wide latitude distribution revealed remarkably low genomic diversity in the estuarine oyster compared with its sister species and fine population structures shaped by historical glaciation, geological events and oceanographic forces. Genes from regions under selection were mostly involved in responding to temperature and salinity stress, demonstrating selection by these two environmental factors is a strong evolutionary force. Genes under selection included a large cluster of tandemly duplicated members of the solute carrier membrane transport protein families which are also expanded in two other low-salinity oyster species, highlighting the significance of membrane transporter expansion in estuarine adaptation. Genes exhibiting high plasticity showed strong selection in upstream regulatory regions that modulate transcription, indicating selection favoring plasticity. This study revealed genomic signatures of past glaciation and fine population structures shaped by climate history, physical forces and selection in a bivalve mollusc. Our results show gene expansion and selection in regulatory regions enhance phenotypic plasticity that is critical for organisms to survive and adapt to rapidly changing environments.