Population genomics, gut microbiota, and transcriptional response to heat shock in Hong Kong oyster Magallana hongkongensis

The Hong Kong oyster Magallana hongkongensis, previously known as Crassostrea hongkongensis, is a true oyster species that native to the estuary-coast of Pearl River Delta in southern China. The species has long been farmed for hundreds of years, and with scientific, ecological, cultural and nutritional importance. However, there is only limited information on the genetic background and stress adaptation mechanism of M. hongkongensis, restricting the sustainable production and utilisation of the local oyster resources. Here, we presented the population structure analysis on oysters collected from Deep Bay (Shenzhen Bay) and Lantau Island in Hong Kong, the transcriptome analysis on heat shock responses and the gut microbiota profile of M. hongkongensis. A conserved genetic background of local oysters was uncovered by the whole genome resequencing on 49 individuals, and the results indicated a close relationship and adaptation process in local oyster populations. Genetic variants in homeobox and heat shock protein genes were identified and predicted with regulatory function. Oysters had also been incubated under temperate (25 °C) and heat shock (32 °C) conditions for 24 hours to investigate the stress responses. Transcriptome profiles revealed the heat-induced regulation on heat shock protein, protein binding genes and signal transduction genes. We also found the differential expression of two splicing factors might be regulated by alternative splicing, and their expression levels were higher under heat stress. In addition, the gut microbe community were detected by 16S rRNA sequencing, and Cyanobacteria, Proteobacteria and Spirochaetes were the top phyla found in local oysters. Our results provided the knowledge on transcriptomic responses to heat shock in local oyster and implied the molecular basis for the divergent adaptation to the changeable aquatic environment. We also suggested that gut microbiota might participate in the regulation of stress response in M. hongkongensis. These findings give new insights on different mechanisms of local adaptation in Hong Kong oysters and other molluscs.