Abstract:

Population genetics study focuses on genetic variation within populations and it is a research hotspot of examining biological questions like adaptation, speciation and population structure. Deep-sea squat lobster Shinkaia crosnieri is a dominate macrobenthos discovered in both hydrothermal vents and methane seeps. In this study, S. crosnieri samples were collected from one methane seep in the South China Sea (SCS) and one hydrothermal vent in the Okinawa Trough (OT) used for RNA-Seq. Among them, the RNA-Seq data of five organs from two individuals were used to assemble a transcriptome reference and the RNA-Seq data of muscle from all individuals were mapped to this transcriptome reference, resulting in single nucleotide polymorphisms (SNPs) as the molecular marker. Population genetic analyses based on these SNPs revealed a clear genetic differentiation between the SCS and the OT populations. Outlier SNP analysis demonstrated some genes, such as sulfide:quinone oxidoreductase (SQR) and Calcineurin (CN), were potentially under positive selection. Overall, this study firstly applied transcriptome-wide SNPs markers to explore the population structure of S. crosnieri in the Northwest Pacific and generated valuable molecular resources to understand their environmental adaptation in vent and seep ecosystems.

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