Population Genetic Structure and Gene Expression Plasticity of the Deep-Sea Vent and Seep Squat Lobster Shinkaia crosnieri

Yao Xiao, Ting Xu, Jin Sun, Yan Wang, Wai Chuen Wong, Yick Hang Kwan, Chong Chen, Jianwen Qiu*, Pei Yuan Qian*

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

17 Citations (Scopus)


Shinkaia crosnieri (Decapoda: Munidopsidae) is a squat lobster that dominates both deep-sea hydrothermal vent and methane seep communities in the Western Pacific. Previous studies comparing S. crosnieri living in these two types of habitats have suffered from methodological and/or sample size limits. Here, using transcriptome-wide single nucleotide polymorphisms (SNPs) markers from 44 individuals of S. crosnieri, we reveal the extent of genetic connectivity between a methane seep population in the South China Sea and a hydrothermal vent population in the Okinawa Trough, as well as their signatures of local adaptation. Analysis of differentially expressed genes (DEGs) between these two populations and population-specific genes (PSGs) revealed that a large number of unigenes, such as cytochrome P450 (CYP), glutathione S-transferase (GST) and peroxiredoxin 6 (Prdx6) related to oxidoreductase, and sulfur dioxygenase (ETHE1) and chondroitin 4-sulfotransferase 11 (CHST11) related to sulfur metabolism, showed opposite expression patterns in these two populations. Data subsampling in this study revealed that at least five individuals of S. crosnieri per site are required to generate reliable results from the differential gene expression analysis. Population genetic analyses based on 32,452 SNPs revealed clear genetic differentiation between these two populations with an FST value of 0.07 (p < 0.0005), and physical oceanographic modeling of the ocean currents in middle and deep layers also suggests a weak connection between these two sites. Analysis of outlier SNPs revealed 345 unigenes potentially under positive selection, such as sarcosine oxidase/L-pipecolate oxidase (PIPOX), alanine-glyoxylate transaminase/serine-glyoxylate transaminase/serine-pyruvate transaminase (AGXT), and Cu-Zn superoxide dismutase (SOD1). Among the differentially expressed genes and genes with amino acid substitutions between the two sites are those related to oxidation resistance and xenobiotic detoxification, indicating local adaptation to the specific environmental conditions of each site. Overall, exploring the population structure of S. crosnieri using transcriptome-wide SNP markers resulted in an improved understanding of its molecular adaptation and expression plasticity in vent and seep ecosystems.

Original languageEnglish
Article number587686
Number of pages16
JournalFrontiers in Marine Science
Publication statusPublished - 2 Nov 2020

Scopus Subject Areas

  • Oceanography
  • Global and Planetary Change
  • Aquatic Science
  • Water Science and Technology
  • Environmental Science (miscellaneous)
  • Ocean Engineering

User-Defined Keywords

  • deep sea
  • gene expression
  • population connectivity
  • RNA-seq
  • single-nucleotide polymorphism


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