Abstract
Shinkaia crosnieri (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 the two types of habitats have suffered from methodological and/or sample size limits. Here, using transcriptome-wide genetic markers from 44 individuals, we reveal the extent of genetic connectivity between a population of S. crosnieri collected from a methane seep in the South China Sea (SCS) and another collected from a hydrothermal vent in the Okinawa Trough (OT), as well as their signatures of local adaptation. Analysis of differentially expressed genes (DEGs) between these two populations and analysis of population-specific genes (PSGs) revealed that a great 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 revealed that at least five individuals per site are required to generate reliable results from differential gene expression analysis. Population genetic analyses based on 32,452 single-nucleotide polymorphisms (SNPs) revealed clear genetic differentiation between these two populations with an FST value of 0.07. 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). Different gene expressions and amino acid substitutions of some genes between the two sites related to oxidation resistance and xenobiotic detoxification may indicate 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.
Highlights
Deep-sea hydrothermal vents, often distributed along active midocean ridges and back-arc spreading centers, are well known for discharging sulfur-rich geofluids into the water column (Corliss et al, 1979; German et al, 2000)
Results of principal component analysis (PCA) based on the unigene expression matric revealed that all the South China Sea (SCS) seep individuals were separated from all the Okinawa Trough (OT) vent individuals along the first eigenvector (Figure 1A)
Further analyses showed that a total of 4,854 (16.6%) unigenes were differentially expressed between S. crosnieri from the SCS and the OT
Summary
Deep-sea hydrothermal vents, often distributed along active midocean ridges and back-arc spreading centers, are well known for discharging sulfur-rich geofluids into the water column (Corliss et al, 1979; German et al, 2000). Usually found along the continental margins and in trenches, typically release methane-rich geofluids from the seabed more slowly (Van Dover et al, 2002). These two types of ecosystems share some similar features, such as lack of light to support photosynthesis, high pressure, and high concentration of chemically reduced compounds as well as heavy metals (Levin, 2005; German et al, 2011). Only a small fraction of them inhabit both hydrothermal vents and methane seeps (Watanabe et al, 2010; Vrijenhoek, 2013), indicating that thriving in both types of environments requires specific adaptation and gene expression (Watanabe et al, 2010)
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