TY - JOUR
T1 - Population Genetic Structure and Gene Expression Plasticity of the Deep-Sea Vent and Seep Squat Lobster Shinkaia crosnieri
AU - Xiao, Yao
AU - Xu, Ting
AU - Sun, Jin
AU - Wang, Yan
AU - Wong, Wai Chuen
AU - Kwan, Yick Hang
AU - Chen, Chong
AU - Qiu, Jianwen
AU - Qian, Pei Yuan
N1 - Funding Information:
We thank the captains and crews of Xiangyanghong 9, R/V Kairei, and R/V Tan Ka Kee, as well as the operation team of the deep-submergence vehicle Jiaolong, ROV KAIKO, and ROV ROPOS for helping us with sample collection during the relevant cruises. Hiroyuki Yamamoto (JAMSTEC) is thanked for serving as the chief scientist of the research cruise KR15-17. The data for physical oceanographic modeling in this study can be found on the http://www.hycom.org data server under the ?HYCOM + NCODA Global 1/12? Reanalysis? link. Funding. This work was supported by grants from the Major Basic and Applied Research Projects of Guangdong Province (2019B030302004-04), the Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) (SMSEGL20SC01), and Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) (GML2019ZD0409) as well as by a grant from China Ocean Mineral Resources Research and Development Association (DY135-E2-1-03). The R/V Kairei research cruise KR15-17 (PI: Hiroyuki Yamamoto) was supported by the Council for Science, Technology, and Innovation (CSTI) in Japan as part of the Cross Ministerial Strategic Innovation Promotion Program (SIP), Next-generation Technology for Ocean Resource Exploration.
Funding Information:
This work was supported by grants from the Major Basic and Applied Research Projects of Guangdong Province (2019B030302004-04), the Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) (SMSEGL20SC01), and Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)
PY - 2020/11/2
Y1 - 2020/11/2
N2 - 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.
AB - 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.
KW - deep sea
KW - gene expression
KW - population connectivity
KW - RNA-seq
KW - single-nucleotide polymorphism
UR - http://www.scopus.com/inward/record.url?scp=85096103018&partnerID=8YFLogxK
U2 - 10.3389/fmars.2020.587686
DO - 10.3389/fmars.2020.587686
M3 - Journal article
AN - SCOPUS:85096103018
SN - 2296-7745
VL - 7
JO - Frontiers in Marine Science
JF - Frontiers in Marine Science
M1 - 587686
ER -
