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BMC Genomics
2020 Jan 21;211:68. doi: 10.1186/s12864-020-6480-9.
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Insights into high-pressure acclimation: comparative transcriptome analysis of sea cucumber Apostichopus japonicus at different hydrostatic pressure exposures.
Liang L
,
Chen J
,
Li Y
,
Zhang H
.
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BACKGROUND: Global climate change is predicted to force the bathymetric migrations of shallow-water marine invertebrates. Hydrostatic pressure is proposed to be one of the major environmental factors limiting the vertical distribution of extant marine invertebrates. However, the high-pressure acclimation mechanisms are not yet fully understood.
RESULTS: In this study, the shallow-water sea cucumber Apostichopus japonicus was incubated at 15 and 25 MPa at 15 °C for 24 h, and subjected to comparative transcriptome analysis. Nine samples were sequenced and assembled into 553,507 unigenes with a N50 length of 1204 bp. Three groups of differentially expressed genes (DEGs) were identified according to their gene expression patterns, including 38 linearly related DEGs whose expression patterns were linearly correlated with hydrostatic pressure, 244 pressure-sensitive DEGs which were up-regulated at both 15 and 25 MPa, and 257 high-pressure-induced DEGs which were up-regulated at 25 MPa but not up-regulated at 15 MPa.
CONCLUSIONS: Our results indicated that the genes and biological processes involving high-pressure acclimation are similar to those related to deep-sea adaptation. In addition to representative biological processes involving deep-sea adaptation (such as antioxidation, immune response, genetic information processing, and DNA repair), two biological processes, namely, ubiquitination and endocytosis, which can collaborate with each other and regulate the elimination of misfolded proteins, also responded to high-pressure exposure in our study. The up-regulation of these two processes suggested that high hydrostatic pressure would lead to the increase of misfolded protein synthesis, and this may result in the death of shallow-water sea cucumber under high-pressure exposure.
XDA22040502 Strategic Priority Research Program of CAS, 2018YFC0309804 The National Key Research and Development Program of China, 2016YFC0304905 The National Key Research and Development Program of China, ZDKJ2016012 Major scientific and technological projects of Hainan Province
Fig. 1. Venn diagram of DEGs among different combinations (P15 vs. P0.1, P25 vs. P0.1, and P25 vs. P15). P0.1: experimental group incubated at atmospheric pressure; P15: experimental group incubated at 15 MPa; P25: experimental group incubated at 25 MPa; DEGs: differentially expressed genes; LRGs: linearly related DEGs; PSGs: pressure-sensitive DEGs; HPGs: high-pressure-induced DEGs
Fig. 2. Line graphs of the expression patterns of LRGs, PSGs, and HPGs. Points represent the mean of log2 (RFC) of all genes. Error bars represent standard deviation. LRGs: linearly related DEGs; PSGs: pressure-sensitive DEGs; HPGs: high-pressure-induced DEGs; RFC: relative fold change
Fig. 3. Heatmaps of DEGs annotated in Swiss-Prot. a Heatmap of linearly related DEGs. b Heatmap of pressure-sensitive DEGs. c Heatmap of high-pressure-induced DEGs. P0.1: experimental group incubated at atmospheric pressure; P15: experimental group incubated at 15 MPa; P25: experimental group incubated at 25 MPa; DEGs: differentially expressed genes
Fig. 4. Pathway of clathrin-dependent endocytosis. This pathway is a part of KEGG pathway map (map04144). The proteins involved in this pathway are shown in boxes and their descriptions are listed in the Additional file 6: Table S5. The proteins significantly up-regulated at high-pressure condition in our results are highlighted in red boxes
Fig. 5. The statistics of gene family analysis. a Gene family analysis of linearly related DEGs. b Gene family analysis of pressure-sensitive DEGs. c Gene family analysis of high-pressure-induced DEGs. DEGs: differentially expressed genes
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