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Front Genet
2020 Apr 30;11:355. doi: 10.3389/fgene.2020.00355.
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Molecular Response to High Hydrostatic Pressure: Time-Series Transcriptomic Analysis of Shallow-Water Sea Cucumber Apostichopus japonicus.
Chen J
,
Liang L
,
Li Y
,
Zhang H
.
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Hydrostatic pressure is a key environmental factor constraining the benthic migration of shallow-water invertebrates. Although many studies have examined the physiological effects of high hydrostatic pressure on shallow-water invertebrates, the molecular response to high pressure is not fully understood. This question has received increasing attention because ocean warming is forcing the bathymetric migrations of shallow-water invertebrates. Here, we applied time-series transcriptomic analysis to high-pressure incubated and atmospheric pressure-recovered shallow-water sea cucumber (Apostichopus japonicus) to address this question. A total of 44 samples from 15 experimental groups were sequenced. Our results showed that most genes responded to pressure stress at the beginning when pressure was changed, but significant differences of gene expression appeared after 4 to 6 h. Transcription was the most sensitive biological process responding to high-pressure exposure, which was enriched among up-regulated genes after 2 h, followed by ubiquitination (4 h), endocytosis (6 h), stress response (6 h), methylation regulation (24 h), and transmembrane transportation (24 h). After high-pressure incubation, all these biological processes remained up-regulated within 4-6 h at atmospheric pressure. Overall, our results revealed the dynamic transcriptional response of A. japonicus to high-pressure exposure. Additionally, few quantitative or functional responses related to A. japonicus on transcriptional level were introduced by hydrostatic pressure changes after 1 h, and main biological responses were introduced after 4 h, suggesting that, when hydrostatic pressure is the mainly changed environmental factor, it will be better to fix sea cucumber samples for transcriptomic analysis within 1 h, but 4 h will be also acceptable.
FIGURE 1. Results of hierarchical clustering (HCL), differential expression analysis, and principal component analysis (PCA). (A) Hierarchical clustering analysis of seven experimental groups, including P0, P1, P2, P4, P6, P12, and P24. The high-pressure incubated duration of each group is shown via bar chart. (B) Hierarchical clustering analysis of 10 experimental groups, including P0, P24, R0.5, R1, R2, R4, R6, R12, R24, and R48. The atmospheric pressure recovered duration of each group is shown via bar chart. (C) The number of differentially expressed genes (DEGs) in different high-pressure incubations. (D) The number of DEGs in different atmospheric pressure recoveries. (E) Principal component analysis of all experimental groups according to their enrichment analysis results. less-resp, less-responding period; main-resp, main-responding period.
FIGURE 2. Results of enrichment analysis. (A) Gene Ontology enrichment analysis of up-regulated differentially expressed genes (DEGs). (B) Gene Ontology enrichment analysis of down-regulated DEGs. (C) Kyoto Encyclopedia of Genes and Genomes enrichment analysis of up-regulated DEGs. (D) Kyoto Encyclopedia of Genes and Genomes enrichment analysis of down-regulated DEGs. (E) Protein family enrichment analysis of up-regulated DEGs. (F) Protein family enrichment analysis of down-regulated DEGs. (I) Experimental groups of high-pressure incubations. (II) Experimental groups of atmospheric pressure recoveries. (III) Major expression profiles. Pf.A, profile A; Pf.B, profile B; Pf.C, profile C; Pf.D, profile D.
FIGURE 3. The linkage heatmap of differentially expressed genes (DEGs) and significantly up-regulated enriched items. The cells colored in dark red indicate that their corresponding DEGs are involved in their corresponding enriched items. Clustering results of k-means method are shown on the top of the heatmap.
FIGURE 4. The linkage heatmap of differentially expressed genes (DEGs) and significantly down-regulated enriched items. The cells colored in dark blue indicate that their corresponding DEGs are involved in their corresponding enriched items. Clustering results of k-means method are shown on the top of the heatmap.
FIGURE 5. Significant gene expression profiles. The number of genes of each profile is shown at left bottom of each frame. The red curves represent the expression patterns of each gene. The black line represents the model expression pattern. The y axis represents log2 (RFC) of expression values, and the x axis represents the time points. RFC, relative fold change.
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