Dataset Information

Molecular Response to High Hydrostatic Pressure: Time-Series Transcriptomic Analysis of Shallow-Water Sea Cucumber Apostichopus japonicus.

ABSTRACT: 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.

SUBMITTER: Chen J

PROVIDER: S-EPMC7203883 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Publications

Molecular Response to High Hydrostatic Pressure: Time-Series Transcriptomic Analysis of Shallow-Water Sea Cucumber <i>Apostichopus japonicus</i>.

Chen Jiawei J Liang Linying L Li Yanan Y Zhang Haibin H

Frontiers in genetics 20200430

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 t ...[more]

PMID: 32425972

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Project description:The sea cucumber Apostichopus japonicus is a foodstuff with very high economic value in China, Japan and other countries in south-east Asia. It is at the heart of a multibillion-dollar industry and to meet demand for this product, aquaculture methods and facilities have been established. However, there are challenges associated with optimization of reproduction, feeding and growth in non-natural environments. Therefore, we need to learn more about the biology of A. japonicus, including processes such as aestivation, evisceration, regeneration and albinism. One of the major classes of molecules that regulate physiology and behaviour in animals are neuropeptides, and a few bioactive peptides have already been identified in A. japonicus. To facilitate more comprehensive investigations of neuropeptide function in A. japonicus, here we have analysed genomic and transcriptomic sequence data and proteomic data to identify neuropeptide precursors and neuropeptides in this species. We identified 44 transcripts encoding neuropeptide precursors or putative neuropeptide precursors, and in some instances neuropeptides derived from these precursors were confirmed by mass spectrometry. Furthermore, analysis of genomic sequence data enabled identification of the location of neuropeptide precursor genes on genomic scaffolds and linkage groups (chromosomes) and determination of gene structure. Many of the precursors identified contain homologs of neuropeptides that have been identified in other bilaterian animals. Precursors of neuropeptides that have thus far only been identified in echinoderms were identified, including L- and F-type SALMFamides, AN peptides and others. Precursors of several peptides that act as modulators of neuromuscular activity in A. japonicus were also identified. The discovery of a large repertoire of neuropeptide precursors and neuropeptides provides a basis for experimental studies that investigate the physiological roles of neuropeptide signaling systems in A. japonicus. Looking ahead, some of these neuropeptides may have effects that could be harnessed to enable improvements in the aquaculture of this economically important species.

Project description:BACKGROUND: Sea cucumbers are a special group of marine invertebrates. They occupy a taxonomic position that is believed to be important for understanding the origin and evolution of deuterostomes. Some of them such as Apostichopus japonicus represent commercially important aquaculture species in Asian countries. Many efforts have been devoted to increasing the number of expressed sequence tags (ESTs) for A. japonicus, but a comprehensive characterization of its transcriptome remains lacking. Here, we performed the large-scale transcriptome profiling and characterization by pyrosequencing diverse cDNA libraries from A. japonicus. RESULTS: In total, 1,061,078 reads were obtained by 454 sequencing of eight cDNA libraries representing different developmental stages and adult tissues in A. japonicus. These reads were assembled into 29,666 isotigs, which were further clustered into 21,071 isogroups. Nearly 40% of the isogroups showed significant matches to known proteins based on sequence similarity. Gene ontology (GO) and KEGG pathway analyses recovered diverse biological functions and processes. Candidate genes that were potentially involved in aestivation were identified. Transcriptome comparison with the sea urchin Strongylocentrotus purpuratus revealed similar patterns of GO term representation. In addition, 4,882 putative orthologous genes were identified, of which 202 were not present in the non-echinoderm organisms. More than 700 simple sequence repeats (SSRs) and 54,000 single nucleotide polymorphisms (SNPs) were detected in the A. japonicus transcriptome. CONCLUSION: Pyrosequencing was proven to be efficient in rapidly identifying a large set of genes for the sea cucumber A. japonicus. Through the large-scale transcriptome sequencing as well as public EST data integration, we performed a comprehensive characterization of the A. japonicus transcriptome and identified candidate aestivation-related genes. A large number of potential genetic markers were also identified from the A. japonicus transcriptome. This transcriptome resource would lay an important foundation for future genetic or genomic studies on this species.

Dataset Information

Molecular Response to High Hydrostatic Pressure: Time-Series Transcriptomic Analysis of Shallow-Water Sea Cucumber Apostichopus japonicus.

Publications

Molecular Response to High Hydrostatic Pressure: Time-Series Transcriptomic Analysis of Shallow-Water Sea Cucumber <i>Apostichopus japonicus</i>.

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