ArticlePloS one2012
Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867).
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
- Transcriptome Analysis Reveals the lncRNA-mRNA Co-expression Network Regulating the Aestivation of Sea Cucumber.Marine biotechnology (New York, N.Y.) · 2024Article
- Sea cucumbers: an emerging system in evo-devo.EvoDevo · 2024Review
- Biosynthesis of saponin defensive compounds in sea cucumbers.Nature chemical biology · 2022Article
- Development of Microsatellite Markers Based on Transcriptome Sequencing and Evaluation of Genetic Diversity in Swimming Crab (Frontiers in genetics · 2022Article
- Comparative Transcriptomes of the Body Wall of Wild and Farmed Sea CucumberInternational journal of molecular sciences · 2021Article
- Developmental gene regulatory network connections predicted by machine learning from gene expression data alone.PloS one · 2021Article
- De novo transcriptome analysis of stressed blood clam (Anadara broughtonii) and identification of genes associated with hemoglobin.Genes & genomics · 2020Article
- Lysine Acetylation is an Important Post-Translational Modification that Modulates Heat Shock Response in the Sea CucumberInternational journal of molecular sciences · 2019Article
- Identification and sequencing of the gene encoding DNA methyltransferase 3 (DNMT3) from sea cucumber, Apostichopus japonicus.Molecular biology reports · 2019Article
- Neuropeptide precursors and neuropeptides in the sea cucumber Apostichopus japonicus: a genomic, transcriptomic and proteomic analysis.Scientific reports · 2019Article
- De novo transcriptomic analysis of gonad of Strongylocentrotus nudus and gene discovery for biosynthesis of polyunsaturated fatty acids.Genes & genomics · 2019Article
- Reference assembly and gene expression analysis of Apostichopus japonicus larval development.Scientific reports · 2019Article
- Evaluation of two independent protocols for the extraction of DNA and RNA from different tissues of sea cucumberMethodsX · 2019Article
- Article
- Comparative Phospho- and Acetyl Proteomics Analysis of Posttranslational Modifications Regulating Intestine Regeneration in Sea Cucumbers.Frontiers in physiology · 2018Article
- Sea cucumber genome provides insights into saponin biosynthesis and aestivation regulation.Cell discovery · 2018Article
- Evidence for a Saponin Biosynthesis Pathway in the Body Wall of the Commercially Significant Sea Cucumber Holothuria scabra.Marine drugs · 2017Article
- Differential Expression of miRNAs in the Respiratory Tree of the Sea CucumberG3 (Bethesda, Md.) · 2017Article
- Identification and functional characterisation of 5-HT4 receptor in sea cucumber Apostichopus japonicus (Selenka).Scientific reports · 2017Article
- Transcriptome profiling of claw muscle of the mud crab (Scylla paramamosain) at different fattening stages.PloS one · 2017Article
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSea 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.
resultsIn 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.
conclusionPyrosequencing 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.
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