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PLoS One
2017 Jan 01;127:e0181471. doi: 10.1371/journal.pone.0181471.
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Transcriptome analysis of the sea cucumber (Apostichopus japonicus) with variation in individual growth.
Gao L
,
He C
,
Bao X
,
Tian M
,
Ma Z
.
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The sea cucumber (Apostichopus japonicus) is an economically important aquaculture species in China. However, the serious individual growth variation often caused financial losses to farmers and the genetic mechanisms are poorly understood. In the present study, the extensively analysis at the transcriptome level for individual growth variation in sea cucumber was carried out. A total of 118946 unigenes were assembled from 255861 transcripts, with N50 of 1700. Of all unigenes, about 23% were identified with at least one significant match to known databases. In all four pair of comparison, 1840 genes were found to be expressed differently. Global hypometabolism was found to be occurred in the slow growing population, based on which the hypothesis was raised that growth retardation in individual growth variation of sea cucumber is one type of dormancy which is used to be against to adverse circumstances. Besides, the pathways such as ECM-receptor interaction and focal adhesion were enriched in the maintenance of cell and tissue structure and communication. Further, 76645 SSRs, 765242 SNPs and 146886 ins-dels were detected in the current study providing an extensive set of data for future studies of genetic mapping and selective breeding. In summary, these results will provides deep insight into the molecular basis of individual growth variation in marine invertebrates, and be valuable for understanding the physiological differences of growth process.
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28715451
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Fig 1. GO (Gene Ontology) categorization (Biological process, Cellular component and Molecular function) of unigenes in sea cucumber.Each annotated sequence is assigned at least one GO term. The x-axis represents GO subcategories. The left y-axis indicates the percentage of genes. The right y-axis indicates the number of DEGs.
Fig 2. KOG classification of putative proteins.
Fig 3. Venn diagram of differential gene expression in body wall and intestine of sea cucumber with different growth rate.The different colors represent four different subsets: blue indicates AJ_2SB vs. AJ_1SB; yellow indicates AJ_2SI vs. AJ_1SI; purple indicates AJ_2SI vs. AJ_2LI; green indicates AJ_2SB vs. AJ_2LB.
Fig 4. KEGG annotation of putative proteins.A, Cellular Processes; B, Enviromental Information Processing; C, Genetic Information Processing; D, Metabolism; E, Organismal Systems.
Fig 5. Comparison of relative fold changes between RNA-seq and qRT-PCR results between AJ_2SB and AJ_2LB.Positive values represent the up-regulated expression level in AJ_2SB; negative values represent the down-regulated expression level in AJ_2SB. TLR2: toll-like receptor 2; FST: follistatin; PFN: profilin; ANK1: ankyrin-1; MTF: melanotransferrin; ST2: stromelysin-2; PPI: pacifastin proteinase inhibitor; LA: lactadherin.
Fig 6. Distribution of SSR motifs.Different colors represent different repeat types.
Anchordoguy,
Acute blockage of the ubiquitin-mediated proteolytic pathway during invertebrate quiescence.
1994, Pubmed
Anchordoguy,
Acute blockage of the ubiquitin-mediated proteolytic pathway during invertebrate quiescence.
1994,
Pubmed
Arocho,
Validation of the 2-DeltaDeltaCt calculation as an alternate method of data analysis for quantitative PCR of BCR-ABL P210 transcripts.
2006,
Pubmed
Bakir,
Global Transcriptome Analysis Reveals Differences in Gene Expression Patterns Between Nonhyperhydric and Hyperhydric Peach Leaves.
2016,
Pubmed
Bentley,
Accurate whole human genome sequencing using reversible terminator chemistry.
2008,
Pubmed
Du,
Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867).
2012,
Pubmed
,
Echinobase
Grabherr,
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
2011,
Pubmed
Götz,
High-throughput functional annotation and data mining with the Blast2GO suite.
2008,
Pubmed
Hahn,
Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis.
2009,
Pubmed
Huang,
Differential expression patterns of growth-related microRNAs in the skeletal muscle of Nile tilapia (Oreochromis niloticus).
2012,
Pubmed
Kanehisa,
KEGG: kyoto encyclopedia of genes and genomes.
2000,
Pubmed
Liu,
Identification of the pathogens associated with skin ulceration and peristome tumescence in cultured sea cucumbers Apostichopus japonicus (Selenka).
2010,
Pubmed
,
Echinobase
Lv,
Transcriptome analysis of the Portunus trituberculatus: de novo assembly, growth-related gene identification and marker discovery.
2014,
Pubmed
Meyer,
Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx.
2009,
Pubmed
Mustoe,
Accelerated healing of incisional wounds in rats induced by transforming growth factor-beta.
1987,
Pubmed
Ramnanan,
Regulation of global protein translation and protein degradation in aerobic dormancy.
2009,
Pubmed
Reilly,
Frogs and estivation: transcriptional insights into metabolism and cell survival in a natural model of extended muscle disuse.
2013,
Pubmed
Sporn,
Transforming growth factor-beta: biological function and chemical structure.
1986,
Pubmed
Storey,
Aestivation: signaling and hypometabolism.
2012,
Pubmed
Straume,
Suppression of heat shock protein 27 induces long-term dormancy in human breast cancer.
2012,
Pubmed
Sun,
Large scale gene expression profiling during intestine and body wall regeneration in the sea cucumber Apostichopus japonicus.
2011,
Pubmed
,
Echinobase
Tang,
mRNA-Seq whole-transcriptome analysis of a single cell.
2009,
Pubmed
Tombuloglu,
High-throughput transcriptome analysis of barley (Hordeum vulgare) exposed to excessive boron.
2015,
Pubmed
Wang,
RNA-Seq: a revolutionary tool for transcriptomics.
2009,
Pubmed
Wang,
The diploid genome sequence of an Asian individual.
2008,
Pubmed
Zhang,
De novo assembly of the sea cucumber Apostichopus japonicus hemocytes transcriptome to identify miRNA targets associated with skin ulceration syndrome.
2013,
Pubmed
,
Echinobase
Zhao,
RNA-seq dependent transcriptional analysis unveils gene expression profile in the intestine of sea cucumber Apostichopus japonicus during aestivation.
2014,
Pubmed
,
Echinobase
van der Merwe,
Differential growth-related gene expression in abalone (Haliotis midae).
2011,
Pubmed
