Du H et al. (2012), Transcriptome sequencing and characterization f...

ECB-ART-42368

PLoS One 2012 Jan 01;73:e33311. doi: 10.1371/journal.pone.0033311.

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Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867).

Du H , Bao Z , Hou R , Wang S , Su H , Yan J , Tian M , Li Y , Wei W , Lu W , Hu X , Wang S , Hu J .

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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.

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Species referenced: Echinodermata
Genes referenced: LOC100887844 LOC100891497 LOC115919211 LOC115925415 LOC575704 LOC579000 LOC583082 LOC586122 LOC591221 mgat4c tubgcp2

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	Figure 1. Overview of the de novo assembly of the Apostichopus japonicus transcriptome.(A) Size distribution of raw reads. (B) Size distribution of contigs. (C) Log-log plot showing the dependence of contig lengths on the number of reads assembled into each. (D) Size distribution of isotigs.
	Figure 2. Gene ontology (GO) comparison (level 3) between the sea cucumber Apostichopus japonicus and the sea urchin Strongylocentrotus purpuratus.Transcriptome comparison revealed similar GO term representations between the two species.
	Figure 3. Quantitative real-time PCR (Q-PCR) validation of 12 genes that were differentially expressed between the active (white bar) and aestivating (grey bar) adult sea cucumbers.CTSL1, Cathepsin L1; API5, Apoptosis inhibitor 5; SAP18, Histone deacetylase complex subunit SAP18; GNMT, Glycine N-methyltransferase; SODC, Superoxide dismutase [Cu-Zn]; HSPB1, Heat shock protein beta-1; CD163, Scavenger receptor cysteine-rich type 1 protein M130; SMAD3, Mothers against decapentaplegic homolog 3; TUBA1, Tubulin alpha-1 chain; PSTI, aqualysin-1; CBPA1, Carboxypeptidase A1; CBPB, Carboxypeptidase B. For each Q-PCR validation, six technical replications were performed. Significant levels are indicated by * (p<0.05) and ** (p<0.01).