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

• Published in: PloS one 2012-03, Vol.7 (3), p.e33311-e33311
• Main Authors: Du, Huixia, Bao, Zhenmin, Hou, Rui, Wang, Shan, Su, Hailin, Yan, Jingjing, Tian, Meilin, Li, Yan, Wei, Wen, Lu, Wei, Hu, Xiaoli, Wang, Shi, Hu, Jingjie
• Format: Article
• Language: English
• Subjects: Abiotic stress; Acropora millepora; Aestivation; Age Factors; Agriculture; Analysis; Animals; Apostichopus japonicus; Aquaculture; Aquaculture industry; Base Sequence; Biological activity; Biology; China; Chromosomes; Crassostrea gigas; Ctenopharyngodon idella; Data integration; Data mining; Developmental stages; Echinodermata; Echinoidea; Estivation - genetics; Evolution; Expressed Sequence Tags; Fish; Gene expression; Gene Expression Profiling; Gene Library; Gene sequencing; Genes; Genetic engineering; Genetic markers; Genomes; Genomic libraries; Genomics; Heat shock proteins; Holothurioidea; Holothuroidea; Invertebrates; Laboratories; Life sciences; Marine; Marine invertebrates; Microsatellite Repeats - genetics; Molecular Sequence Data; Polymorphism, Single Nucleotide - genetics; Proteins; Real-Time Polymerase Chain Reaction; Sea Cucumbers - classification; Sea Cucumbers - genetics; Sea Cucumbers - metabolism; Sequence Analysis, DNA; Simple sequence repeats; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Stress response; Strongylocentrotus purpuratus; Tissues; Transcriptome - genetics; Trends
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0033311

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. 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. 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.