De Novo assembly of the Japanese flounder (Paralichthys olivaceus) spleen transcriptome to identify putative genes involved in immunity

• Published in: PloS one Vol. 10; no. 2; p. e0117642
• Main Authors: Huang, Lin, Li, Guiyang, Mo, Zhaolan, Xiao, Peng, Li, Jie, Huang, Jie
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 27-02-2015; Public Library of Science (PLoS)
• Subjects: Animals; Bioinformatics; Breeding; Chemokines; Commercial fishing; Complement System Proteins - metabolism; Computational Biology - methods; Cytokines; Cytokines - metabolism; Databases, Nucleic Acid; Disease control; Encyclopedias; Epidemics; Fish; Fishery sciences; Fishes; Fishing; Flounder; Flounder - genetics; Flounder - immunology; Flounder - metabolism; Gene expression; Gene Expression Profiling; Gene sequencing; Genes; Genomes; Genomics; Immune response; Immune system; Immunity; Immunity - genetics; Laboratories; Marine biology; Marine fish; Microsatellite Repeats; Molecular Sequence Annotation; Outbreaks; Paralichthys olivaceus; Polymorphism, Single Nucleotide; Proteins; Receptors, Antigen, B-Cell - metabolism; Receptors, Antigen, T-Cell - metabolism; Scophthalmus maximus; Signal Transduction; Simple sequence repeats; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Spleen; Spleen - immunology; Spleen - metabolism; Sustainable development; Toll-Like Receptors - metabolism; Transcriptome; Zebrafish; Yellow Sea; China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0117642

Japanese flounder (Paralichthys olivaceus) is an economically important marine fish in Asia and has suffered from disease outbreaks caused by various pathogens, which requires more information for immune relevant genes on genome background. However, genomic and transcriptomic data for Japanese flounder remain scarce, which limits studies on the immune system of this species. In this study, we characterized the Japanese flounder spleen transcriptome using an Illumina paired-end sequencing platform to identify putative genes involved in immunity.
A cDNA library from the spleen of P. olivaceus was constructed and randomly sequenced using an Illumina technique. The removal of low quality reads generated 12,196,968 trimmed reads, which assembled into 96,627 unigenes. A total of 21,391 unigenes (22.14%) were annotated in the NCBI Nr database, and only 1.1% of the BLASTx top-hits matched P. olivaceus protein sequences. Approximately 12,503 (58.45%) unigenes were categorized into three Gene Ontology groups, 19,547 (91.38%) were classified into 26 Cluster of Orthologous Groups, and 10,649 (49.78%) were assigned to six Kyoto Encyclopedia of Genes and Genomes pathways. Furthermore, 40,928 putative simple sequence repeats and 47, 362 putative single nucleotide polymorphisms were identified. Importantly, we identified 1,563 putative immune-associated unigenes that mapped to 15 immune signaling pathways.
The P. olivaceus transciptome data provides a rich source to discover and identify new genes, and the immune-relevant sequences identified here will facilitate our understanding of the mechanisms involved in the immune response. Furthermore, the plentiful potential SSRs and SNPs found in this study are important resources with respect to future development of a linkage map or marker assisted breeding programs for the flounder.