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


RESULTS
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.


CONCLUSIONS
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.
Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; College of Life Science, Qingdao University, Qingdao, China.
Lin
L
Huang
Key Laboratory of Sustainable Development of Marine Fisheries, The Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; National Laboratory for Marine Science and Technology, Qingdao, China.
Guiyang
G
Li
Key Laboratory of Sustainable Development of Marine Fisheries, The Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; National Laboratory for Marine Science and Technology, Qingdao, China.
Zhaolan
Z
Mo
Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
Peng
P
Xiao
Key Laboratory of Sustainable Development of Marine Fisheries, The Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; National Laboratory for Marine Science and Technology, Qingdao, China.
Jie
J
Li
Key Laboratory of Sustainable Development of Marine Fisheries, The Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; National Laboratory for Marine Science and Technology, Qingdao, China.
Jie
J
Huang
D000818:Animals; D003165:Complement System Proteins / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D016207:Cytokines / Q000378:metabolism; D030561:Databases, Nucleic Acid; D005432:Flounder / Q000235:genetics* / Q000276:immunology* / Q000378:metabolism; D020869:Gene Expression Profiling; D007109:Immunity / Q000235:genetics*; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D011947:Receptors, Antigen, B-Cell / Q000378:metabolism; D011948:Receptors, Antigen, T-Cell / Q000378:metabolism; D015398:Signal Transduction; D013154:Spleen / Q000276:immunology* / Q000378:metabolism*; D051193:Toll-Like Receptors / Q000378:metabolism; D059467:Transcriptome
D016207:Cytokines; D011947:Receptors, Antigen, B-Cell; D011948:Receptors, Antigen, T-Cell; D051193:Toll-Like Receptors; D003165:Complement System Proteins