日本牙鲆（Paralichthys olivaceus）脾脏转录组的从头组装，以鉴定参与免疫的假定基因。
De Novo assembly of the Japanese flounder (Paralichthys olivaceus) spleen transcriptome to identify putative genes involved in immunity.
作者信息
Huang Lin, Li Guiyang, Mo Zhaolan, Xiao Peng, Li Jie, Huang Jie
机构信息
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.
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.
出版信息
PLoS One. 2015 Feb 27;10(2):e0117642. doi: 10.1371/journal.pone.0117642. eCollection 2015.
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.
METHODOLOGY/PRINCIPAL FINDINGS: 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/SIGNIFICANCE: 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.
背景
牙鲆是亚洲一种具有重要经济价值的海水鱼类，遭受了由各种病原体引起的疾病爆发，这需要在基因组背景下获取更多与免疫相关基因的信息。然而，牙鲆的基因组和转录组数据仍然匮乏，这限制了对该物种免疫系统的研究。在本研究中，我们使用Illumina双末端测序平台对牙鲆脾脏转录组进行了表征，以鉴定参与免疫的假定基因。
方法/主要发现：构建了来自牙鲆脾脏的cDNA文库，并使用Illumina技术进行随机测序。去除低质量读段后产生了12,196,968条修剪后的读段，这些读段组装成了96,627个单基因。共有21,391个单基因（22.14%）在NCBI Nr数据库中得到注释，且BLASTx最佳匹配中只有1.1%与牙鲆蛋白质序列匹配。大约12,503个（58.45%）单基因被分类到三个基因本体组中，19,547个（91.38%）被归类到26个直系同源簇中，10,649个（49.78%）被分配到六个京都基因与基因组百科全书途径中。此外，鉴定出了40,928个假定的简单序列重复和47,362个假定的单核苷酸多态性。重要的是，我们鉴定出了1,563个假定的免疫相关单基因，它们映射到15条免疫信号通路。
结论/意义：牙鲆转录组数据为发现和鉴定新基因提供了丰富资源，此处鉴定出的免疫相关序列将有助于我们理解免疫反应所涉及的机制。此外，本研究中发现的大量潜在SSR和SNP是牙鲆未来构建连锁图谱或标记辅助育种计划的重要资源。
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