title: Transcriptome analysis of the Larimichthys crocea liver in response to Cryptocaryon irritans.
abstract: The large yellow croaker (Larimichthys crocea) is an economically important marine fish cultured in China and East Asian countries and is facing a serious threat from Cryptocaryon irritans, which is a protozoan ectoparasite that infects most reared marine fish species. To understand the molecular immune mechanisms underlying the response to C. irritans, we first performed a comparative gene transcription analysis using livers from C. irritans-immunized L. croceas and from a control group through RNA-Seq technology. After the removal of low-quality sequences and assembly, 51360 contigs were obtained, with an average length of 1066.93 bp. Further, a blast analysis indicates that 30747 contigs can be annotated based on homology with matches in the NT, NR, gene, and string databases. A gene ontology analysis was used to classify 21598 genes according to three major functional categories: molecular function, cellular component, and biological process. Moreover, 14470 genes were found in 303 KEGG pathways. We used RSEM and EdgeR to determine that 3841 genes were significantly differentially expressed (FDR < 0.001), including 2129 up-regulated genes and 1712 down-regulated genes. A significant enrichment analysis of these differentially expressed genes and isogenes revealed major immune-related pathways, including the toll-like receptor, complement and coagulation cascades, and chemokine signaling pathways. In addition, 28748 potential simple sequence repeats (SSRs) were detected from 12776 transcripts, and 62992 candidate single nucleotide polymorphisms (SNPs) were identified in the L. croceas liver transcriptome. This study characterized a gene expression pattern for normal and C. irritans-immunized L. croceas for the first time and not only sheds new light on the molecular mechanisms underlying the host-C. irritans interaction but also facilitates future studies on L. croceas gene expression and functional genomics.
authors.affiliation: College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.
authors.forename: Panpan
authors.initials: P
authors.lastname: Wang
authors.affiliation: College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.
authors.forename: Yong-Quan
authors.initials: YQ
authors.lastname: Su
authors.affiliation: College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China. Electronic address: maoyong@xmu.edu.cn.
authors.forename: Yong
authors.initials: Y
authors.lastname: Mao
authors.affiliation: Zhejiang Ocean University, Zhoushan, 316022, China.
authors.forename: Jian-She
authors.initials: JS
authors.lastname: Zhang
authors.affiliation: Zhejiang Ocean University, Zhoushan, 316022, China.
authors.forename: Chang-Wen
authors.initials: CW
authors.lastname: Wu
authors.affiliation: Ningde Fufa Fisheries Co., LTD, Ningde, 352002, China.
authors.forename: Qiao-Zhen
authors.initials: QZ
authors.lastname: Ke
authors.affiliation: Ningde Fufa Fisheries Co., LTD, Ningde, 352002, China.
authors.forename: Kun-Huang
authors.initials: KH
authors.lastname: Han
authors.affiliation: Ningde Fufa Fisheries Co., LTD, Ningde, 352002, China.
authors.forename: Wei-Qiang
authors.initials: WQ
authors.lastname: Zheng
authors.affiliation: Ningde Fufa Fisheries Co., LTD, Ningde, 352002, China.
authors.forename: Nen-di
authors.initials: ND
authors.lastname: Xu
mesh_terms: D000818:Animals; D018925:Chemokines / Q000235:genetics; D016798:Ciliophora; D016770:Ciliophora Infections / Q000235:genetics* / Q000276:immunology / Q000662:veterinary; D005393:Fish Diseases / Q000235:genetics* / Q000276:immunology; D029941:Fish Proteins / Q000235:genetics*; D020869:Gene Expression Profiling / Q000662:veterinary; D008099:Liver / Q000378:metabolism*; D010473:Perciformes / Q000235:genetics* / Q000469:parasitology; D017423:Sequence Analysis, RNA
chemical_list: D018925:Chemokines; D029941:Fish Proteins
keywords: Cryptocaryon irritans; Immune mechanism; Infection; Larimichthys crocea; Transcriptome