title: De novo annotation of the immune-enriched transcriptome provides insights into immune system genes of Chinese sturgeon (Acipenser sinensis).
abstract: Chinese sturgeon (Acipenser sinensis), one of the oldest extant actinopterygian fishes with very high evolutionary, economical and conservation interest, is considered to be one of the critically endangered aquatic animals in China. Up to date, the immune system of this species remains largely undetermined with little sequence information publicly available. Herein, the first comprehensive transcriptome of immune tissues for Chinese sturgeon was characterized using Illumina deep sequencing. Over 67 million high-quality reads were generated and de novo assembled into the final set of 91,739 unique sequences. The annotation pipeline revealed that 25,871 unigenes were successfully annotated in the public databases, of which only 2002 had significant match to the existing sequences for the genus Acipenser. Overall 22,827 unigenes were categorized into 52 GO terms, 12,742 were classified into 26 KOG categories, and 4968 were assigned to 339 KEGG pathways. A more detailed annotation search showed the presence of a notable representation of immune-related genes, which suggests that this non-teleost actinopterygian fish harbors the same intermediates as in the well known immune pathways from mammals and teleosts, such as pattern recognition receptor (PRR) signaling pathway, JAK-STAT signaling pathway, complement and coagulation pathway, T-cell receptor (TCR) and B-cell receptor (BCR) signaling pathways. Additional genetic marker discovery led to the retrieval of 20,056 simple sequence repeats (SSRs) and 327,140 single nucleotide polymorphisms (SNPs). This immune-enriched transcriptome of Chinese sturgeon represents a rich resource that adds to the currently nascent field of chondrostean fish immunogenetics and furthers the conservation and management of this valuable fish.
authors.affiliation: Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
authors.forename: Rong
authors.initials: R
authors.lastname: Zhu
authors.affiliation: Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Institute of Chinese Sturgeon, China Three Gorges Corporation, Yichang, Hubei 443100, China.
authors.forename: He-Jun
authors.initials: HJ
authors.lastname: Du
authors.affiliation: Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
authors.forename: Shun-Yi
authors.initials: SY
authors.lastname: Li
authors.affiliation: Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
authors.forename: Ya-Dong
authors.initials: YD
authors.lastname: Li
authors.affiliation: Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Ni
authors.affiliation: Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
authors.forename: Xue-Jing
authors.initials: XJ
authors.lastname: Yu
authors.affiliation: Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
authors.forename: Yan-Yan
authors.initials: YY
authors.lastname: Yang
authors.affiliation: Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.
authors.forename: Yu-Ding
authors.initials: YD
authors.lastname: Fan
authors.affiliation: Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.
authors.forename: Nan
authors.initials: N
authors.lastname: Jiang
authors.affiliation: Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China. Electronic address: zlb@yfi.ac.cn.
authors.forename: Ling-Bing
authors.initials: LB
authors.lastname: Zeng
authors.affiliation: Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China. Electronic address: xgwang@hubu.edu.cn.
authors.forename: Xing-Guo
authors.initials: XG
authors.lastname: Wang
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D029941:Fish Proteins / Q000235:genetics* / Q000378:metabolism; D005399:Fishes / Q000235:genetics*; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D051193:Toll-Like Receptors / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
chemical_list: D029941:Fish Proteins; D051193:Toll-Like Receptors
keywords: Chinese sturgeon (Acipenser sinensis); De novo assembly; Immune-related gene; Microsatellites; Transcriptome