title: Identification of Immune-Related Genes and Development of SSR/SNP Markers from the Spleen Transcriptome of Schizothorax prenanti.
abstract: Schizothorax prenanti (S. prenanti) is mainly distributed in the upstream regions of the Yangtze River and its tributaries in China. This species is indigenous and commercially important. However, in recent years, wild populations and aquacultures have faced the serious challenges of germplasm variation loss and an increased susceptibility to a range of pathogens. Currently, the genetics and immune mechanisms of S. prenanti are unknown, partly due to a lack of genome and transcriptome information. Here, we sought to identify genes related to immune functions and to identify molecular markers to study the function of these genes and for trait mapping. To this end, the transcriptome from spleen tissues of S. prenanti was analyzed and sequenced. Using paired-end reads from the Illumina Hiseq2500 platform, 48,517 transcripts were isolated from the spleen transcriptome. These transcripts could be clustered into 37,785 unigenes with an N50 length of 2,539 bp. The majority of the unigenes (35,653, 94.4%) were successfully annotated using non-redundant nucleotide sequence analysis (nt), and the non-redundant protein (nr), Swiss-Prot, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. KEGG pathway assignment identified more than 500 immune-related genes. Furthermore, 7,545 putative simple sequence repeats (SSRs), 857,535 single nucleotide polymorphisms (SNPs), and 53,481 insertion/deletion (InDels) were detected from the transcriptome. This is the first reported high-throughput transcriptome analysis of S. prenanti, and it provides valuable genetic resources for the investigation of immune mechanisms, conservation of germplasm, and molecular marker-assisted breeding of S. prenanti.
authors.affiliation: College of Animal Science & Technology, Hunan Agricultural University, Changsha, Hunan, China.|Fisheries Breeding and Healthy Cultivation Research Centre, Southwest University, Chongqing, China.|Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, P.R. China, Fisheries College, Jimei University, Xiamen, Fujian, China.|Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde, Hunan, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Luo
authors.affiliation: Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, P.R. China, Fisheries College, Jimei University, Xiamen, Fujian, China.
authors.forename: Shijun
authors.initials: S
authors.lastname: Xiao
authors.affiliation: Fisheries Breeding and Healthy Cultivation Research Centre, Southwest University, Chongqing, China.
authors.forename: Hua
authors.initials: H
authors.lastname: Ye
authors.affiliation: Fisheries Breeding and Healthy Cultivation Research Centre, Southwest University, Chongqing, China.
authors.forename: Zhengshi
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, P.R. China, Fisheries College, Jimei University, Xiamen, Fujian, China.
authors.forename: Changhuan
authors.initials: C
authors.lastname: Lv
authors.affiliation: Fisheries Breeding and Healthy Cultivation Research Centre, Southwest University, Chongqing, China.
authors.forename: Shuming
authors.initials: S
authors.lastname: Zheng
authors.affiliation: Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, P.R. China, Fisheries College, Jimei University, Xiamen, Fujian, China.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Wang
authors.affiliation: College of Animal Science & Technology, Hunan Agricultural University, Changsha, Hunan, China.|Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde, Hunan, China.
authors.forename: Xiaoqing
authors.initials: X
authors.lastname: Wang
mesh_terms: D000818:Animals; D018925:Chemokines / Q000378:metabolism; D003530:Cyprinidae / Q000235:genetics* / Q000378:metabolism; D018076:DNA, Complementary / Q000737:chemistry / Q000276:immunology; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats / Q000235:genetics*; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D012313:RNA / Q000302:isolation & purification / Q000378:metabolism; D017422:Sequence Analysis, DNA; D015398:Signal Transduction / Q000235:genetics; D013154:Spleen / Q000378:metabolism*; D051193:Toll-Like Receptors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D018925:Chemokines; D018076:DNA, Complementary; D051193:Toll-Like Receptors; D012313:RNA