title: De novo assembly and characterization of the spleen transcriptome of common carp (Cyprinus carpio) using Illumina paired-end sequencing.
abstract: Common carp (Cyprinus carpio) is one of the most important aquacultured species of the family Cyprinidae, and breeding this species for disease resistance is becoming more and more important. However, at the genome or transcriptome levels, study of the immunogenetics of disease resistance in the common carp is lacking. In this study, 60,316,906 and 75,200,328 paired-end clean reads were obtained from two cDNA libraries of the common carp spleen by Illumina paired-end sequencing technology. Totally, 130,293 unique transcript fragments (unigenes) were assembled, with an average length of 1400.57 bp. Approximately 105,612 (81.06%) unigenes could be annotated according to their homology with matches in the Nr, Nt, Swiss-Prot, COG, GO, or KEGG databases, and they were found to represent 46,747 non-redundant genes. Comparative analysis showed that 59.82% of the unigenes have significant similarity to zebrafish Refseq proteins. Gene expression comparison revealed that 10,432 and 6889 annotated unigenes were, respectively, up- and down-regulated with at least twofold changes between two developmental stages of the common carp spleen. Gene ontology and KEGG analysis were performed to classify all unigenes into functional categories for understanding gene functions and regulation pathways. In addition, 46,847 simple sequence repeats (SSRs) were detected from 35,618 unigenes, and a large number of single nucleotide polymorphism (SNP) and insertion/deletion (INDEL) sites were identified in the spleen transcriptome of common carp. This study has characterized the spleen transcriptome of the common carp for the first time, providing a valuable resource for a better understanding of the common carp immune system and defense mechanisms. This knowledge will also facilitate future functional studies on common carp immunogenetics that may eventually be applied in breeding programs.
authors: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province 450002, PR China. Electronic address: liguoxi0914@126.com.
authors: Guoxi
authors: G
authors: Li
authors: College of Biological Engineering, Henan University of Technology, Zhengzhou, Henan Province 450001, PR China. Electronic address: zhaoyinli73@aliyun.com.
authors: Yinli
authors: Y
authors: Zhao
authors: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province 450002, PR China. Electronic address: Liuzhonghu2001@126.com.
authors: Zhonghu
authors: Z
authors: Liu
authors: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province 450002, PR China. Electronic address: gchsheng00@163.com.
authors: Chunsheng
authors: C
authors: Gao
authors: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province 450002, PR China. Electronic address: yanfb790811@sina.com.
authors: Fengbin
authors: F
authors: Yan
authors: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province 450002, PR China. Electronic address: Liubianzhi@126.com.
authors: Bianzhi
authors: B
authors: Liu
authors: Laboratory of Aquaculture and Genetic Breeding, Henan Academy of Fishery Science, Zhengzhou, Henan Province 450044, PR China. Electronic address: Fnjaxn@163.com.
authors: Jianxin
authors: J
authors: Feng
mesh_terms: D000818:Animals; D001483:Base Sequence; D002347:Carps / Q000235:genetics / Q000378:metabolism*; D019295:Computational Biology; D020869:Gene Expression Profiling / Q000662:veterinary; D005786:Gene Expression Regulation / Q000235:genetics / Q000502:physiology*; D015723:Gene Library; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D013045:Species Specificity; D013154:Spleen / Q000378:metabolism*; D059467:Transcriptome / Q000235:genetics*; D015027:Zebrafish / Q000235:genetics
keywords: Characterization; Common carp (Cyprinus carpio); Illumina paired-end sequencing; Spleen; Transcriptome