Li Guoxi, Zhao Yinli, Liu Zhonghu, Gao Chunsheng, Yan Fengbin, Liu Bianzhi, Feng Jianxin
College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province 450002, PR China.
College of Biological Engineering, Henan University of Technology, Zhengzhou, Henan Province 450001, PR China.
Fish Shellfish Immunol. 2015 Jun;44(2):420-9. doi: 10.1016/j.fsi.2015.03.014. Epub 2015 Mar 21.
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.
鲤鱼（Cyprinus carpio）是鲤科中最重要的水产养殖物种之一，培育具有抗病能力的该物种变得越来越重要。然而，在基因组或转录组水平上，鲤鱼抗病免疫遗传学的研究尚显不足。在本研究中，通过Illumina双末端测序技术从鲤鱼脾脏的两个cDNA文库中获得了60,316,906和75,200,328条双末端纯净读段。总共组装得到了130,293个独特的转录片段（单基因），平均长度为1400.57 bp。约105,612个（81.06%）单基因可根据其与Nr、Nt、Swiss-Prot、COG、GO或KEGG数据库中匹配序列的同源性进行注释，发现它们代表46,747个非冗余基因。比较分析表明，59.82%的单基因与斑马鱼Refseq蛋白具有显著相似性。基因表达比较显示，在鲤鱼脾脏的两个发育阶段之间，10,432个和6889个注释单基因分别上调和下调至少两倍。进行了基因本体论和KEGG分析，将所有单基因分类到功能类别中，以了解基因功能和调控途径。此外，从35,618个单基因中检测到46,847个简单序列重复（SSR），并在鲤鱼脾脏转录组中鉴定出大量单核苷酸多态性（SNP）和插入/缺失（INDEL）位点。本研究首次对鲤鱼脾脏转录组进行了表征，为更好地理解鲤鱼免疫系统和防御机制提供了宝贵资源。这些知识也将促进未来鲤鱼免疫遗传学的功能研究，最终可能应用于育种计划。
