Characterization of common carp transcriptome: sequencing, de novo assembly, annotation and comparative genomics.
Characterization of common carp transcriptome: sequencing, de novo assembly, annotation and comparative genomics.
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DOI：
10.1371/journal.pone.0035152
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Sun X
中科院分区：
文献类型：
--
作者：
Ji P;Liu G;Xu J;Wang X;Li J;Zhao Z;Zhang X;Zhang Y;Xu P;Sun X
鲤鱼（Cyprinus carpio）是鲤科鱼类中最重要的水产养殖品种之一，全球年产量约340万吨，占世界淡水养殖产量的近14%。由于鲤鱼在经济和生态上的重要性，迫切需要基因组数据进行遗传改良。然而，仍然没有足够的转录组数据可用。本项目的目标是对鲤鱼转录组进行深入测序，为鲤鱼研究提供组装良好的转录组序列。采用Roche 454平台进行鲤鱼转录组测序。共收集到1，418，591条干净的ESTs，组装成36，811个cDNA重叠群，平均长度为888 bp，N50长度为1，002 bp。进行注释，并从组装的重叠群中鉴定出总共19，165个独特的蛋白质。进行基因本体和KEGG分析，并将所有重叠群分类为功能类别，以了解基因功能和调控途径。从29，869个（81.1%）重叠群中检测到开放阅读框（ORF），平均ORF长度为763 bp。从这些重叠群中，鉴定了9，625个全长cDNA，其序列长度为201 bp至9，956 bp。比较分析显示，27，693个（75.2%）重叠群与斑马鱼Refseq蛋白具有显著相似性，24，371个（66.2%）、24，501个（66.5%）和25，025个（70.0%）重叠群与teraodon、medaka和三刺鱼refseq蛋白具有显著相似性。从1,730个重叠群中初步鉴定出总共2,064个微卫星，1,639个独特序列在两侧具有足够的侧翼序列用于引物设计。对鲤鱼的转录组进行了深度测序、从头组装和鉴定，为深入了解鲤鱼基因组提供了宝贵的资源。转录组数据将有助于鲤鱼基因组功能的进一步研究，并逐步应用于鲤鱼以及其他鲤科鱼类的育种。
Common carp (Cyprinus carpio) is one of the most important aquaculture species of Cyprinidae with an annual global production of 3.4 million tons, accounting for nearly 14% of the freshwater aquaculture production in the world. Due to the economical and ecological importance of common carp, genomic data are eagerly needed for genetic improvement purpose. However, there is still no sufficient transcriptome data available. The objective of the project is to sequence transcriptome deeply and provide well-assembled transcriptome sequences to common carp research community. Transcriptome sequencing of common carp was performed using Roche 454 platform. A total of 1,418,591 clean ESTs were collected and assembled into 36,811 cDNA contigs, with average length of 888 bp and N50 length of 1,002 bp. Annotation was performed and a total of 19,165 unique proteins were identified from assembled contigs. Gene ontology and KEGG analysis were performed and classified all contigs into functional categories for understanding gene functions and regulation pathways. Open Reading Frames (ORFs) were detected from 29,869 (81.1%) contigs with an average ORF length of 763 bp. From these contigs, 9,625 full-length cDNAs were identified with sequence length from 201 bp to 9,956 bp. Comparative analysis revealed that 27,693(75.2%) contigs have significant similarity to zebrafish Refseq proteins, and 24,371(66.2%), 24,501(66.5%) and 25,025(70.0%) to teraodon, medaka and three-spined stickleback refseq proteins. A total of 2,064 microsatellites were initially identified from 1,730 contigs, and 1,639 unique sequences had sufficient flanking sequences on both sides for primer design. The transcriptome of common carp had been deep sequenced, de novo assembled and characterized, providing the valuable resource for better understanding of common carp genome. The transcriptome data will facilitate future functional studies on common carp genome, and gradually apply in breeding programs of common carp, as well as closely related other Cyprinids.
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