凡纳滨对虾大量EST的生物信息学分析

孙政; 柳承璋; 李富花; 张晓军; 张俊彬; 相建海

doi:10.3969/j.issn.0253-4193.2013.05.014

凡纳滨对虾大量EST的生物信息学分析

doi: 10.3969/j.issn.0253-4193.2013.05.014

1.
上海海洋大学水产与生命学院, 上海 201306;中国科学院海洋研究所实验海洋生物学重点实验室, 山东青岛 266071
2.
中国科学院海洋研究所实验海洋生物学重点实验室, 山东青岛 266071
3.
上海海洋大学水产与生命学院, 上海 201306

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出版历程
- 收稿日期: 2012-06-06

Bioinformatic processing of a large number of Litopenaeus vannamei ESTs and analysis of tissue-specific gene expression

1.
College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China;Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
2.
Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
3.
College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China

摘要

摘要: 凡纳滨对虾是我国乃至世界最重要的对虾养殖种。EST(expressed sequence tags)测序是对没有基因组背景的生物进行功能基因分析最为有效的方法之一。为了研究凡纳滨对虾重要功能基因、以及为筛选分子标记奠定基础,本文集成了一套快速高效的EST信息深度挖掘的方法,并对公共数据库中161 241条凡纳滨对虾EST序列进行分析,获得了20 410 条unigenes,包括14 236条contigs和6 174条singlets。通过与NR数据库比对发现有注释的基因7 984条,并对其余12 426条未知基因中的4 702条进行了功能域注释。对有NR注释的基因的GO 分类分析获得其中2 715条基因的生物学过程、细胞定位和分子功能分类信息。此外,通过与模式生物通路图进行比对和定位,将3738条基因定位到270个KEGG通路图中,发现凡纳滨对虾的9条unigenes与果蝇丝裂原活化蛋白激酶(MAPK)通路的5个关键基因对应,提示凡纳滨对虾很可能存在类似的重要信号转导通路。另外,通过对6种组织,包括肝胰腺、淋巴器官、血细胞、鳃、眼柄和神经的EST进行比较分析,筛选获得了组织特异性转录本共7 000余条,并对这些特异性转录本进行了功能分类。本研究不仅开发了公共基因资源发掘的方法,也为对虾功能基因的研究利用提供了重要参考数据。
- 凡纳滨对虾 /
- EST /
- 基因组织特异性表达
Abstract: As the most important maricultured Penaeid species, Litopenaeus vannamei holds a pivotal position in the development of the shrimp aquaculture. EST (Expressed Sequence Tags) sequencing is an effective way to study functional genes of a species without genome background. Focusing on discovery and cloning of important functional genes, also laying the foundation for development of molecule marker, we summarized a set of bioinformatics methods to efficiently dig for profound EST information using the 161 241 EST sequences of L. vannamei form dbEST. EST assembly resulted in 20 410 unigenes (including 14 236 contigs and 6 174 singlets) among which 7 984 matched with known proteins by comparison with NR database. RPS-blast search identified functional domains of 4 702 unigenes which had no match in the NR database. Downstream Gene Ontology (GO) analysis classified 2 715 known unigenes into categories of biological process, cellular component and molecular function. Gene comparison with model organisms mapped 3 738 unigenes into 270 KEGG pathway maps, conveyed useful information of important L. vannamei pathways such as the mitogen-activated protein kinases (MAPK) pathway. Nine L. vannamei unigenes showed high similarity to 5 proteins in the Drosophila MAPK pathway, indicating its existence in L. vannamei. Comparative analysis among six tissues, including hepatopancreas, lymphoid organs, haematocytes, gill, eyestalk and the nerve cord provided about 7 000 suspected tissue-specific expressed genes, which were classified into GO categories. This work developed a methodology for public gene resource exploration and provided clues for gene function study of L. vannamei.
- Litopenaeus vannamei /
- EST /
- tissue-specific gene expression

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参考文献(26)

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