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

SUN Zheng; LIU Chengzhang; LI Fuhua; ZHANG Xiaojun; ZHANG Junbin; XIANG Jianhai

doi:10.3969/j.issn.0253-4193.2013.05.014

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SUN Zheng, LIU Chengzhang, LI Fuhua, ZHANG Xiaojun, ZHANG Junbin, XIANG Jianhai. Bioinformatic processing of a large number of Litopenaeus vannamei ESTs and analysis of tissue-specific gene expression[J]. Haiyang Xuebao, 2013, 35(5): 128-136. doi: 10.3969/j.issn.0253-4193.2013.05.014

Citation:

SUN Zheng, LIU Chengzhang, LI Fuhua, ZHANG Xiaojun, ZHANG Junbin, XIANG Jianhai. Bioinformatic processing of a large number of Litopenaeus vannamei ESTs and analysis of tissue-specific gene expression[J]. Haiyang Xuebao, 2013, 35(5): 128-136. doi: 10.3969/j.issn.0253-4193.2013.05.014

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

doi: 10.3969/j.issn.0253-4193.2013.05.014

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

Received Date: 2012-06-06

Abstract

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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References(26)

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