ShrimpGPAT: a gene and protein annotation tool for knowledge sharing and gene discovery in shrimp

BMC Genomics

Anuphap Prachumwat⁴  Burachai Sonthayanon¹  Sudsanguan Ngamsuriyaroj³  Timothy W Flegel¹  Sirintra Vaiwsri³  Parpakron Korshkari² 

[1] National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, 113 Paholyothin Road, Tambon Khlong 1, Amphoe Khlong Luang, Pathum Thani 12120, Thailand;Center of Excellence for Shrimp Molecular Biology and Biotechnology (CENTEX Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400, Thailand;Faculty of Information and Communication Technology, Mahidol University, Salaya Campus, Phutthamonthon District, Nakhon Pathom 73170, Thailand;Shrimp-Virus Interaction Laboratory, Agricultural Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, 113 Paholyothin Road, Tambon Khlong 1, Amphoe Khlong Luang, Pathum Thani 12120, Thailand

关键词: Community-based functional annotation;    Knowledge base;    Transcriptomes;    EST;    Decapoda;    Penaeid shrimp;   

Others  :  857067
DOI  :  10.1186/1471-2164-15-506

 received in 2014-01-22, accepted in 2014-06-17,  发布年份 2014

【 摘 要 】

Background

Although captured and cultivated marine shrimp constitute highly important seafood in terms of both economic value and production quantity, biologists have little knowledge of the shrimp genome and this partly hinders their ability to improve shrimp aquaculture. To help improve this situation, the Shrimp Gene and Protein Annotation Tool (ShrimpGPAT) was conceived as a community-based annotation platform for the acquisition and updating of full-length complementary DNAs (cDNAs), Expressed Sequence Tags (ESTs), transcript contigs and protein sequences of penaeid shrimp and their decapod relatives and for in-silico functional annotation and sequence analysis.

Description

ShrimpGPAT currently holds quality-filtered, molecular sequences of 14 decapod species (~500,000 records for six penaeid shrimp and eight other decapods). The database predominantly comprises transcript sequences derived by both traditional EST Sanger sequencing and more recently by massive-parallel sequencing technologies. The analysis pipeline provides putative functions in terms of sequence homologs, gene ontologies and protein-protein interactions. Data retrieval can be conducted easily either by a keyword text search or by a sequence query via BLAST, and users can save records of interest for later investigation using tools such as multiple sequence alignment and BLAST searches against pre-defined databases. In addition, ShrimpGPAT provides space for community insights by allowing functional annotation with tags and comments on sequences. Community-contributed information will allow for continuous database enrichment, for improvement of functions and for other aspects of sequence analysis.

Conclusions

ShrimpGPAT is a new, free and easily accessed service for the shrimp research community that provides a comprehensive and up-to-date database of quality-filtered decapod gene and protein sequences together with putative functional prediction and sequence analysis tools. An important feature is its community-based functional annotation capability that allows the research community to contribute knowledge and insights about the properties of molecular sequences for better, shared, functional characterization of shrimp genes. Regularly updated and expanded with data on more decapods, ShrimpGPAT is publicly available at http://shrimpgpat.sc.mahidol.ac.th/ webcite.

【 授权许可】

   
2014 Korshkari et al.; licensee BioMed Central Ltd.

【 图 表 】

【 参考文献 】

• [1]Flegel TW: Historic emergence, impact and current status of shrimp pathogens in Asia. J Invertebr Pathol 2012, 110:166-173.
• [2]Stentiford GD, Neil DM, Peeler EJ, Shields JD, Small HJ, Flegel TW, Vlak JM, Jones B, Morado F, Moss S, Lotz J, Bartholomay L, Behringer DC, Hauton C, Lightner DV: Disease will limit future food supply from the global crustacean fishery and aquaculture sectors. J Invertebr Pathol 2012, 110:141-157.
• [3]Tassanakajon A, Klinbunga S, Paunglarp N, Rimphanitchayakit V, Udomkit A, Jitrapakdee S, Sritunyalucksana K, Phongdara A, Pongsomboon S, Supungul P, Tang S, Kuphanumart K, Pichyangkura R, Lursinsap C: Penaeus monodon gene discovery project: the generation of an EST collection and establishment of a database. Gene 2006, 384:104-112.
• [4]Robalino J, Almeida JS, McKillen D, Colglazier J, Trent HF, Chen YA, Peck ME, Browdy CL, Chapman RW, Warr GW, Gross PS: Insights into the immune transcriptome of the shrimp Litopenaeus vannamei: tissue-specific expression profiles and transcriptomic responses to immune challenge. Physiol Genomics 2007, 29:44-56.
• [5]Leu JH, Chang CC, Wu JL, Hsu CW, Hirono I, Aoki T, Juan HF, Lo CF, Kou GH, Huang HC: Comparative analysis of differentially expressed genes in normal and white spot syndrome virus infected Penaeus monodon. BMC Genomics 2007, 8:120.
• [6]Jung H, Lyons RE, Dinh H, Hurwood DA, McWilliam S, Mather PB: Transcriptomics of a giant freshwater prawn (Macrobrachium rosenbergii): de novo assembly, annotation and marker discovery. PLoS One 2011, 6:e27938.
• [7]Lehnert SA, Wilson KJ, Byrne K, Moore SS: Tissue-specific expressed sequence tags from the black tiger shrimp penaeus monodon. Mar Biotechnol (NY) 1999, 1:465-0476.
• [8]Leu JH, Chen SH, Wang YB, Chen YC, Su SY, Lin CY, Ho JM, Lo CF: A review of the major penaeid shrimp EST studies and the construction of a shrimp transcriptome database based on the ESTs from four penaeid shrimp. Mar Biotechnol (NY) 2011, 13(4):608-621.
• [9]McKillen DJ, Chen YA, Chen C, Jenny MJ, Trent HF, Robalino J, McLean DC, Gross PS, Chapman RW, Warr GW, Almeida JS: Marine genomics: a clearing-house for genomic and transcriptomic data of marine organisms. BMC Genomics 2005, 6:34.
• [10]Leekitcharoenphon P, Taweemuang U, Palittapongarnpim P, Kotewong R, Supasiri T, Sonthayanon B: Predicted sub-populations in a marine shrimp proteome as revealed by combined EST and cDNA data from multiple Penaeus species. BMC Res Notes 2010, 3:295.
• [11]Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T: A travel guide to cytoscape plugins. Nat Methods 2012, 9:1069-1076.
• [12]Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL: BLAST+: architecture and applications. BMC Bioinformatics 2009, 10:421.
• [13]Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797.
• [14]Katoh K, Standley DM: MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013, 30:772-780.
• [15]Maglott D, Ostell J, Pruitt KD, Tatusova T: Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 2011, 39:D52-D57.
• [16]The Sequence Read Archive (SRA) http://www.ncbi.nlm.nih.gov/Traces/sra/ webcite
• [17]Ewing B, Green P: Base-calling of automated sequencer traces using phred. II Error probabilities. Genome Res 1998, 8:186-194.
• [18]Phred, Phrap and Consed http://www.phrap.org/ webcite
• [19]Huang X, Madan A: CAP3: A DNA sequence assembly program. Genome Res 1999, 9:868-877.
• [20]Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B: RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res 2012, 40:W622-W627.
• [21]The UniVec Database http://www.ncbi.nlm.nih.gov/tools/vecscreen/univec/ webcite
• [22]Huang H, McGarvey PB, Suzek BE, Mazumder R, Zhang J, Chen Y, Wu CH: A comprehensive protein-centric ID mapping service for molecular data integration. Bioinformatics 2011, 27:1190-1191.
• [23]Yu J, Pacifico S, Liu G, Finley RL: DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. BMC Genomics 2008, 9:461.
• [24]Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, Jandrasits C, Jimenez RC, Khadake J, Mahadevan U, Masson P, Pedruzzi I, Pfeiffenberger E, Porras P, Raghunath A, Roechert B, Orchard S, Hermjakob H: The IntAct molecular interaction database in 2012. Nucleic Acids Res 2012, 40:D841-D846.