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

Abstract

BackgroundAlthough 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.DescriptionShrimpGPAT 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.ConclusionsShrimpGPAT 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/.

New Paradigms to Help Solve the Global Aquaculture Disease Crisis

“…Particularly for shrimp, the problems associated with high-frequency genomic sequence repeats [ 34 ] may be overcome by application of longer-read sequencing technologies alongside other shorter-read technologies to allow for accurate assembly and characterisation. Open publication of such data as a “public good” will fast track new therapeutics [ 36 ] and provide increased acceptance of the importance of endogenous, viral-like elements in genetic immunity [ 37 ] (and, when deemed socially acceptable, in the production of edited-genome lines of fish [ 38 ], molluscs [ 39 ], and crustaceans [ 40 ]). Standardised approaches to pathogen (or pathobiome) sequencing and open data access must coincide with these developments [ 36 ].…”

“…Open publication of such data as a “public good” will fast track new therapeutics [ 36 ] and provide increased acceptance of the importance of endogenous, viral-like elements in genetic immunity [ 37 ] (and, when deemed socially acceptable, in the production of edited-genome lines of fish [ 38 ], molluscs [ 39 ], and crustaceans [ 40 ]). Standardised approaches to pathogen (or pathobiome) sequencing and open data access must coincide with these developments [ 36 ]. The basis for controlling progression from infection to disease in farmed hosts will benefit from a better understanding of fundamental mechanisms for pathogen tolerance in wild hosts where host background genetic diversity is higher [ 41 ] and where exposure to pathogens may have left an inherited legacy of natural resistance [ 42 , 43 ].…”

Hsp70 expression in shrimp Litopenaeus vannamei in response to IHHNV and WSSV infection

“…Marine shrimp in the family Penaeidae have gained status as a very important international seafood trade product of particular economic importance in shrimp farming countries [9]. During the past 20 years, viral diseases have been among the main causes of economic looses in shrimp farming, particularly in Asia and South America [2].…”