Abstract
BackgroundOil crop seeds are important sources of fatty acids (FAs) for human and animal nutrition. Despite their importance, there is a lack of an essential bioinformatics resource on gene transcription of oil crops from a comparative perspective. In this study, we developed ocsESTdb, the first database of expressed sequence tag (EST) information on seeds of four large-scale oil crops with an emphasis on global metabolic networks and oil accumulation metabolism that target the involved unigenes.DescriptionA total of 248,522 ESTs and 106,835 unigenes were collected from the cDNA libraries of rapeseed (Brassica napus), soybean (Glycine max), sesame (Sesamum indicum) and peanut (Arachis hypogaea). These unigenes were annotated by a sequence similarity search against databases including TAIR, NR protein database, Gene Ontology, COG, Swiss-Prot, TrEMBL and Kyoto Encyclopedia of Genes and Genomes (KEGG). Five genome-scale metabolic networks that contain different numbers of metabolites and gene–enzyme reaction–association entries were analysed and constructed using Cytoscape and yEd programs. Details of unigene entries, deduced amino acid sequences and putative annotation are available from our database to browse, search and download. Intuitive and graphical representations of EST/unigene sequences, functional annotations, metabolic pathways and metabolic networks are also available. ocsESTdb will be updated regularly and can be freely accessed at http://ocri-genomics.org/ocsESTdb/.ConclusionocsESTdb may serve as a valuable and unique resource for comparative analysis of acyl lipid synthesis and metabolism in oilseed plants. It also may provide vital insights into improving oil content in seeds of oil crop species by transcriptional reconstruction of the metabolic network.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0399-8) contains supplementary material, which is available to authorized users.
Highlights
Oil crop seeds are important sources of fatty acids (FAs) for human and animal nutrition
The ocsESTdb database is the first integrated comparative analysis database of expressed sequence tag (EST) sequences from the seed of four oil crops. This database supplies a user-friendly interface, in which data can be freely accessed and downloaded. ocsESTdb is a uniquely comprehensive world-wide oil crop seed EST database, which includes sufficient information on unigenes that represent the characteristics of oil crops in terms of oil content
Information necessary to investigate the properties of oil crop genes at the molecular and function levels is supplied in the database
Summary
Oil crop seeds are important sources of fatty acids (FAs) for human and animal nutrition. Description: A total of 248,522 ESTs and 106,835 unigenes were collected from the cDNA libraries of rapeseed (Brassica napus), soybean (Glycine max), sesame (Sesamum indicum) and peanut (Arachis hypogaea). These unigenes were annotated by a sequence similarity search against databases including TAIR, NR protein database, Gene Ontology, COG, Swiss-Prot, TrEMBL and Kyoto Encyclopedia of Genes and Genomes (KEGG). More than 2,328,985 EST sequence entries are available in the public database (dbEST database of NCBI, as of October 2013) for the important oil crops B. napus (643,944), G. max (1,461,723), S. indicum (44,820) and A. hypogaea (178,498) These huge data sets are under-utilised due to the scarcity of informatics databases. A handful of such informatics resources are currently available, which provide high-level analysis of crop functional genomics in searchable forms [9,10,11]
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