ARS | Publication request: RoBuST: An Integrated Resource of Genomics Information for Plants in the Root and Bulb Crop Families Apiaceae and Alliaceae

Submitted to: Biomed Central (BMC) Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 6, 2010
Publication Date: August 6, 2010
Citation: Bhasi, A., Simon, P.W., Senalik, D.A., Kumar, B., Manikandan, V., Philip, P., Senapathy, P. 2010. RoBuST: An Integrated Resource of Genomics Information for Plants in the Root and Bulb Crop Families Apiaceae and Alliaceae. Biomed Central (BMC) Plant Biology. 10:161.

Interpretive Summary: Rapid advancements in DNA sequencing and molecular genetics techniques have generated a wealth of plant genomics, genetics, and breeding data. The rapid proliferation of plant genome information generated by these efforts has led to the development of several data analysis platforms focused on specific plant groups – for example a database called ‘Gramene’ for grain crops like corn and rice. Such integrated repositories of data with active input from the plant research community can greatly aid researchers to gain a deeper understanding of plant genetics, plant taxonomy, plant pathology and plant physiology and are valuable tools for supporting research initiatives focused on addressing challenges confronted in agriculture. Interestingly, most of the available plant data analysis platforms available today are focused on plant groups with high economic value and are associated with data collection from genome sequencing projects. For less-studied “minor” and “orphan” crops, with no ongoing genome sequencing efforts, very few data analysis tools are available. Root and bulb vegetables (RBV) represent one such group of orphan crops. These include carrots, celeriac (root celery), parsnips, onions, garlic, and leek – food crops common to virtually all agricultural regions and consumers' plates around the world. Yet the community of plant scientists working on RBV crops is a small one, perhaps as small as 10 and 25 full-time equivalent scientists in academic and government programs world-wide devoted to each of these crops. Most of this effort comes from breeders, geneticists, taxonomists, plant pathologists, and plant physiologists. A similar level of effort also comes from seed companies worldwide To initiate a platform to collect and organize genomic information useful for genetics, breeding, taxonomy, plant physiology and other data highly relevant to root and bulb vegetables, the RoBuST database has been developed. The current release of RoBuST provides a comprehensive collection of genomic information relevant to two root and bulb orphan crop families – Alliaceae and Apiaceae. RoBuST also has a unique data collection of Alliaceae/Apiaceae- specific genomic information and tools. A variety of sequence analysis and visualization tools are available in the RoBuST web interface for integrated analysis of these diverse data sets. RoBuST is of interest to researchers and seed companies working on root and bulb crops and their relatives.

Technical Abstract: Root and bulb vegetables (RBV) include carrots, celeriac (root celery), parsnips (Apiaceae), onions, garlic, and leek (Alliaceae) – food crops grown globally and consumed worldwide. Few data analysis platforms are currently available where data collection, annotation and integration initiatives are focused on RBV plant groups. Scientists working on RBV include breeders, geneticists, taxonomists, plant pathologists, and plant physiologists who use genomic data for a wide range of activities including the development of molecular genetic maps, delineation of taxonomic relationships, and investigation of molecular aspects of gene expression in biochemical pathways and disease responses. With genomic data coming from such diverse areas of plant science, availability of a community resource focused on these RBV data types would be of great interest to this scientific community. To initiate a platform to collect and organize genomic information useful for RBV researchers, the RoBuST database has been developed (www.robustdb.com) The current release of RoBuST contains genomics data for 294 Alliaceae and 816 Apiaceae plant species and has the following features: (1) comprehensive sequence annotations of 3,663 genes 5,959 RNAs, 22,723 ESTs and 11,438 regulatory sequence elements from Apiaceae and Alliaceae plant families; (2) graphical tools for visualization and analysis of sequence data; (3) access to traits, biosynthetic pathways, genetic linkage maps and molecular taxonomy data associated with Alliaceae and Apiaceae plants; (4) comprehensive plant splice signal repository of 659,369 splice signals collected from 6,015 plant species for comparative analysis of plant splicing patterns.