P0325LIS (Legume Information System): A Clade Based Web Resource for Legumes
A major effort at LIS is to leverage data from information-rich species, such as soybean and Medicago, to aid the interpretation of data from other species, using phylogenetic and synteny-based approaches. Genes from all hosted genomes have been placed into ~18,500 gene families - searchable and viewable as gene trees and multiple alignments. These families enable traversal among orthologous and paralogous sequences across the legumes. This complements functional annotations based on protein domains and multi-species microsynteny views using a genome “context viewer” showing genomic regions with similar local gene content and ordering. Chromosome-scale synteny blocks are presented in per-species genome browsers.
The other emphasis at LIS is integration of genetic and genomic data. QTLs from many studies (so far focused on common bean and peanut) have been collected and integrated into a common database, and projected onto composite genetic maps (in CMap) when possible. Molecular markers are being mapped on to the genome to make possible traversal from traits to genome, and vice versa. Germplasm data is also being incorporated in readiness for future sequence-based genotyping and phenotype data.
LIS, funded by the USDA-ARS and jointly developed with NCGR, is a major component of the NSF-funded Legume Federation project that promotes sharing common resources and standards among its member databases.