National Center for Genome Resources,Santa Fe,NM,USAMini-biographyMichael received his BS in Microbiology from New Mexico State University in 1999. Upon graduating, Michael joined the National Center for Genome Resources (NCGR) assisting with curation of Arabidopsis thaliana metabolic pathway data, software testing and data quality control. Michael quickly realized the importance and power that bioinformatics would bring to science and has returned to the University of New Mexico to pursue his MS in Computer Science. Michael is currently working as a software engineer programmer analyst and has contributed to the development of the Phytophthora Functional Genomics Database (PFGD: http://www.pfgd.org) as well as the Legume Information System (LIS: http://www.comparative-legumes.org). LIS developed by the National Center for Genome Resources in cooperation with the USDA Agricultural Research Service (ARS), is a comparative legume resource that integrates genetic and molecular data from multiple legume species enabling cross-species genomic and transcript comparisons.
The Legume Information System (LIS): an integrated, dynamic comparative legume information resourceGregory D. May
1, Michael D. Gonzales
1, Kamal Gajendran
1, Andrew D. Farmer
1, David Grant
2, Randy Shoemaker
2, William D. Beavis
11National Center for Genome Resources, Santa Fe, NM, USA
2USDA-ARS & Department of Agronomy, Iowa State University, Ames, IA, USA
gdm@ncgr.orgComparative genomics is the comparison and analysis of genomes of different species to gain a better understanding of how species have evolved and to determine gene function. Clade-oriented information resources such as LIS offer data and applications enabling comparative genomics approaches that utilise bioinformatics to leverage genomic information from model and reference organisms for the benefit of legume breeders and researchers.
LIS (www.comparative-legumes.org/) is a publicly accessible legume resource that integrates molecular and genetic data from phylogenetically diverse legume species enabling cross-species transcript, genomic and map comparisons. The intent of the LIS is to help researchers leverage data-rich model plants to fill knowledge gaps across crop legume species and provide the ability to traverse between interrelated data types.
The LIS virtual plant user interface facilitates intuitive navigation of
M. truncatula, Lotus, soybean and Arabidopsis EST and consensus transcript data. Currently, the sequence import functionality at LIS makes use of NCGR’s computational pipeline, XGI that uses a variety of algorithms for sequence pattern recognition, comparison and annotation (www.ncgr.org/xgi) and can handle genomic, EST or ORF sequence data types.
The XGI genomic pipeline (XGIg) processes LIS genomic data uploaded from GenBank as provided by the genome sequencing centers. The Comparative Functional Genomics Browser (CFGB) provides visualisation of comparative genomics analysis results including alignment of transcript data with genomic contigs. CFGB also enables dynamic visualisation of comparative alignments between genomic contigs through zooming, panning and sorting functions.
LIS incorporates a CMap-based viewer (www.gmod.org/cmap) that provides users with detailed sequence and annotation viewing that is provided by a custom sequence viewing module developed for LIS. CMap provides LIS users access to, where available, the genetic and physical maps of Medicago, soybean and Phaseolus. For comparative analyses, a map is selected from the database for use as a reference map. Other maps can be subsequently added so that alignments relative to the selected reference map can be compared.
Future implementations of LIS will utilise semantic web services to traverse between data types allowing users to following phenotype through genetic maps to annotated genome sequence to linkage groups of other species.
