Genome duplication (polyploidy) is common during speciation among crop plants and their pathogens. The Gbrowse sites at SIUC, including SoyGD, shows the first physical map of a dicot since Arabidopsis, some of the first physical maps of soybean pathogens. The sites are being developed to show the first maps of a legume cell, tissue, organ and whole plant. SoyGD provides the best representation of a polyploid genome to date. The goal is to develop database tools that improve representations of polyploid genomic regions for soybean, other legumes and other plants. To address the goal there are three objectives:
Objective 1: To enhance the soybean (Glycine max) genome browser by integrating the cultivar ‘Forrest’ and ‘Williams’ physical maps with community resources at LIS and Soybase. Discoveries will derive from integration.
Objective 2: To improve the utility of the contigs and linked DNA sequence for identifying homeologous and conserved syntenic regions using Medicago truncatulata and Lotus japonicus genome sequences. Homeology is localized polyploidy. Conserved syntenty may help explain homeology’s function.
Objective 3: To provide researchers, businesses and educators with user-friendly access to fingerprints, maps, genome sequences and clones. Outreach will enrich the project
Approaches: Working with bioinformatics researchers as clients and users, to develop priorities for annotations and creative interactions that enhance the understanding of genomic data. Using agile software development methods, incrementally add features to the system building on users’ priorities and feedback.