PlantsDB

PlantsDB provides integrated genomic data and comparative-genomics tools to enable comparative analysis and interpretation of plant genomes across model organisms and crop species.

Key Features:

• Species coverage: Genomic instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley, and wheat.
• Comparative genomics integration: Integration of comparative-genomics tools, including CrowsNest, for cross-species analyses.
• Synteny visualization: Visualization and investigation of syntenic relationships between monocot genomes using CrowsNest.
• Repeat element resources: Inclusion of the MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) for repeat element annotation and analysis.
• Complex/repetitive genome support: Framework for cross-linking results from genome analysis strategies targeting complex and repetitive genomes, particularly Triticeae species such as wheat and barley.
• Interoperability: Interconnection with external resources via web services to enable integration of diverse genomic data.

Scientific Applications:

• Comparative genome analysis: Comparative analyses across model organisms and crop species to investigate genome structure and evolution.
• Synteny studies: Visualization and analysis of syntenic relationships among monocot genomes to study conserved genomic architecture.
• Repeat element research: Identification and characterization of repeat elements in plant genomes using mips-REdat and mips-REcat.
• Triticeae genome analysis: Interpretation and analysis of complex and repetitive Triticeae genomes, including wheat and barley.
• Integration of genome analyses: Cross-linking and consolidation of results from diverse genome analysis strategies to support integrative genomic interpretation.

Methodology:

Integration of CrowsNest for synteny visualization; cross-linking of genome analysis results via web services; incorporation of MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat).