MIPS PlantsDB is a database framework for integrative and comparative plant genome research and provides data and information resources for individual plant species (including Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat). Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB.