Structural and Functional Genomic Resources and Database Development

In-depth analysis of the Brassica oleracea genome is continually improving the structural and functional genomic resources and databases available to the Brassica oleracea research community. In this chapter, we highlight Bolbase as one such example. Bolbase is a comprehensive database which provides access to B. oleracea genomic and comparative genomic information. The B. oleracea genomic data includes nine fully assembled chromosomes and 1,848 scaffolds, with 45,758 protein-coding genes, 13,382 transposable elements, and 3,581 non-coding RNAs. Comparative genomic information includes syntenic regions among B. oleracea, B. rapa, and A. thaliana, synonymous (Ks) and non-synonymous (Ka) substitution rates between orthologous gene pairs, gene families, or clusters, and differences in quantity, category, and distribution of transposable elements on different chromosomes. Additionally, Bolbase also provides search and data mining tools, including a keyword search, a local BLAST server, and a customized GBrowse tool, which can extract annotations of genomic components identify similar sequences, and visualize syntenic regions among different plant species.