The Key Laboratory of Oil Crops Biology and Genetic Breeding, the Ministry of Agriculture, Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
BMC Genomics. 2013 Sep 30;14:664. doi: 10.1186/1471-2164-14-664.
Brassica oleracea is a morphologically diverse species in the family Brassicaceae and contains a group of nutrition-rich vegetable crops, including common heading cabbage, cauliflower, broccoli, kohlrabi, kale, Brussels sprouts. This diversity along with its phylogenetic membership in a group of three diploid and three tetraploid species, and the recent availability of genome sequences within Brassica provide an unprecedented opportunity to study intra- and inter-species divergence and evolution in this species and its close relatives.
We have developed a comprehensive database, Bolbase, which provides access to the B. oleracea genome data and comparative genomics information. The whole genome of B. oleracea is available, including nine fully assembled chromosomes and 1,848 scaffolds, with 45,758 predicted genes, 13,382 transposable elements, and 3,581 non-coding RNAs. Comparative genomics information is available, including syntenic regions among B. oleracea, Brassica rapa and Arabidopsis 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 chromosomes. Bolbase provides useful search and data mining tools, including a keyword search, a local BLAST server, and a customized GBrowse tool, which can be used to extract annotations of genome components, identify similar sequences and visualize syntenic regions among species. Users can download all genomic data and explore comparative genomics in a highly visual setting.
Bolbase is the first resource platform for the B. oleracea genome and for genomic comparisons with its relatives, and thus it will help the research community to better study the function and evolution of Brassica genomes as well as enhance molecular breeding research. This database will be updated regularly with new features, improvements to genome annotation, and new genomic sequences as they become available. Bolbase is freely available at http://ocri-genomics.org/bolbase.
芸薹属是十字花科中形态多样的物种，包含一组营养丰富的蔬菜作物，包括普通结球甘蓝、菜花、西兰花、球茎甘蓝、羽衣甘蓝、抱子甘蓝。这种多样性，加上其在三个二倍体和三个四倍体物种组中的系统发育成员地位，以及芸薹属内基因组序列的最新可用性，为研究该物种及其近缘种的种内和种间分化和进化提供了前所未有的机会。
我们开发了一个综合数据库 Bolbase，提供对 B. oleracea 基因组数据和比较基因组学信息的访问。B. oleracea 的整个基因组是可用的，包括九个完全组装的染色体和 1848 个支架，有 45758 个预测基因、13382 个转座元件和 3581 个非编码 RNA。比较基因组学信息是可用的，包括 B. oleracea、芸薹属和拟南芥之间的共线性区域、同源基因对、基因家族或簇之间的同义（Ks）和非同义（Ka）取代率，以及染色体上转座元件数量、类别和分布的差异。Bolbase 提供了有用的搜索和数据挖掘工具，包括关键字搜索、本地 BLAST 服务器和定制的 GBrowse 工具，可用于提取基因组组件的注释，识别相似序列并可视化物种间的共线性区域。用户可以下载所有基因组数据，并在高度可视化的环境中探索比较基因组学。
Bolbase 是 B. oleracea 基因组及其与亲缘物种基因组比较的第一个资源平台，因此它将帮助研究界更好地研究芸薹属基因组的功能和进化，并增强分子育种研究。该数据库将定期更新，增加新的功能、改进基因组注释，并在新的基因组序列可用时进行更新。Bolbase 可在 http://ocri-genomics.org/bolbase 免费获取。
