School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
Bioinformatics. 2012 Dec 1;28(23):3141-3. doi: 10.1093/bioinformatics/bts586. Epub 2012 Oct 7.
The Brassicaceae family includes the most important plant model Arabidopsis thaliana and many cruciferous vegetable crops. A number of close relatives of Arabidopsis and economically important Brassica species are being sequenced with whole-genome shotgun sequencing technologies. However, de novo assembly of full chromosomes is difficult, since many non-model Brassicaceae species are lacking genetic and/or physical maps. As a unique feature for Brassicaceae, the genome of each member is composed of 24 conserved chromosomal blocks, and the arrangement of the 24 blocks can be obtained from karyotype analysis via comparative chromosome painting experiments. Taking this advantage, we developed a bioinformatic tool named KGBassembler to automatically finalize assembly of full chromosomes from contigs and/or scaffolds based on available karyotypes of Brassicaceae species.
KGBassembler was implemented in C++ with a graphical user interface. It is freely available to academic users at http://www.cmbb.arizona.edu/KGBassembler/.
芸薹科植物包括最重要的植物模式拟南芥和许多十字花科蔬菜作物。许多与拟南芥亲缘关系密切的物种和经济上重要的芸薹属物种正在使用全基因组鸟枪法测序技术进行测序。然而，由于许多非模式芸薹科物种缺乏遗传和/或物理图谱，因此完整染色体的从头组装是困难的。作为芸薹科的一个独特特征，每个成员的基因组由 24 个保守的染色体块组成，并且可以通过比较染色体涂染实验从核型分析中获得 24 个块的排列。利用这一优势，我们开发了一种名为 KGBassembler 的生物信息学工具，该工具可以根据芸薹科物种的现有核型，自动完成基于 contigs 和/或 scaffolds 的完整染色体组装。
KGBassembler 是用 C++编写的，带有图形用户界面。它可以在 http://www.cmbb.arizona.edu/KGBassembler/ 上免费提供给学术用户。
