The Brassicaceae family includes the most important plant model Arabidopsis thaliana and many cruciferous vegetable crops. Due to the lack of genetic and/or physical maps for many non-model Brassicaceae species, de novo assembly of full chromosomes is difficult in many experiments designed with short sequencing data. To address this problem, we developed a bioinformatics tool named KGBassembler to automatically finalize assembly of full chromosomes from contigs and/or scaffolds based on available karyotypes of Brassicaceae species (Figure 1). KGBassembler has been successfully applied to the assembly of Eutrema salsugineum, an extremophile model for abiotic stress tolerance studies.
Figure. Flowchart of karyotype-based genome assembly
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- Please cite the following article:
Ma C, Chen H, Xin M, et al. KGBassembler: a karyotype-based genome assembler for Brassicaceae species.[J]. Bioinformatics, 2012, 28(23):3141-3143.