Paritosh Kumar, Pradhan Akshay Kumar, Pental Deepak
Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India.
Department of Genetics, University of Delhi South Campus, New Delhi, 110021, India.
BMC Genomics. 2020 Dec 11;21(1):887. doi: 10.1186/s12864-020-07271-w.
Brassica nigra (BB), also called black mustard, is grown as a condiment crop in India. B. nigra represents the B genome of U's triangle and is one of the progenitor species of B. juncea (AABB), an important oilseed crop of the Indian subcontinent. We report the genome assembly of B. nigra variety Sangam.
The genome assembly was carried out using Oxford Nanopore long-read sequencing and optical mapping. A total of 1549 contigs were assembled, which covered ~ 515.4 Mb of the estimated ~ 522 Mb of the genome. The final assembly consisted of 15 scaffolds that were assigned to eight pseudochromosomes using a high-density genetic map of B. nigra. Around 246 Mb of the genome consisted of the repeat elements; LTR/Gypsy types of retrotransposons being the most predominant. The B genome-specific repeats were identified in the centromeric regions of the B. nigra pseudochromosomes. A total of 57,249 protein-coding genes were identified of which 42,444 genes were found to be expressed in the transcriptome analysis. A comparison of the B genomes of B. nigra and B. juncea revealed high gene colinearity and similar gene block arrangements. A comparison of the structure of the A, B, and C genomes of U's triangle showed the B genome to be divergent from the A and C genomes for gene block arrangements and centromeric regions.
A highly contiguous genome assembly of the B. nigra genome reported here is an improvement over the previous short-read assemblies and has allowed a comparative structural analysis of the A, B, and C genomes of the species belonging to the U's triangle. Based on the comparison, we propose a new nomenclature for B. nigra pseudochromosomes, taking the B. rapa pseudochromosome nomenclature as the reference.
黑芥（BB），也称为黑芥末，在印度作为一种调味品作物种植。黑芥代表了U三角中的B基因组，是印度次大陆重要油料作物芥菜（AABB）的祖先物种之一。我们报道了黑芥品种Sangam的基因组组装。
使用牛津纳米孔长读长测序和光学图谱进行基因组组装。共组装了1549个重叠群，覆盖了估计约522 Mb基因组中的约515.4 Mb。最终组装由15个支架组成，这些支架使用黑芥的高密度遗传图谱被分配到8条假染色体上。基因组中约246 Mb由重复元件组成；LTR/Gypsy类型的逆转座子最为主要。在黑芥假染色体的着丝粒区域鉴定出了B基因组特异性重复序列。共鉴定出57249个蛋白质编码基因，其中42444个基因在转录组分析中被发现表达。黑芥和芥菜的B基因组比较显示出高度的基因共线性和相似的基因块排列。对U三角中A、B和C基因组结构的比较表明，B基因组在基因块排列和着丝粒区域与A和C基因组不同。
本文报道的黑芥基因组高度连续的组装比以前的短读长组装有所改进，并允许对属于U三角的物种的A、B和C基因组进行比较结构分析。基于比较，我们以白菜的假染色体命名法为参考，提出了黑芥假染色体的新命名法。
