Li Ying, Liu Gao-Feng, Ma Li-Ming, Liu Tong-Kun, Zhang Chang-Wei, Xiao Dong, Zheng Hong-Kun, Chen Fei, Hou Xi-Lin
State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
Biomarker Technologies Corporation, Beijing, 101300, China.
Hortic Res. 2020 Dec 28;7(1):212. doi: 10.1038/s41438-020-00449-z.
Non-heading Chinese cabbage (NHCC) is an important leafy vegetable cultivated worldwide. Here, we report the first high-quality, chromosome-level genome of NHCC001 based on PacBio, Hi-C, and Illumina sequencing data. The assembled NHCC001 genome is 405.33 Mb in size with a contig N50 of 2.83 Mb and a scaffold N50 of 38.13 Mb. Approximately 53% of the assembled genome is composed of repetitive sequences, among which long terminal repeats (LTRs, 20.42% of the genome) are the most abundant. Using Hi-C data, 97.9% (396.83 Mb) of the sequences were assigned to 10 pseudochromosomes. Genome assessment showed that this B. rapa NHCC001 genome assembly is of better quality than other currently available B. rapa assemblies and that it contains 48,158 protein-coding genes, 99.56% of which are annotated in at least one functional database. Comparative genomic analysis confirmed that B. rapa NHCC001 underwent a whole-genome triplication (WGT) event shared with other Brassica species that occurred after the WGD events shared with Arabidopsis. Genes related to ascorbic acid metabolism showed little variation among the three B. rapa subspecies. The numbers of genes involved in glucosinolate biosynthesis and catabolism were higher in NHCC001 than in Chiifu and Z1, due primarily to tandem duplication. The newly assembled genome will provide an important resource for research on B. rapa, especially B. rapa ssp. chinensis.
小白菜是一种在全球广泛种植的重要叶菜类蔬菜。在此，我们基于PacBio、Hi-C和Illumina测序数据，报道了小白菜品种NHCC001的首个高质量染色体水平基因组。组装得到的NHCC001基因组大小为405.33 Mb，contig N50为2.83 Mb，scaffold N50为38.13 Mb。组装基因组中约53%由重复序列组成，其中长末端重复序列（LTRs，占基因组的20.42%）最为丰富。利用Hi-C数据，97.9%（396.83 Mb）的序列被分配到10条假染色体上。基因组评估表明，该白菜型油菜NHCC001基因组组装质量优于目前其他可用的白菜型油菜组装，它包含48,158个蛋白质编码基因，其中99.56%至少在一个功能数据库中得到注释。比较基因组分析证实，白菜型油菜NHCC001经历了一次全基因组三倍化（WGT）事件，该事件与其他芸苔属物种共享，且发生在与拟南芥共享的全基因组加倍（WGD）事件之后。与抗坏血酸代谢相关的基因在三个白菜型油菜亚种间变化不大。参与硫代葡萄糖苷生物合成和分解代谢的基因数量在NHCC001中高于Chiifu和Z1，主要是由于串联重复。新组装的基因组将为白菜型油菜尤其是白菜亚种的研究提供重要资源。
