Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China.
Sci Rep. 2020 Jul 24;10(1):12394. doi: 10.1038/s41598-020-69389-x.
Cabbage (Brassica oleracea var. capitata) is an important vegetable crop widely grown throughout the world, providing plentiful nutrients and health-promoting substances. To facilitate further genetics and genomic studies and crop improvement, we present here a high-quality reference genome for cabbage. We report a de novo genome assembly of the cabbage double-haploid line D134. A combined strategy of single-molecule real-time (SMRT) sequencing, 10× Genomics and chromosome conformation capture (Hi-C) produced a high quality cabbage draft genome. The chromosome-level D134 assembly is 529.92 Mb in size, 135 Mb longer than the current 02-12 reference genome, with scaffold N50 length being raised as high as 38 times. We annotated 44,701 high-quality protein-coding genes, and provided full-length transcripts for 45.59% of the total predicted gene models. Moreover, we identified novel genomic features like underrated TEs, as well as gene families and gene family expansions and contractions during B. oleracea evolution. The D134 draft genome is a cabbage reference genome assembled by SMRT long-read sequencing combined with the 10× Genomics and Hi-C technologies for scaffolding. This high-quality cabbage reference genome provides a valuable tool for improvement of Brassica crops.
结球甘蓝（Brassica oleracea var. capitata）是一种在世界各地广泛种植的重要蔬菜作物，提供丰富的营养物质和促进健康的物质。为了促进进一步的遗传学和基因组学研究和作物改良，我们在这里呈现了一个结球甘蓝的高质量参考基因组。我们报告了结球甘蓝双单倍体系 D134 的从头基因组组装。单分子实时（SMRT）测序、10× Genomics 和染色体构象捕获（Hi-C）的组合策略产生了高质量的结球甘蓝草案基因组。染色体水平的 D134 组装大小为 529.92 Mb，比当前的 02-12 参考基因组长 135 Mb，支架 N50 长度高达 38 倍。我们注释了 44701 个高质量的蛋白质编码基因，并为 45.59%的总预测基因模型提供了全长转录本。此外，我们鉴定了新的基因组特征，如被低估的转座元件，以及在 B. oleracea 进化过程中的基因家族和基因家族扩张和收缩。D134 草案基因组是通过 SMRT 长读测序与 10× Genomics 和 Hi-C 技术结合组装的结球甘蓝参考基因组。这个高质量的结球甘蓝参考基因组为芸薹属作物的改良提供了一个有价值的工具。
