Xuequn Chen: Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China. ORCID
Chaobo Tong: The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China. ORCID
Xingtan Zhang: Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China. ORCID
Aixia Song: Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China. ORCID
Ming Hu: The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China.
Wei Dong: Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China. ORCID
Fei Chen: College of Horticulture, Nanjing Agricultural University, Nanjing, China.
Youping Wang: Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China.
Jinxing Tu: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, China.
Shengyi Liu: The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China.
Haibao Tang: Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China. ORCID
Liangsheng Zhang: Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China. ORCID
Rapeseed (Brassica napus L.) is a recent allotetraploid crop, which is well known for its high oil production. Here, we report a high-quality genome assembly of a typical semi-winter rapeseed cultivar, 'Zhongshuang11' (hereafter 'ZS11'), using a combination of single-molecule sequencing and chromosome conformation capture (Hi-C) techniques. Most of the high-confidence sequences (93.1%) were anchored to the individual chromosomes with a total of 19 centromeres identified, matching the exact chromosome count of B. napus. The repeat sequences in the A and C subgenomes in B. napus expanded significantly from 500 000 years ago, especially over the last 100 000 years. These young and recently amplified LTR-RTs showed dispersed chromosomal distribution but significantly preferentially clustered into centromeric regions. We exhaustively annotated the nucleotide-binding leucine-rich repeat (NLR) gene repertoire, yielding a total of 597 NLR genes in B. napus genome and 17.4% of which are paired (head-to-head arrangement). Based on the resequencing data of 991 B. napus accessions, we have identified 18 759 245 single nucleotide polymorphisms (SNPs) and detected a large number of genomic regions under selective sweep among the three major ecotype groups (winter, semi-winter and spring) in B. napus. We found 49 NLR genes and five NLR gene pairs colocated in selective sweep regions with different ecotypes, suggesting a rapid diversification of NLR genes during the domestication of B. napus. The high quality of our B. napus 'ZS11' genome assembly could serve as an important resource for the study of rapeseed genomics and reveal the genetic variations associated with important agronomic traits.
