Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies

Lei Zhang; Xu Cai; Jian Wu; Min Liu; Stefan Grob; Feng Cheng; Jianli Liang; Chengcheng Cai; Zhiyuan Liu; Bo Liu; Fan Wang; Song Li; Fuyan Liu; Xuming Li; Lin Cheng; Wencai Yang; Mai-He Li; Ueli Grossniklaus; Hongkun Zheng; Xiaowu Wang

doi:10.1038/s41438-018-0071-9

Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies

Hortic Res. 2018 Aug 15:5:50. doi: 10.1038/s41438-018-0071-9. eCollection 2018.

Authors

Lei Zhang^#^{1

2}, Xu Cai^#¹, Jian Wu^#¹, Min Liu^#³, Stefan Grob⁴, Feng Cheng¹, Jianli Liang¹, Chengcheng Cai¹, Zhiyuan Liu¹, Bo Liu¹, Fan Wang³, Song Li³, Fuyan Liu³, Xuming Li³, Lin Cheng⁵, Wencai Yang², Mai-He Li⁶, Ueli Grossniklaus⁴, Hongkun Zheng³, Xiaowu Wang^{1

5}

Affiliations

¹ 1Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, 100081 Beijing, China.
² 2College of Horticulture, China Agricultural University, 100193 Beijing, China.
³ 3Biomarker Technologies Corporation, 101300 Beijing, China.
⁴ 4Department of Plant and Microbial Biology, University of Zürich, 8008 Zürich, Switzerland.
⁵ Shandong Provincial Key Laboratory of Protected Vegetable Molecular Breeding, Shandong Shouguang Vegetable Seed Industry Group Co. Ltd, 262700 Shouguang, Shandong Province China.
⁶ 6Forest Dynamics, Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland.

^# Contributed equally.

Abstract

Brassica rapa comprises several important cultivated vegetables and oil crops. Current reference genome assemblies of Brassica rapa are quite fragmented and not highly contiguous, thereby limiting extensive genetic and genomic analyses. Here, we report an improved assembly of the B. rapa genome (v3.0) using single-molecule sequencing, optical mapping, and chromosome conformation capture technologies (Hi-C). Relative to the previous reference genomes, our assembly features a contig N50 size of 1.45 Mb, representing a ~30-fold improvement. We also identified a new event that occurred in the B. rapa genome ~1.2 million years ago, when a long terminal repeat retrotransposon (LTR-RT) expanded. Further analysis refined the relationship of genome blocks and accurately located the centromeres in the B. rapa genome. The B. rapa genome v3.0 will serve as an important community resource for future genetic and genomic studies in B. rapa. This resource will facilitate breeding efforts in B. rapa, as well as comparative genomic analysis with other Brassica species.