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Article|15 Aug 2018|OPEN
Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies
Lei Zhang1,2, Xu Cai1, Jian Wu1, Min Liu3, 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 Wang1,5,
1Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, 100081 Beijing, China
2College of Horticulture, China Agricultural University, 100193 Beijing, China
3Biomarker Technologies Corporation, 101300 Beijing, China
4Department of Plant and Microbial Biology, University of Zürich, 8008 Zürich, Switzerland
5Shandong Provincial Key Laboratory of Protected Vegetable Molecular Breeding, Shandong Shouguang Vegetable Seed Industry Group Co. Ltd, 262700 Shouguang, Shandong Province, China
6Forest Dynamics, Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland

Horticulture Research 5,
Article number: 50 (2018)
doi: 10.1038/hortres.2018.50
Views: 765

Received: 27 Feb 2018
Revised: 21 May 2018
Accepted: 11 Jun 2018
Published online: 15 Aug 2018

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.