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

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

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.

Journal: Horticulture research
DOI: 10.1038/s41438-018-0071-9
Year: 2018

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