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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-12

AUTHORS

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

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. More... »

PAGES

50

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/s41438-018-0071-9

DOI

http://dx.doi.org/10.1038/s41438-018-0071-9

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1105814076

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30131865


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