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

2018-08-15

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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17 schema:description 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.
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24 B. rapa genome
25 Brassica rapa
26 Brassica species
27 Further analysis
28 MB
29 N50 size
30 analysis
31 assembly
32 block
33 breeding efforts
34 capture technology
35 centromeres
36 chromosome conformation capture technology
37 community resources
38 comparative genomic analysis
39 comprises
40 contig N50 size
41 crops
42 efforts
43 events
44 fold improvement
45 genome
46 genome assembly
47 genome blocks
48 genomic analysis
49 genomic studies
50 important community resource
51 improved assembly
52 improvement
53 long terminal repeat retrotransposons
54 mapping
55 news events
56 oil crops
57 optical mapping
58 previous reference genome
59 rapa
60 rapa genome
61 reference genome
62 reference genome assembly
63 relationship
64 repeat retrotransposons
65 resources
66 retrotransposons
67 sequencing
68 single-molecule sequencing
69 size
70 species
71 study
72 technology
73 terminal repeat retrotransposons
74 v3.0
75 vegetables
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