Data

Assembly and comparison of two closely related Brassica napus genomes

The University of Western Australia
Bayer, Philipp Emanuel ; Hurgobin, Bhavna ; Golicz, Agnieszka A. ; Chan, Chon-Kit Kenneth ; Yuan, Yuxuan ; Lee, HueyTyng ; Renton, Michael ; Meng, Jinling ; Li, Ruiyuan ; Long, Yan ; Zou, Jun ; Bancroft, Ian ; Chalhoub, Boulos ; King, Graham J. ; Batley, Jacqueline ; Edwards, David
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ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=info:doi10.5281/zenodo.400371&rft.title=Assembly and comparison of two closely related Brassica napus genomes&rft.identifier=10.5281/zenodo.400371&rft.publisher=Zenodo&rft.description=Here we present the de novo assembly of the B. napus cultivar Tapidor and comparison with an improved assembly of the B. napus cultivar Darmor-bzh. Both cultivars were annotated using the same method to allow comparison of gene content. We identified genes unique to each cultivar and differentiate these from artefacts due to variation in the assembly and annotation. We demonstrate that using a common annotation pipeline can result in different gene predictions, even for closely related cultivars, and repeat regions which collapse during assembly impact whole genome comparison. After accounting for differences in assembly and annotation, we demonstrate that the genome of Darmor-bzh contains a greater number of genes than the genome of Tapidor.&rft.creator=Bayer, Philipp Emanuel &rft.creator=Hurgobin, Bhavna &rft.creator=Golicz, Agnieszka A. &rft.creator=Chan, Chon-Kit Kenneth &rft.creator=Yuan, Yuxuan &rft.creator=Lee, HueyTyng &rft.creator=Renton, Michael &rft.creator=Meng, Jinling &rft.creator=Li, Ruiyuan &rft.creator=Long, Yan &rft.creator=Zou, Jun &rft.creator=Bancroft, Ian &rft.creator=Chalhoub, Boulos &rft.creator=King, Graham J. &rft.creator=Batley, Jacqueline &rft.creator=Edwards, David &rft.date=2017&rft.relation=http://research-repository.uwa.edu.au/en/publications/c4cf55a5-c69a-4815-8bee-696ba59891fb&rft_subject=Brassica napus&rft_subject=plant genome&rft_subject=genome assembly&rft.type=dataset&rft.language=English Access the data
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Here we present the de novo assembly of the B. napus cultivar Tapidor and comparison with an improved assembly of the B. napus cultivar Darmor-bzh. Both cultivars were annotated using the same method to allow comparison of gene content. We identified genes unique to each cultivar and differentiate these from artefacts due to variation in the assembly and annotation. We demonstrate that using a common annotation pipeline can result in different gene predictions, even for closely related cultivars, and repeat regions which collapse during assembly impact whole genome comparison. After accounting for differences in assembly and annotation, we demonstrate that the genome of Darmor-bzh contains a greater number of genes than the genome of Tapidor.

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External Organisations
The University of Western Australia; University of Queensland; Huazhong Agricultural University; York University Toronto; Université Evry Val d'Essonne); Southern Cross University
Associated Persons
Bhavna Hurgobin (Creator); Chon-Kit Kenneth Chan (Creator); HueyTyng Lee (Creator); David Edwards (Creator)Agnieszka A. Golicz (Creator); Jinling Meng (Creator); Ruiyuan Li (Creator); Yan Long (Creator); Jun Zou (Creator); Ian Bancroft (Creator); Boulos Chalhoub (Creator); Graham J. King (Creator)

Issued: 2017-03-17

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Subjects
Brassica napus | genome assembly | plant genome |

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