Assembly and comparison of two closely related Brassica napus genomes

Philipp E Bayer, Bhavna Hurgobin, Agnieszka A. Golicz, Chon-Kit Kenneth Chan, Yuxuan Yuan, Hueytyng Lee, Michael Renton, Jinling Meng, Ruiyuan Li, Yan Long, Jun Zou, Ian Bancroft, Boulos Chalhoub, Graham J King, Jacqueline Batley, David Edwards

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

As an increasing number of plant genome sequences become available, it is clear that gene content varies between individuals, and the challenge arises to predict the gene content of a species. However, genome comparison is often confounded by variation in assembly and annotation. Differentiating between true gene absence and variation in assembly or annotation is essential for the accurate identification of conserved and variable genes in a species. 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. Our results are the first step towards comparison of the true differences between B. napus genomes and highlight the potential sources of error in the future production of a B. napus pangenome. This article is protected by copyright. All rights reserved.

Original languageEnglish
Pages (from-to)1-9
Number of pages9
JournalPlant Biotechnology Journal
Volume15
Issue number12
DOIs
Publication statusE-pub ahead of print - 14 Jun 2017

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Brassica napus
Genome
genome
Genes
genes
cultivars
Plant Genome
Artifacts
Research Design
prediction

Cite this

Bayer, Philipp E ; 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. / Assembly and comparison of two closely related Brassica napus genomes. In: Plant Biotechnology Journal. 2017 ; Vol. 15, No. 12. pp. 1-9.
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Bayer, PE, Hurgobin, B, Golicz, AA, Chan, C-KK, Yuan, Y, Lee, H, Renton, M, Meng, J, Li, R, Long, Y, Zou, J, Bancroft, I, Chalhoub, B, King, GJ, Batley, J & Edwards, D 2017, 'Assembly and comparison of two closely related Brassica napus genomes' Plant Biotechnology Journal, vol. 15, no. 12, pp. 1-9. https://doi.org/10.1111/pbi.12742

Assembly and comparison of two closely related Brassica napus genomes. / Bayer, Philipp E; 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.

In: Plant Biotechnology Journal, Vol. 15, No. 12, 14.06.2017, p. 1-9.

Research output: Contribution to journalArticle

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T1 - Assembly and comparison of two closely related Brassica napus genomes

AU - Bayer, Philipp E

AU - Hurgobin, Bhavna

AU - Golicz, Agnieszka A.

AU - Chan, Chon-Kit Kenneth

AU - Yuan, Yuxuan

AU - Lee, Hueytyng

AU - Renton, Michael

AU - Meng, Jinling

AU - Li, Ruiyuan

AU - Long, Yan

AU - Zou, Jun

AU - Bancroft, Ian

AU - Chalhoub, Boulos

AU - King, Graham J

AU - Batley, Jacqueline

AU - Edwards, David

N1 - This article is protected by copyright. All rights reserved.

PY - 2017/6/14

Y1 - 2017/6/14

N2 - As an increasing number of plant genome sequences become available, it is clear that gene content varies between individuals, and the challenge arises to predict the gene content of a species. However, genome comparison is often confounded by variation in assembly and annotation. Differentiating between true gene absence and variation in assembly or annotation is essential for the accurate identification of conserved and variable genes in a species. 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. Our results are the first step towards comparison of the true differences between B. napus genomes and highlight the potential sources of error in the future production of a B. napus pangenome. This article is protected by copyright. All rights reserved.

AB - As an increasing number of plant genome sequences become available, it is clear that gene content varies between individuals, and the challenge arises to predict the gene content of a species. However, genome comparison is often confounded by variation in assembly and annotation. Differentiating between true gene absence and variation in assembly or annotation is essential for the accurate identification of conserved and variable genes in a species. 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. Our results are the first step towards comparison of the true differences between B. napus genomes and highlight the potential sources of error in the future production of a B. napus pangenome. This article is protected by copyright. All rights reserved.

KW - Journal Article

U2 - 10.1111/pbi.12742

DO - 10.1111/pbi.12742

M3 - Article

VL - 15

SP - 1

EP - 9

JO - Plant Biotechnology Journal

JF - Plant Biotechnology Journal

SN - 1467-7644

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