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Assembly and comparison of two closely related Brassica napus genomes

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Assembly and comparison of two closely related Brassica napus genomes. / Bayer, Philippe 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, 21.11.2017, p. 1602-1610.

Research output: Contribution to journal › Article › peer-review

Harvard

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. 1602-1610. https://doi.org/10.1111/pbi.12742

APA

Bayer, P. E., Hurgobin, B., Golicz, A. A., Chan, C-K. K., Yuan, Y., Lee, H., Renton, M., Meng, J., Li, R., Long, Y., Zou, J., Bancroft, I., Chalhoub, B., King, G. J., Batley, J., & Edwards, D. (2017). Assembly and comparison of two closely related Brassica napus genomes. Plant biotechnology journal, 15(12), 1602-1610. https://doi.org/10.1111/pbi.12742

Vancouver

Bayer PE, Hurgobin B, Golicz AA, Chan C-KK, Yuan Y, Lee H et al. Assembly and comparison of two closely related Brassica napus genomes. Plant biotechnology journal. 2017 Nov 21;15(12):1602-1610. https://doi.org/10.1111/pbi.12742

Author

Bayer, Philippe 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. 1602-1610.

Bibtex - Download

@article{db51cafa7b12455bb7acda3476291828,
title = "Assembly and comparison of two closely related Brassica napus genomes",
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 Brassica 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 future production of a B. napus pangenome.",
keywords = "Brassica napus, Tapidor, contigPlacer, genome assembly, genome assembly improvement, genotyping by sequencing, whole genome comparison, Genes, Plant, Molecular Sequence Annotation, Genome, Plant, Brassica napus/genetics, Repetitive Sequences, Nucleic Acid, Expressed Sequence Tags",
author = "Bayer, {Philippe E} and Bhavna Hurgobin and Golicz, {Agnieszka A} and Chan, {Chon-Kit Kenneth} and Yuxuan Yuan and HueyTyng Lee and Michael Renton and Jinling Meng and Ruiyuan Li and Yan Long and Jun Zou and Ian Bancroft and Boulos Chalhoub and King, {Graham J.} and Jacqueline Batley and David Edwards",
note = "{\textcopyright} 2017 The Authors.",
year = "2017",
month = nov,
day = "21",
doi = "10.1111/pbi.12742",
language = "English",
volume = "15",
pages = "1602--1610",
journal = "Plant biotechnology journal",
issn = "1467-7644",
publisher = "Wiley-Blackwell",
number = "12",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

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

AU - Bayer, Philippe 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 - © 2017 The Authors.

PY - 2017/11/21

Y1 - 2017/11/21

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 Brassica 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 future production of a B. napus pangenome.

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 Brassica 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 future production of a B. napus pangenome.

KW - Brassica napus

KW - Tapidor

KW - contigPlacer

KW - genome assembly

KW - genome assembly improvement

KW - genotyping by sequencing

KW - whole genome comparison

KW - Genes, Plant

KW - Molecular Sequence Annotation

KW - Genome, Plant

KW - Brassica napus/genetics

KW - Repetitive Sequences, Nucleic Acid

KW - Expressed Sequence Tags

UR - http://www.scopus.com/inward/record.url?scp=85020740237&partnerID=8YFLogxK

U2 - 10.1111/pbi.12742

DO - 10.1111/pbi.12742

M3 - Article

C2 - 28403535

VL - 15

SP - 1602

EP - 1610

JO - Plant biotechnology journal

JF - Plant biotechnology journal

SN - 1467-7644

IS - 12

ER -

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