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Assembly and comparison of two closely related Brassica napus genomes

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Author(s)

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

Department/unit(s)

Publication details

JournalPlant biotechnology journal
DateAccepted/In press - 9 Apr 2017
DateE-pub ahead of print - 12 Apr 2017
DatePublished (current) - 21 Nov 2017
Issue number12
Volume15
Number of pages9
Pages (from-to)1602-1610
Early online date12/04/17
Original languageEnglish

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.

Bibliographical note

© 2017 The Authors.

    Research areas

  • 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

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