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.
authors.affiliation: School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia.
authors.forename: Philipp E
authors.initials: PE
authors.lastname: Bayer
authors.affiliation: School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia.|School of Agriculture and Food Sciences, University of Queensland, St. Lucia, Qld, Australia.
authors.forename: Bhavna
authors.initials: B
authors.lastname: Hurgobin
authors.affiliation: Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, Vic., Australia.
authors.forename: Agnieszka A
authors.initials: AA
authors.lastname: Golicz
authors.affiliation: School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia.
authors.forename: Chon-Kit Kenneth
authors.initials: CK
authors.lastname: Chan
authors.affiliation: School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia.
authors.forename: Yuxuan
authors.identifier: http://orcid.org/0000-0002-0684-586X
authors.initials: Y
authors.lastname: Yuan
authors.affiliation: School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia.|School of Agriculture and Food Sciences, University of Queensland, St. Lucia, Qld, Australia.
authors.forename: HueyTyng
authors.initials: H
authors.lastname: Lee
authors.affiliation: School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia.|School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia.
authors.forename: Michael
authors.initials: M
authors.lastname: Renton
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, China.
authors.forename: Jinling
authors.initials: J
authors.lastname: Meng
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, China.
authors.forename: Ruiyuan
authors.initials: R
authors.lastname: Li
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Long
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Zou
authors.affiliation: Department of Biology, University of York, York, UK.
authors.forename: Ian
authors.initials: I
authors.lastname: Bancroft
authors.affiliation: Organization and Evolution of Complex Genomes (OECG), Institut National de la Recherche agronomique (INRA), Université d'Evry Val d'Essonne (UEVE), Evry, France.|Institute of System and Synthetic Biology, Genopole, Centre National de la Recherche Scientifique, Université d'Evry Val d'Essonne, Université Paris-Saclay, Evry, France.
authors.forename: Boulos
authors.initials: B
authors.lastname: Chalhoub
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, China.|Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia.
authors.forename: Graham J
authors.initials: GJ
authors.lastname: King
authors.affiliation: School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Batley
authors.affiliation: School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia.
authors.forename: David
authors.initials: D
authors.lastname: Edwards
mesh_terms: D029688:Brassica napus / Q000235:genetics; D020224:Expressed Sequence Tags; D017343:Genes, Plant; D018745:Genome, Plant; D058977:Molecular Sequence Annotation; D012091:Repetitive Sequences, Nucleic Acid
keywords: 
  Brassica napus
  ; Tapidor; contigPlacer; genome assembly; genome assembly improvement; genotyping by sequencing; whole genome comparison