10.5281/zenodo.400371
https://zenodo.org/records/400371
oai:zenodo.org:400371
Bayer, Philipp Emanuel
Philipp Emanuel
Bayer
School of Plant Biology, The University of Western Australia, Stirling Highway, Crawley, WA 6009, Australia
Hurgobin, Bhavna
Bhavna
Hurgobin
School of Plant Biology, The University of Western Australia, Stirling Highway, Crawley, WA 6009, Australia, Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
Golicz, Agnieszka A.
Agnieszka A.
Golicz
Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
Chan, Chon-Kit Kenneth
Chon-Kit Kenneth
Chan
School of Plant Biology, The University of Western Australia, Stirling Highway, Crawley, WA 6009, Australia
Yuan, Yuxuan
Yuxuan
Yuan
School of Plant Biology, The University of Western Australia, Stirling Highway, Crawley, WA 6009, Australia
Lee, HueyTyng
HueyTyng
Lee
School of Plant Biology, The University of Western Australia, Stirling Highway, Crawley, WA 6009, Australia, Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
Renton, Michael
Michael
Renton
chool of Plant Biology, The University of Western Australia, Stirling Highway, Crawley, WA 6009, Australia
Meng, Jinling
Jinling
Meng
National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, China
Li, Ruiyuan
Ruiyuan
Li
National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, China
Long, Yan
Yan
Long
National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, China
Zou, Jun
Jun
Zou
National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, China
Bancroft, Ian
Ian
Bancroft
Department of Biology, University of York, York, UK
Chalhoub, Boulos
Boulos
Chalhoub
Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Recherche 1165 (Institut National de Recherche Agronomique, Centre National de la Recherche Scientifique, Université Evry Val d'Essonne), Evry 91057, France
King, Graham J.
Graham J.
King
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 2480, Australia
Batley, Jacqueline
Jacqueline
Batley
School of Plant Biology, The University of Western Australia, Stirling Highway, Crawley, WA 6009, Australia
Edwards, David
David
Edwards
School of Plant Biology, The University of Western Australia, Stirling Highway, Crawley, WA 6009, Australia
Assembly and comparison of two closely related Brassica napus genomes
Zenodo
2017
genome assembly
plant genome
Brassica napus
2017-03-17
Creative Commons Attribution 4.0 International
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.
The authors would like to acknowledge funding support from the Australian Research Council (Projects LP110100200, LP130100925, LP140100537 and DP160104497), from the UK Biotechnology and Biological Sciences Research Council (BBSRC) to GK (BB/E017797/1) and IB (BB/E017363/1) and from the National Basic Research and Development Programme of China (2006CB101600). This work was supported by resources provided by the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia, the Australian Genome Research Facility (AGRF), the Queensland Cyber Infrastructure Foundation (QCIF) and the Australian Partnership for Advanced Computing (APAC).