Service Incident: New DOI registrations are working again. Re-registration of failed DOI registrations (~500) are still affected by the service incident at DataCite (our DOI registration agency).
Published March 17, 2017 | Version v1
Dataset Open

Assembly and comparison of two closely related Brassica napus genomes

  • 1. School of Plant Biology, The University of Western Australia, Stirling Highway, Crawley, WA 6009, Australia
  • 2. 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
  • 3. Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
  • 4. chool of Plant Biology, The University of Western Australia, Stirling Highway, Crawley, WA 6009, Australia
  • 5. National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, China
  • 6. Department of Biology, University of York, York, UK
  • 7. 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
  • 8. 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

Description

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.

Notes

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).

Files

Darmor_v81_Tapidor_Ningyou_SNPs.zip

Files (563.6 MB)

Name Size Download all
md5:b1e82c0e73a756d032731104419e428c
18.2 MB Download
md5:e59043a5e5d1f513ffcba88f47c783ae
28.2 MB Download
md5:15204096f1e30d9bb8e82bdaf7593366
11.5 MB Download
md5:fb05e8a600bc921cf2c2ecdd3ce2237f
225.8 MB Download
md5:3936ed7e811a328f4382f5d63b416eee
17.8 MB Preview Download
md5:cf391adc16d9ef27a973440d47d1a4b9
986.8 kB Preview Download
md5:d588bfee2b37e922bb854b4f52c9f059
137.2 kB Preview Download
md5:cd984306b8b1c22f8dedb8b230050ac2
50.4 kB Download
md5:c47e6d1fa1b16163d5c2dfef1f851433
29.4 kB Preview Download
md5:5b0907ab6b8f6f988397df6c6fab4ed7
816.1 kB Preview Download
md5:9c8051f3dab47b152645a9907d5b9e42
408.4 kB Preview Download
md5:4086a436ffd876f0de401311706e6180
14.5 MB Download
md5:24f54b23f55a4f267994643057e005a7
6.0 MB Download
md5:f056173e753add31f4834d4e9568c55c
22.8 MB Download
md5:92068fa0c05d6be4c1a6ae53a2a36baa
9.9 MB Download
md5:152d059ebaa4201fa846cdee25c618e9
190.4 MB Download
md5:1352c0cd5f2057dbd5d2f2181fa1a089
16.1 MB Preview Download