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Abstract
The organisation of the Sinapis alba genome, comprising 12 linkage groups (n = 12), was compared with the Brassicaceae ancestral karyotype (AK) genomic blocks previously described in other crucifer species. Most of the S. alba genome falls into conserved triplicated genomic blocks that closely match the AK-defined genomic blocks found in other crucifer species including the A, B, and C genomes of closely related Brassica species. In one instance, an S. alba linkage group (S05) was completely collinear with one AK chromosome (AK1), the first time this has been observed in a member of the Brassiceae tribe. However, as observed for other members of the Brassiceae tribe, ancestral genomic blocks were fragmented in the S. alba genome, supporting previously reported comparative chromosome painting describing rearrangements of the AK karyotype prior to the divergence of the Brassiceae from other crucifers. The presented data also refute previous phylogenetic reports that suggest S. alba was more closely related to Brassica nigra (B genome) than to B. rapa (A genome) and B. oleracea (C genome). A comparison of the S. alba and Arabidopsis thaliana genomes revealed many regions of conserved gene order, which will facilitate access to the rich genomic resources available in the model species A. thaliana for genetic research in the less well-resourced crop species S. alba.
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Affiliation(s)
- Matthew N. Nelson
- School of Plant Biology, Faculty of Natural and Agricultural Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Isobel A.P. Parkin
- School of Plant Biology, Faculty of Natural and Agricultural Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Derek J. Lydiate
- School of Plant Biology, Faculty of Natural and Agricultural Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
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Parkin IA, Clarke WE, Sidebottom C, Zhang W, Robinson SJ, Links MG, Karcz S, Higgins EE, Fobert P, Sharpe AG. Towards unambiguous transcript mapping in the allotetraploid Brassica napusThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”. Genome 2010; 53:929-38. [DOI: 10.1139/g10-053] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The architecture of the Brassica napus genome is marked by its evolutionary origins. The genome of B. napus was formed from the hybridization of two closely related diploid Brassica species, both of which evolved from an hexaploid ancestor. The extensive whole genome duplication events in its near and distant past result in the allotetraploid genome of B. napus maintaining multiple copies of most genes, which predicts a highly complex and redundant transcriptome that can confound any expression analyses. A stringent assembly of 142 399 B. napus expressed sequence tags allowed the development of a well-differentiated set of reference transcripts, which were used as a foundation to assess the efficacy of available tools for identifying and distinguishing transcripts in B. napus ; including microarray hybridization and 3′ anchored sequence tag capture. Microarray platforms cannot distinguish transcripts derived from the two progenitors or close homologues, although observed differential expression appeared to be biased towards unique transcripts. The use of 3′ capture enhanced the ability to unambiguously identify homologues within the B. napus transcriptome but was limited by tag length. The ability to comprehensively catalogue gene expression in polyploid species could be transformed by the application of cost-efficient next generation sequencing technologies that will capture millions of long sequence tags.
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Affiliation(s)
- Isobel A.P. Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Wayne E. Clarke
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Christine Sidebottom
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Wentao Zhang
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Stephen J. Robinson
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Matthew G. Links
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Steve Karcz
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Erin E. Higgins
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Pierre Fobert
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Andrew G. Sharpe
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
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