Analysis of the Brassica ´A´ and ´C´ genomes and comparison with the genome of Arabidopsis Thaliana

Love, C., Logan, E., Erwin, T., Spangenberg, G. and Edwards, D. (2006). Analysis of the Brassica ´A´ and ´C´ genomes and comparison with the genome of Arabidopsis Thaliana. In: Y. P. Lim, Acta Horticulturae. Proceedings of the Joint Meeting of the Fourteenth Crucifer Genetics Workshop and Fourth ISHS Symposium on Brassicas. 4th International Symposium on Brassicas and 14th Crucifer Genetics Workshop, Daejeon, Korea, (99-104). 24 - 28 October 2004.


Author(s) Love, C.
Logan, E.
Erwin, T.
Spangenberg, G.
Edwards, D.
Title of paper Analysis of the Brassica ´A´ and ´C´ genomes and comparison with the genome of Arabidopsis Thaliana
Formatted title  Analysis of the Brassica ´A´ and ´C´ genomes and comparison with the genome of Arabidopsis Thaliana
Conference name 4th International Symposium on Brassicas and 14th Crucifer Genetics Workshop
Conference location Daejeon, Korea
Conference dates 24 - 28 October 2004
Convener Y.P. Lim
Proceedings title Acta Horticulturae. Proceedings of the Joint Meeting of the Fourteenth Crucifer Genetics Workshop and Fourth ISHS Symposium on Brassicas
Editor(s) Y. P. Lim
Place published Leuven, Belgium
Publisher International Society for Horticultural Science
Publication date 2006
Volume number 706
ISBN 978-90-66054-45-5
ISSN 0567-7572
Start page 99
End page 104
Total pages 6
Language eng
Abstract/Summary The growing availability of Brassica genomic sequence data presents the opportunity of conducting a detailed analysis into the relationships between the Brassica A and C genomes as well as a comparison between these two Brassica genomes and the complete genome sequence of the model plant Arabidopsis thaliana. Through the Multinational Brassica Genome Project, there are a growing number of Brassica rapa (A genome) BAC end sequences being produced, with the aim of delivering the end sequences of 110,000 BACs by 2005. We have developed a computational tool for the comparative mapping of these Brassica BACs onto the Arabidopsis genome. The tool electronically maps BACs onto Arabidopsis by aligning the end sequences for each BAC with regions of the Arabidopsis genome sequence, followed by filtering for BAC ends aligning in an inverse orientation within a specified genomic distance (<500,000 bp). Furthermore, we have compared the publicly available B. oleracea (C genome) shotgun sequences both with the Arabidopsis genome and the B. rapa BAC end sequences. An analysis of the resulting data provides the opportunity to identify regions of conservation between the three genomes, regions of gene duplication, as well as regions of conserved synteny between B. rapa and Arabidopsis. The results provide an insight into the comparative structure of the three genomes and assist in the efficient selection of candidate B. rapa BACs to be sequenced as part of the Multinational Brassica Genome Project.
Subjects 060408 Genomics
060407 Genome Structure and Regulation
060102 Bioinformatics
0604 Genetics
Keyword(s) Brassica
Computational biology
Arabidopsis
Comparative genomics
 
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