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Plant Physiology 135:735-744 (2004)
© 2004 American Society of Plant Biologists

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GENOME ANALYSIS

The Arabidopsis Genome Sequence as a Tool for Genome Analysis in Brassicaceae. A Comparison of the Arabidopsis and Capsella rubella Genomes1,[w]

Karine Boivin2, Adile Acarkan3, Rosa-Stella Mbulu4, Oliver Clarenz5 and Renate Schmidt6,*

Max-Delbrück-Laboratorium in der Max-Planck-Gesellschaft, 50829 Cologne, Germany

The annotated Arabidopsis genome sequence was exploited as a tool for carrying out comparative analyses of the Arabidopsis and Capsella rubella genomes. Comparison of a set of random, short C. rubella sequences with the corresponding sequences in Arabidopsis revealed that aligned protein-coding exon sequences differ from aligned intron or intergenic sequences in respect to the degree of sequence identity and the frequency of small insertions/deletions. Molecular-mapped markers and expressed sequence tags derived from Arabidopsis were used for genetic mapping in a population derived from an interspecific cross between Capsella grandiflora and C. rubella. The resulting eight Capsella linkage groups were compared to the sequence maps of the five Arabidopsis chromosomes. Fourteen colinear segments spanning approximately 85% of the Arabidopsis chromosome sequence maps and 92% of the Capsella genetic linkage map were detected. Several fusions and fissions of chromosomal segments as well as large inversions account for the observed arrangement of the 14 colinear blocks in the analyzed genomes. In addition, evidence for small-scale deviations from genome colinearity was found. Colinearity between the Arabidopsis and Capsella genomes is more pronounced than has been previously reported for comparisons between Arabidopsis and different Brassica species.

1 This work was supported by the Bundesministerium für Bildung und Forschung (grant no. 0311107) and by the European Union EudicotMap program (grant no. BIO–4CT–97–2170).

2 Present address: INRA-URGV, 2 rue Gaston Crémieux-CP 5708, 91057 Évry cedex, France.

3 Present address: Bayer AG, Landwirtschaftszentrum, PF-F-MWF, Geb. 6240, Alfred-Nobel-Strasse 50, 40789 Monheim, Germany.

4 Present address: Ministry of Agriculture, Water and Rural Development, Private Bag 13187, Windhoek, Namibia.

5 Present address: Max-Planck-Institut für Züchtungsforschung, Carl-von-Linné-Weg 10, 50829 Cologne, Germany.

6 Present address: Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14424 Potsdam, Germany.

[w] The online version of this article contains Web-only data.

Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.104.040030.

* Corresponding author; e-mail rschmidt{at}mpimp-golm.mpg.de; fax 49–331–567–8408.

Received January 20, 2004; returned for revision March 23, 2004; accepted March 24, 2004.




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