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Published online before print June 12, 2001, 10.1101/gr.GR-1617R
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Vol. 11, Issue 7, 1167-1174, July 2001

REPORTS
Conservation of Microstructure between a Sequenced Region of the Genome of Rice and Multiple Segments of the Genome of Arabidopsis thaliana

Klaus Mayer,1 George Murphy,2 Renato Tarchini,3,11 Rolf Wambutt,4 Guido Volckaert,5 Thomas Pohl,6 Andreas Düsterhöft,7 Willem Stiekema,8 Karl-Dieter Entian,9 Nancy Terryn,10 Kai Lemcke,1 Dirk Haase,1 Caroline R. Hall,2 Anne-Marie van Dodeweerd,2 Scott V. Tingey,3 Hans-Werner Mewes,1 Michael W. Bevan,2 and Ian Bancroft2,12

1 National Research Center for Environment and Health, Institute for Bioinformatics, Munich Information Centre for Protein Sequences, 85764 Neuherberg, Germany; 2 John Innes Centre, Colney, Norwich, NR7 4UH, United Kingdom; 3 DuPont Agricultural Biotechnology, Newark, Delaware 19711, USA; 4 AGOWA GmbH, D-12489 Berlin, Germany; 5 Katholieke Universiteit Leuven, Laboratory of Gene Technology, B-3001 Leuven, Belgium; 6 GATC GmbH, D-78467 Konstanz, Germany; 7 QIAGEN GmbH, Max-Volmer-Str.4, D-40724 Hilden, Germany; 8 Plant Research International, NL 6708 PB, Wageningen, The Netherlands; 9 Institut für Mikrobiologie, D-60439 Frankfurt/M., Germany; 10 Department of Genetics, University of Ghent, B-9000 Ghent, Belgium

The nucleotide sequence was determined for a 340-kb segment of rice chromosome 2, revealing 56 putative protein-coding genes. This represents a density of one gene per 6.1 kb, which is higher than was reported for a previously sequenced segment of the rice genome. Sixteen of the putative genes were supported by matches to ESTs. The predicted products of 29 of the putative genes showed similarity to known proteins, and a further 17 genes showed similarity only to predicted or hypothetical proteins identified in genome sequence data. The region contains a few transposable elements: one retrotransposon, and one transposon. The segment of the rice genome studied had previously been identified as representing a part of rice chromosome 2 that may be homologous to a segment of Arabidopsis chromosome 4. We confirmed the conservation of gene content and order between the two genome segments. In addition, we identified a further four segments of the Arabidopsis genome that contain conserved gene content and order. In total, 22 of the 56 genes identified in the rice genome segment were represented in this set of Arabidopsis genome segments, with at least five genes present, in conserved order, in each segment. These data are consistent with the hypothesis that the Arabidopsis genome has undergone multiple duplication events. Our results demonstrate that conservation of the genome microstructure can be identified even between monocot and dicot species. However, the frequent occurrence of duplication, and subsequent microstructure divergence, within plant genomes may necessitate the integration of subsets of genes present in multiple redundant segments to deduce evolutionary relationships and identify orthologous genes.

11 Present address: Plant Research International, Droevendaalsesleeg 1, 6708 PB, Wageningen, The Netherlands.

12 Corresponding author.

11:1167-1174 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00
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