PAG-X  Plant, Animal & Microbe Genomes X Conference

January 12-16, 2002
Town & Country Convention Center
San Diego, CA

Poster: Genome Sequencing & ESTs
            

COMPARATIVE SEQUENCE ANALYSIS OF HOMOLOGOUS WX1 REGIONS IN BARLEY, MAIZE, PEARL MILLET, RICE, SORGHUM AND DIPLOID WHEAT

JIANXIN MA1 , Phillip J. SanMiguel2 , Jorge Dubcovsky3 , Bryan A. Shiloff4 , Nils Rostocks5 , Zeyu Jiang4 , Carlos S. Busso3 , Andris Kleinhofs5 , Katrien M. Devos6 , Wusirika Ramakrishna1 , Jeffrey L. Bennetzen1

1 Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
2 Purdue University Genomics Core, S004 WSLR, Purdue University, West Lafayette, IN 47907, USA
3 Department of Agronomy & Range Science, University of California, Davis, CA 95616, USA
4 National Centre for Genome Resources, Santa Fe, NM 87505, USA
5 Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
6 John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK

Single BACs containing homologous wx1 genomic regions in six grasses (barley, maize, pearl millet, rice, sorghum, and diploid wheat) were sequenced and analyzed. We found that these regions contain several small rearrangements of gene content, order and/or orientation. Depending on the criteria used for gene identification, even close relatives like maize/sorghum and barley/diploid wheat exhibited common gene content for only 23-75% and 13-33%, respectively, of the predicted genes. Some of the rearrangements appear to mark specific lineages. For instance, a cluster of five genes that are 5´ to wx1 appear to be in the same relative order in the lineage that gave rise to maize, sorghum and pearl millet, but are in the inverted orientation in rice. None of the genes around the wx1 homologues in barley or diploid wheat are homologues of any of the genes in the other four grass species studied. Barley and diploid wheat also appear to be highly rearranged relative to each other, sharing only one gene that is the most 3' proximal to wx1. Just 5´ to wx1 in maize, a triplication of an ~10kb segment containing 2 predicted genes per repeat was observed in maize, with one repeat in inverted orientation relative to the other two. These genes are not seen in the wx1 BACs for any of the other species investigated. Our data provide the first molecular description of a pearl millet genomic segment, and we found that retrotransposons account for more than 70% of this region.

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