PAG-X  Plant, Animal & Microbe Genomes X Conference

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

Workshop: Comparative Genomics
            

FREQUENT GENIC REARRANGEMENTS IN TWO REGIONS OF GRASS GENOMES IDENTIFIED BY COMPARATIVE SEQUENCE ANALYSIS

Wusirika Ramakrishna1 , Jianxin Ma1 , Phillip SanMiguel1 , John Emberton1 , Bryan Shiloff2 , Zeyu Jiang2 , Jorge Dubcovsky3 , Andris Kleinhofs4 , Joachim Messing5 , Jeffrey Bennetzen1 , Nils Rostoks4 , Carlos Busso3 , Matthew Ogden1 , Eric Linton5 , Katrien Devos6

1 Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
2 National Center for Genome Resources, Santa Fe, NM 87505, USA
3 Department of Agronomy & Range Science, University of California, Davis, 95616 CA, USA
4 Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
5 PGIR-Waksman Institute, Rutgers University, Piscataway, NJ 08855, USA
6 John Innes Centre, Norwich Research Park, Colney, Norwich

Grass genomes show extensive colinearity based on comparative genetic maps. Sequence analysis of the two regions, Rp1 and wx1 by sequencing of BACs from different grass genomes revealed frequent genic rearrangements. The Rp1 region contains multiple R genes, and undergoes a high rate of unequal recombination whereas wx1 gene shows a high rate of intragenic recombination. Sequence analysis of maize and sorghum Rp1 BACs revealed two Rp1 genes and twelve other gene-homologous sequences, of which at least ten genes were truncated in one maize segment and eight gene-homologous segments were found in a second maize segment, of which two were Rp1-related and the other six were truncated. A 42 kb region with an Rp1 gene, six truncated genes and three Opie retrotransposons was duplicated on these two BACs. In sorghum, the sequenced region included a cluster of five Rp1 homologues, of which two are truncated with N-terminal deletions. The Rp1-homologous region in sorghum has several genes that are either duplicated, inverted, or both. Sequence analysis of BACs containing homologous wx1 genomic regions in six grasses (barley, maize, pearl millet, rice, sorghum, and diploid wheat) revealed several small rearrangements of gene content, order and/or orientation. A five gene region 5' to wx1 shows inverted orientation in rice compared to sorghum. Variations in gene content were prominent around the wx1 homologues in barley and wheat compared to each other and to the other four grass species studied. A triplication of an ~10kb segment with 2 genes was present only in maize.

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