Frequent genic rearrangements in two regions of grass genomes identified by comparative sequence analysis

Comparative and Functional Genomics Comp Funct Genom 2002; 3: 165–166. Published online 21 March 2002 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002 / cfg.164 Conference Review Frequent genic rearrangements in two regions of grass genomes identified by comparative sequence analysis Wusirika Ramakrishna 1 *, Jianxin Ma 1 , Phillip SanMiguel 2 , John Emberton 1 , Jorge Dubcovsky 3 , Bryan A Shiloff 4 , Zeyu Jiang 4 , Nils Rostoks 5 , Carlos S Busso 3 , Matthew Ogden 1 , Eric Linton 6 , Andris Kleinhofs 5 , Katrien M Devos 7 , Joachim Messing 6 and Jeffrey L Bennetzen 1 Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA Purdue University Genomics Core, S004 WSLR, Purdue University, West Lafayette, IN 47907, USA Department of Agronomy & Range Science, University of California, Davis, 95616 CA, USA National Center for Genome Resources, Santa Fe, NM 87505, USA Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA PGIR-Waksman Institute, Rutgers University, Piscataway, NJ 08855, USA John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK * Correspondence to: Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA. E-mail: wusirika@purdue.edu Grass genomes show extensive colinearity based on comparative genetic maps, although some large chromosomal rearrangements mark particular lineages. Small rearrangements involving one or a few genes would be missed by these comparative maps. Hence, we have undertaken sequence com- parisons between BACs (bacterial artificial chromo- somes) that contain 80–200 kb genomic segments of several grass species. Rp1 is a complex disease resistance locus in maize that provides race-specific resistance to the leaf rust disease caused by the fungus Puccinia sorghi. Sequence analysis of maize and sorghum Rp1 BACs revealed two Rp1 homologues 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. The truncated gene segments may have arisen by break repair, probably through homologous or illegitimate recombination. A 43 kb region with an Rp1 homologue, six truncated genes and three Opie retrotransposons was duplicated on two maize BACs. Estimation of divergence times for the Rp1 Copyright # 2002 John Wiley & Sons, Ltd. homologues, the three Opie elements and the inter- vening regions between duplicated regions are consistent with the duplication having occurred within the last 200 000 years. The Retrotransposons Opie-B, Opie-C and Opie-D were inserted before this duplication. In sorghum, the sequenced region includes a cluster of five Rp1 homologues, of which two are truncated with N-terminal deletions. Of the other three Rp1 homologues, a stop codon is present in one and a retrotransposon is inserted in another. The Rp1-homologous region in sorghum has several genes that are either duplicated, inverted, or both. Five duplicated genes other than the Rp1 homologues are present. Physical mapping revealed the presence of eleven Rp1 homologues that mapped to about 400 kb in B73 maize. Six Rp1 homologues mapped to about 50 kb in sorghum inbred BTr623 to a region on linkage group H that is colinear with maize chromosome 10. The Waxy1 gene encodes UDP-glucose starch glycosyl transferase, an enzyme that converts amy- lose to amylopectin. Wx1 is in syntenic locations in all of these grass species, although the maize Wx1 is within a paracentric inversion that places it near centromeric heterochromatin. Sequence analysis of