ABSTRACT

1. Count of rice loci aligned: Chr 2 71 85 72 48 53 58 89 61 81 54 48 61 44 200 264 Aligned Rice Loci (Loci/Mb) Chr 3 Chr 8 Chr 4 Chr 9 Chr 10 10 kb Chr 5 Chr 11 Chr 6 Orthologue in region Chr 12 Chr 7 Orthologue not in region Chromosome Position (Mb) Target region for BAC skim mapping Rice 1 1 2 3 4 5 6 7 8 9 9 a 10 11 b 12 13 c 14 Sorghum 3 d 1 2 3 4 5 6 7 8 9 e e 10 11 12 13 f 14 Adapted from Lockton & Gaut (2005) Trends Genet 21:60 Maize 3 a a a 4 5 6 7 8 10 11 12 * * b b b Maize 8 3 6 7 9 c c c duplication fractionation d d d e e e Duplicates are no longer under selective pressure and are lost from one homoeologue or the other. f f f f Diploid Homoeologous pair Greater Gene Loss in Maize than Sorghum Skim Sequences Align Predominantly to Rice Loci on Chr. 1 Maize and sorghum regions orthologous to rice chr. 1 (35 - 41 Mb) were targeted for low coverage sequencing. In sorghum, the corresponding region was divided into 13 pools, each comprising 3-4 BAC clones. The corresponding region in maize was divided into two pools of 30 and 37 BAC clones. Each pool was sequenced to ~1.3x coverage. • Based on hits to TE-neg, conserved loci • Rice tandem arrays counted as one locus • Percent calculated over 100 kb sliding window a b Collinearity over targeted region Additional Cluster of Alignments on Rice Chr. 5 * c d e * f Chr. 1 Chr. 5 a b a c c b d * c e d f f e * f Chr. 3 Chr. 10 ABSTRACT Comparative maps between members of the grass family (Poaceae) display a remarkable degree of long-range chromosomal collinearity. However, when compared at the sequence level, this collinearity is punctuated by examples of gene loss, duplication, and long-distance movement. The extent to which such rearrangements have contributed to the 70 million year evolution of cereal genomes is not well understood due to the limited availability of assembled genomic sequences other than rice. We aim to build a high-resolution comparative map of rice chromosome 1 and corresponding regions of maize and sorghum, with a particular interest in documenting disruptions in gene micro-collinearity. Building off of comparative maps available at Gramene (www.gramene.org), we constructed BAC minimum tiling paths for regions of maize chromosome 8 and sorghum chromosome 3 that are orthologous to a 5.5 Mb region of rice chromosome 1. A strategy of low-coverage sequencing and alignment to the rice assembly resulted in a high-resolution comparative map across the region. Gene loss or movement was more prevalent in maize than in sorghum. Our findings are consistent with previous observations that following the tetraploidization in maize many duplicate genes were lost from one homeologous region or the other. This project was funded by NSF#0333074 and USDA-ARS CRIS Project #1907-21000-014-00D. Comparative Mapping of an Orthologous Region Of Rice, Maize, And Sorghum Joshua Stein1, Bonnie Hurwitz1, Patricia Klein2, Scott Jackson3, Theresa Musket4, Georgia Davis4, Lidia Gnoj1, Richard McCombie1, and Doreen Ware1,5 1Cold Spring Harbor Laboratory, 2Texas A&M University, 3Purdue University, 4University of Missouri, Columbia, 5USDA-ARS NAA Plant, Soil & Nutrition Laboratory Research Unit Fractionation in maize homoeologues Collinearity after ~50 M years Comparison of sequenced BACs from maize and sorghum to rice This map exemplifies a general pattern in which segments of a single chromosome in rice map to two chromosomes in maize due to the whole genome duplication in the maize progenitor. Synteny maps are available at www.gramene.org (see poster #181) * * Maize sequence unique to homoeologue • Maize 3 & 8 show complementary losses of genes from region • Sorghum-specific genes have rice orthologues on chr. 10, 3, & 9 • Lineage-specific tandem-duplications Comparative mapping using BAC skim sequences • Skim seq’s aligned to rice non-TE peptides by BLASTX: best significant hits tallied • 50% of loci detected by maize skim reside on rice chr. 1 • 67% of loci detected by sorghum skim reside on rice chr. 1 • Rice chr. 1 accounts for just 13% of all annotated loci in the rice genome • Similar results obtained by BLAT alignments Genome Duplication in Progenitor of Grasses • Skim sequences are detecting a region in rice Chr. 5 that is duplicated in rice Chr. 1 • A whole genome duplication took place prior to the origin of grasses. • An all vs. all blastp analysis of TIGR (Release 3) annotations shows that the rice chr. 1 region under study here has homeologous segments on rice chr. 5. On Rice Chr. 1, 89% of maize and 95% of sorghum hits map to the targeted region Hits on other chromosomes, except Chr. 5, were dispersed. Duplication/fractionation model of loss of collinearity† † Paterson AH et al. 2004. PNAS. 101:9903 Rice Progenitor of the grasses Divergence and continued fractionation duplication fractionation In most cases it was possible to find the true orthologue on chr. 1 for these sequences, and we are following up to ask if these are functional. Diploid Homoeologous pair Sorghum * Loss of collinearity