A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes - PubMed (original) (raw)

Comparative Study

. 2003 Oct 14;100(21):12265-70.

doi: 10.1073/pnas.1434476100. Epub 2003 Oct 6.

Affiliations

Comparative Study

A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes

Katica Ilic et al. Proc Natl Acad Sci U S A. 2003.

Abstract

The sequences of large insert clones containing genomic DNA that is orthologous to the maize adh1 region were obtained for sorghum, rice, and the adh1-homoeologous region of maize, a remnant of the tetraploid history of the Zea lineage. By using all four genomes, it was possible to describe the nature, timing, and lineages of most of the genic rearrangements that have differentiated this chromosome segment over the last 60 million years. The rice genome has been the most stable, sharing 11 orthologous genes with sorghum and exhibiting only one tandem duplication of a gene in this region. The lineage that gave rise to sorghum and maize acquired a two-gene insertion (containing the adh locus), whereas sorghum received two additional gene insertions after its divergence from a common ancestor with maize. The two homoeologous regions of maize have been particularly unstable, with complete or partial deletion of three genes from one segment and four genes from the other segment. As a result, the region now contains only one duplicated locus compared with the eight original loci that were present in each diploid progenitor. Deletion of these maize genes did not remove both copies of any locus. This study suggests that grass genomes are generally unstable in local genome organization and gene content, but that some lineages are much more unstable than others. Maize, probably because of its polyploid origin, has exhibited extensive gene loss so that it is now approaching a diploid state.

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Figures

Fig. 1.

Fig. 1.

Structures of two homoeologous genomic regions in maize. Arrows indicate the location, approximate size, and transcriptional orientation of predicted genes. Colored arrows represent the genes whose homoeologous copies are either completely (green) or partially (purple) deleted from one maize region. Purple boxes show the remaining fragments of partially deleted genes. Gray areas connect conserved sequences between the two maize regions. The only structurally intact candidate gene still present in both regions is gene 10. Orange arrowheads show long interspersed nuclear elements inserted in the intronic region(s) of two homoeologues. Two overlapping gray horizontal lines represent the two BACs (276N13 and 123C01) that were sequenced.

Fig. 2.

Fig. 2.

Colinear genomic regions in rice, sorghum, and two homoeologous segments in maize. The shaded areas connecting the regions represent conserved sequence. Gene content of the central part of rice BAC 84L17 (68.7 kb) is depicted; candidate genes from the 37.2- and 54.6-kb rice segments flanking the compared region are not shown. Orthologous genes (shown as arrows) in all four regions have the same numerical designations. Gray arrows show a unique tandem gene duplication in rice. Also, four sorghum genes that are not shared with rice are shown as gray arrows. The blended-gray regions show orthologous genes (3.5 and 7.5) that are shared between sorghum and one homoeologous maize region (contig 276N13/123C01). Gene fragments and truncated genes in the two maize segments are shown as gray boxes and vertical lines.

Fig. 3.

Fig. 3.

Schematic diagram of the simplest evolutionary model for events that took place in this orthologous region of the rice, sorghum, and maize genomes after their divergence from a common ancestor. Arrows indicate genes, whereas gray bars in the two maize segments show truncated gene fragments. The genic composition of the common ancestor of the three species is proposed, with 11 genes in this region, and is structurally very similar to the rice region.

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