Mosaic organization of orthologous sequences in grass genomes

Abstract

Although comparative genetic mapping studies show extensive genome conservation among grasses, recent data provide many exceptions to gene collinearity at the DNA sequence level. Rice, sorghum, and maize are closely related grass species, once sharing a common ancestor. Because they diverged at different times during evolution, they provide an excellent model to investigate sequence divergence. We isolated, sequenced, and compared orthologous regions from two rice subspecies, sorghum, and maize to investigate the nature of their sequence differences. This study represents the most extensive sequence comparison among grasses, including the largest contiguous genomic sequences from sorghum (425 kb) and maize (435 kb) to date. Our results reveal a mosaic organization of the orthologous regions, with conserved sequences interspersed with nonconserved sequences. Gene amplification, gene movement, and retrotransposition account for the majority of the nonconserved sequences. Our analysis also shows that gene amplification is frequently linked with gene movement. Analyzing an additional 2.9 Mb of genomic sequence from rice not only corroborates our observations, but also suggests that a significant portion of grass genomes may consist of paralogous sequences derived from gene amplification. We propose that sequence divergence started from hotspots along chromosomes and expanded by accumulating small-scale genomic changes during evolution.

Figure 1

Sequence comparison of orthologous regions from rice, sorghum, and maize. Sequences of genomic regions from rice (subspecies japonica and indica), sorghum, and maize have been vertically arranged with a size ruler (in kilobases) for each sequence. Only orthologous regions (CR1–CR4) are highlighted. Light-blue areas indicate the homologous regions. The boxed sections between CR2 and CR3 in sorghum and maize represent an insertion relative to rice. Pink boxes along the rulers indicate conserved sequence regions across species (CR1–CR4, CRa, CRb). In maize, CR4 was divided into CR4-1 and CR4-2, reflecting an insertion relative to sorghum and rice. In sorghum, CRb was split into two pieces because of an insertion relative to maize. Green bars indicate RFLP marker php200725 and its orthologs. The second green bar in the sorghum region marks the duplication of php200725. Small triangles indicate amplified storage-protein gene copies and their orientation (22-kD zein in maize and 22-kD kafirin in sorghum, respectively). Violet arrows indicate Mla1-like disease-resistance genes and their orientation. All other genes are indicated by small red bars. Genes without a pink outer box indicate nonconserved genes. Gray bars indicate areas of retrotransposons, and blue bars DNA transposons. Two hatched boxes in sorghum indicate two MITE-rich regions (5′ region, <1 kb/MITE; 3′ region, <2 kb/MITE). All kafirins and zeins showed homology to each other, but only the oldest copies are indicated. A summary of predicted genes and their positions is given in Table 1 for convenience.