Grass genomes

Abstract

For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that insert between genes. These retroelements are less abundant in smaller genome plants, including rice and sorghum. Although 5- to 200-kb blocks of methylated, presumably heterochromatic, retrotransposons flank most maize genes, rice and sorghum genes are often adjacent. Similar genes are commonly found in the same relative chromosomal locations and orientations in each of these three species, although there are numerous exceptions to this collinearity (i.e., rearrangements) that can be detected at the levels of both the recombinational map and cloned DNA. Evolutionarily conserved sequences are largely confined to genes and their regulatory elements. Our results indicate that a knowledge of grass genome structure will be a useful tool for gene discovery and isolation, but the general rules and biological significance of grass genome organization remain to be determined. Moreover, the nature and frequency of exceptions to the general patterns of grass genome structure and collinearity are still largely unknown and will require extensive further investigation.

Figure 1

Physical map of the Adh1-F region of maize. A 240-kbp region flanking the maize Adh1-F allele has been partially sequenced. Narrow lines indicate the locations of known or predicted genes, and the boxes indicate either confirmed retroelements (filled boxes) or sequences that have not yet been fully characterized (open boxes). Asterisks depict the sites of restriction fragments that cross-hybridized with the orthologous region of sorghum (15). Arrows below the line indicate putative or known transcripts and their orientations. Only one of these transcripts is associated with a gene that has an official designation, Adh1, whereas the others have only our operational names.

Figure 2

Physical maps of the Sh2/A1-homologous regions of rice and sorghum. Maps are based on the completed sequences of these regions from rice (A) (22) and sorghum (B) (24). Arrows above the line indicate the size and orientation of known or predicted transcripts. We have data to unambiguously support the expression of one of these genes, gene X of rice, which exhibits 100% homology with the sequenced portion of a rice cDNA (22). The other genes are thought to be expressed primarily because their predicted exons are well-conserved relative to the maize genes (22, 24). The two-headed arrow depicts the one identified retroelement in these two orthologous regions, a solo long terminal repeat of Leviathan (24, 25).