- American Society of Plant Biologists
Worldwide, there are nearly 10,000 species of grasses, and this group includes many of humanity's most important sources of food, fiber, and forage: rice, wheat, maize, cotton, sorghum, and numerous others. Many of these species have complete genome sequences available and have well-established tools to analyze genome content, complexity, and variation among species. In a recent comprehensive review, Bennetzen (2007) summarized much of the recent progress and future challenges in understanding the genome organization and evolution of members of this important family.
Although all species of grasses diverged from a common ancestor <80 million years ago, there is remarkable variation in genome size and chromosome number. By contrast, there is less variation in gene content. Perhaps surprisingly, >90% of genes are shared between any two members of the grass family, and many distant relatives show colinearity of genes. Much of the variation among grass species results from differences in expression, copy number, or function of shared genes. In addition, significant variation occurs in the intergenic regions, which typically receive less attention than coding regions.
The genus Oryza, which contains 23 species, including cultivated rice, has diverged relatively recently from a common ancestor that existed ∼15 million years ago. Ammiraju et al. (pages 3191–3209) completed a comparative analysis of the architecture of the orthologous Adh1-Adh2 regions (120 to 600 kb) from 10 species of Oryza that represent all six diploid genome types in this genus (see figure ). They determined not only gene content, density, and copy number in this region, but also examined the divergence in coding and intergenic regions. This allowed them to propose a tentative timing of genus radiation from the common ancestor.
Phylogenomic framework of diploid species from the genus Oryza. Representative species from each known Oryza diploid genome type (AA to GG) that is part of Oryza Map alignment Project (www.omap.org). Origins, genome sizes, and seed phenotypes are shown on respective branches (O. sativa includes both subspecies japonica and indica). Image courtesy of Paul Sanchez, Jayson Talag, and Chuanzhu Fan.
The 46 intact genes in this region fell into eight distinct gene families, often organized into tandemly arranged clusters of two to twelve members. Much of the variation in gene colinearity was shown to be a result of lineage-specific gain and loss of family members. In several cases, large (>100 kb) inversions or deletions led to major sequence rearrangements that contributed to genome diversification.
Rapid and ongoing sequence flux was observed in the intergenic regions, much of it mediated by transposable elements, including LTR retrotransposons, MULEs, and MITEs. In some genome lineages, transposable elements were shown to be responsible for movement of entire genes from other chromosomes. In summary, this detailed analysis of the major sources contributing to genome instability provides a unique insight into the mechanism and chronology of Oryza speciation.
