Comparative genomics of grasses promises a bountiful harvest.

Building on a rich history of comparative genomics, scientists are making rapid progress toward a comprehensive framework for comparative genomics of the grass family (Poaceae) that will permit comparative studies at new levels of intricacy. The sequences of each of the two rice (Oryza sativa) subspecies (Goff et al., 2002; Yu et al., 2002, 2005b; Matsumoto et al., 2005), the recent completion of a high-quality genetically and physically anchored whole-genome sequence for sorghum (Sorghum bicolor; Paterson et al., 2009), and the imminent completion of a wholegenome shotgun sequence for Brachypodium distachyon together sample three important grass clades (Fig. 1). The rapidly progressing maize (Zea mays) genome sequence (www.maizegenome.org) provides a second panicoid, distinguished from sorghum by about 12 million years of evolution, including a whole-genome duplication (Swigonova et al., 2004). Comparison of these genomes with one another and with other genomes promises to clarify the grass gene set, providing phylogenetic data helpful to resolving what are sometimes striking differences between independent annotations of the same genome sequence, for example, rice RAP2 (Tanaka et al., 2008) versus TIGR5 (Ouyang et al., 2007), which differ substantially. Grass plastome sequencing is also advancing (Bortiri et al., 2008). The generally similar gene content and order of cereals and related grasses, especially those such as Oryza, Sorghum, and Brachypodium that have not incurred lineage-specific genome duplications, provide a starting point for accelerating progress in the study and improvement of many additional taxa. Indeed, the vast majority of monocots lack sufficient genomic tools to investigate pertinent problems in agricultural productivity, conservation biology, ecology, invasion biology, population biology, and systematic biology. For example, orphan crops, which are collectively planted to 250 million ha year and yield US$100 billion per year farm gate value in the developing world (Naylor et al., 2004), are largely without genomics resources. Many noncultivated monocots that are important as weeds, invasives, or potential new crops are likewise unexplored at the DNA level. Deductions about gene arrangement based on alignments of fully sequenced genomes (Tang et al., 2008) together with use of conserved exon sequences and intron locations to develop generalized monocot genomic tools (Feltus et al., 2006; Lohithaswa et al., 2007) promise to benefit research on monocot model and nonmodel systems alike.