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First published online November 12, 2008; 10.1104/pp.108.128926 Plant Physiology 149:111-116 (2009) © 2009 American Society of Plant Biologists
Poaceae Genomes: Going from Unattainable to Becoming a Model Clade for Comparative Plant GenomicsDepartment of Plant Biology, Michigan State University, East Lansing, Michigan 48824
Genomics has an immense potential for improving our understanding of critical issues in plant growth and development, some of which can be applied to improvement of crop production. Midway into the second decade of genomics, genome and transcriptome sequencing efforts with the Poaceae are impressive given the technical and fiscal challenges presented by the typically large, repetitive genomes found within the Poaceae (Smith and Flavell, 1975
The first genome-scale sequences generated for the Poaceae were ESTs that represent the transcribed portion of a genome and provide a rapid, economic approach to sampling the gene space of an organism. As early access sequence datasets, ESTs can be used for (1) development of genetic markers (for example, see Harushima et al., 1998  ), (2) electronic gene expression analyses (for example, see Ewing et al., 1999), (3) improvement of structural annotation (Haas et al., 2003), and (4) functional genomic resources for use in overexpression, in vitro expression, and gene-silencing studies. In 1997, the first set of ESTs for a Poaceae species was reported for rice (Oryza sativa; Yamamoto and Sasaki, 1997). Now, 11 years later, there are 36 Poaceae species with EST collections greater than 1,000 sequences (Table I); of these, >1 million ESTs are available for three Poaceae species (maize [Zea mays], rice, wheat [Triticum aestivum]). Collectively, as of October 30, 2008, within the dbEST division of GenBank, there were 5,491,939 Poaceae EST sequences totaling 2,764 Mb (2.76 Gb). With the high degree of repetitive sequences within the majority of Poaceae species, coupled with the availability of high-throughput next generation sequencing platforms for transcriptome sequencing (Cloonan et al., 2008; Rosenkranz et al., 2008), ESTs will continue to provide a rich source of genic sequences for grass researchers and it should be fully envisioned that within the coming years, EST collections will be available for thousands of Poaceae species.
With continued advancements in technology and concomitant reductions in costs over the last decade, whole-genome sequences have been generated for multiple species within the Poaceae (Table I). Rice was not only the first crop species but also the second plant species with a genome sequence (Barry, 2001 ; Goff et al., 2002; Yu et al., 2002; The International Rice Genome Sequencing Project, 2005; Yu et al., 2005). Currently, genome sequence is available for two subspecies of rice, indica and japonica. Perhaps most importantly for all current and future Poaceae genome sequences, a high-quality, near-complete genome sequence is available for the Nipponbare cultivar of japonica rice (The International Rice Genome Sequencing Project, 2005) that will most likely provide the only gold standard reference genome for the Poaceae for the near future. Indeed, the reference Nipponbare sequence was used to resequence a set of 20 rice lines using hybridization-based sequencing to identify single nucleotide polymorphisms (McNally et al., 2006; http://irfgc.irri.org/index.php?option=com_content&task=view&id=14&Itemid=106; http://oryzasnp.plantbiology.msu.edu/). Draft genome sequences are also available for sorghum (Sorghum bicolor), Brachypodium distachyon, and maize with analyses and full public release anticipated in 2009 (Table I). A genome project is planned for foxtail millet (Setaria italica) by the U.S. Department of Energy Joint Genome Institute (Table I). Physical resources in the form of bacterial artificial chromosome (BAC) map clones have been developed for a number of Poaceae species in advance of genome sequencing (Table I). Most notably, the OMAP project (Kim et al., 2008) has generated physical maps and BAC end sequences for 12 Oryza species in support of comparative genomics within this important genus.
In addition to transcriptome and whole-genome sequences, large sets of genomic sequences are available within the GSS, HTG, WGS, and PLN divisions of GenBank. Within the GSS division, which includes gene enrichment as well as BAC end sequences, 5,072,454 Poaceae sequences (3,337 Mb) are available. Although the maize and sorghum gene enrichment sequences within the GSS division have now been superceded by draft genome sequences, the gene enrichment approaches of methylation filtration and high Cot were highly successful in generating genic sequences for maize and sorghum, thereby providing early access to the gene space (Palmer et al., 2003
It should be noted that the majority of the sequence available currently for the Poaceae are derived from a few species of high agricultural importance (rice, maize, wheat, and sorghum). As shown in Figure 2
, although 13 of the 47 species with genome-scale datasets, resources, or initiatives listed in Table I have >100 Mb of total sequence in GenBank, three-quarters of the sequence are from maize or Oryza species reflective of the heavy bias in Poaceae genome sequencing projects to date. However, with access to the next generation of genome sequencing technologies (Margulies et al., 2005
Certainly, this is an exciting time to be engaged in Poaceae research as even if genomics is not your research discipline, access to not just one but multiple Poaceae genome sequences provides not only a robust set of resources for biological inquiries, but also provides a perspective of gene function in a phylogenetic context. With this deluge of genomic sequence data, the storage, handling, analysis, and use of the large-scale genomic sequence and annotation data becomes problematic for most researchers. Consequently, resources, databases, and analyses tools need to be developed to ensure these genome datasets can be used in a feasible and intelligent manner, thereby maximizing the return on the investment of obtaining the genome sequence. Certainly, Poaceae researchers are not alone in forging a path through the morass of genome sequence data in the early 21st century, and the tools, resources, software, and knowledge gained from other genomic research endeavors throughout the Tree of Life will be instrumental in obtaining a full understanding of the pan-Poaceae genome.
Efforts in phylogenetic tree construction by E. Kellogg are greatly appreciated. Work on rice genomics was supported by the National Science Foundation (grant nos. DBI–0321538 and DBI–0834043 to C.R.B.). Received September 1, 2008; accepted November 5, 2008; published November 12, 2008.
The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: C. Robin Buell (buell{at}msu.edu). www.plantphysiol.org/cgi/doi/10.1104/pp.108.128926
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