CHAPTER FIVE
Genomics and the Major Transitions in Plant Evolution

There are more than 250,000 species of plants. They represent a wide variety of growth habits, adaptive responses, and useful traits. Such diversity and complexity are increasingly recognized as a reflection of the evolutionary forces driving plant speciation. Plant genomics is increasingly capable of providing DNA-based analytic tools for comparing genomes across great evolutionary distances and for providing insights about the similarities and differences among organisms, the basis of ecologic adaptations, and their origins and persistence. There is untapped value in natural variation as a source of functional information because natural variation has led to variation in function that cannot be uncovered in typical forward or reverse mutant screens. In fact, many important issues in evolutionary and ecologic genomics can be addressed with existing or proposed fully sequenced models, such as Arabidopsis, rice, maize, and Medicago, taking advantage of their large collections of cultivars and wild relatives with diverse life forms (perennial and annual), mating systems, and ploidy levels. Yet, although those species are useful for addressing some questions in ecologic genomics, they do not reflect the widely divergent templates for evolutionary genomics provided by the total breadth of plant or other species.

Current sequencing costs are still too high to invest in the broad set of species currently used in evolutionary biology, so a selection of additional species must be targeted to explore



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The National Plant Genome Initiative: Objectives for 2003–2008 CHAPTER FIVE Genomics and the Major Transitions in Plant Evolution There are more than 250,000 species of plants. They represent a wide variety of growth habits, adaptive responses, and useful traits. Such diversity and complexity are increasingly recognized as a reflection of the evolutionary forces driving plant speciation. Plant genomics is increasingly capable of providing DNA-based analytic tools for comparing genomes across great evolutionary distances and for providing insights about the similarities and differences among organisms, the basis of ecologic adaptations, and their origins and persistence. There is untapped value in natural variation as a source of functional information because natural variation has led to variation in function that cannot be uncovered in typical forward or reverse mutant screens. In fact, many important issues in evolutionary and ecologic genomics can be addressed with existing or proposed fully sequenced models, such as Arabidopsis, rice, maize, and Medicago, taking advantage of their large collections of cultivars and wild relatives with diverse life forms (perennial and annual), mating systems, and ploidy levels. Yet, although those species are useful for addressing some questions in ecologic genomics, they do not reflect the widely divergent templates for evolutionary genomics provided by the total breadth of plant or other species. Current sequencing costs are still too high to invest in the broad set of species currently used in evolutionary biology, so a selection of additional species must be targeted to explore

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The National Plant Genome Initiative: Objectives for 2003–2008 plant biodiversity. We advocate a modest investment in the period 2003–2008 for development of genomics resources in species outside the model, references, and their crop relatives. As an initial step, we recommend the survey of roughly 50 species with EST sequencing. ESTs remain the most rapid and cost-effective way to sample gene content and discover new genes. This effort will go a long way toward making gene discovery and comparative genomics possible. To ensure that genomics investment in additional species builds effectively on existing resources and on the EST sequencing suggested above, we recommend that the evolutionary-genomics community pursue further the selection of a small number of key species (5–10) spanning critical evolutionary nodes in preparation for communitywide genomic investigation over the next 3–10 years. The species should be selected to provide a broad view of the evolutionary potential of genomes and a deep understanding of gene diversity and adaptation. Other federally funded projects—such as Deep Green (2002) and its successor, Deep Gene (2002)—have identified a phylogenetically diverse array of species for application of genomics. The NPGI should give priority to developing tools for species from this set or from among species closely related to them. In the context of evolutionary studies, the genomes of cyanobacteria, from which up to 20% of the genes in contemporary plants originated, and the eukaryotic algae also are legitimate objects of study in the NPGI. The specific approach taken to achieve the goals of evolutionary studies broadly is not immediately obvious and will require consensus building. Our key concern is that, for any given species or evolutionary question, there needs to be at least some minimum concentration of scientists ready to exploit genomics data. Beyond that concern, criteria for choosing any evolutionary-genomics focal species should include: Distributed position in the phylogeny, with emphasis on early branches of the green plant phylogeny. Genome size, with emphasis on small genomes and simple ploidy.

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The National Plant Genome Initiative: Objectives for 2003–2008 Genetic tractability: Ease of crossing and population development. Ease of growth. Short generation time. Availability of existing tools: Germplasm collections. Mapping populations. Genetic and physical maps. BAC or P1-derived artificial chromosome clone collections. EST collections. Mutant collections. Size of the research community vs required investment. Importance of the focal species or close relatives: In terms of agriculture. In ecology and conservation. Tools for genomic studies of diverse focal species should be explicitly comparative and should be developed with nonspecialists in mind, with the aim of broadening the community of researchers who have access to and can effectively use plant-genomics data in the future. By expanding the essential toolkit available to evolutionary biologists interested in diverse taxa in the next 5 years, and by urging the relevant community to coalesce around a set of common goals, the stage can be set for the expansion of plant genomics into evolutionary questions. We hope that this modest investment will prepare the evolutionary genomics community for a much larger investment in genome sequencing in the next 5–10 years.

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