Comparative Sequencing of Plant Genomes: Choices to Make

The first sequenced genome of a plant, Arabidopsis thaliana, was published <6 years ago (Arabidopsis Genome Initiative, 2000). Since that time, the complete rice genome (Oryza sativa; Goff et al., 2002; Yu et al., 2002; International Rice Genome Sequencing Project, 2005) and a draft sequence of the poplar genome (Populus trichocarpa; http://genome.jgi-psf.org/Poptr1/Poptr1.home.html) have also been completed. In addition, the National Center for Biotechnology Information Entrez Genome Projects website reports that sequencing of several more plant genomes is in progress. The first wave of plant genome sequencing has passed, and we are now entering a new era in plant genomics research. Many of the obvious candidates for genome sequencing, model species with small genomes or species of economic importance, have either already been completed or are underway. The next round of choices should be made as part of a coherent strategy based on a mixture of scientific and economic needs and should recognize the value of including phylogenetic position as a selection criterion. There are also new technologies that will change the way we approach future genome sequencing projects. How are we to make appropriate choices with regards to both the species targets and the sequencing technologies we will use?