Most of the species diversity of plants is represented in the crown group, the angiosperms, which encompasses the Monocots and the Eudicots. Consensus phylogenies place paraphyletic gymnosperms basal to angiosperms and ferns as a sister group to this clade (Pryer et al., 2002) (Fig. 17.1D). The placement of some of the basal groups in the Embryophyta (hornworts, liverworts, and mosses) is still unresolved, although lycophytes are now considered the sister group to the clade containing ferns, gymnosperms, and angiosperms (Hedges, 2002; Pryer et al., 2002) (Fig. 17.1D). Finally, multiple sources of evidence point to the green algae as the unicellular sister group to plants (reviewed in Archibald and Keeling, 2002) (Fig. 17.1D).
Genome projects for green plants have been hampered by the larger genome sizes of most members of this group. Nonetheless, the first draft Plantae genome published was from Arabidopsis thaliana, a flowering plant model organism (Arabidopsis Genome Initiative, 2000). Genome drafts of two different rice strains (Oryza sativa) have been recently published (Goff et al., 2002; Yu et al., 2002). This effort is now complemented by the completion of a unicellular alga (Chlamydomonas reinhardtii), the poplar tree (Populus trichocarpa), and partial genome data from corn (Zea mays), whereas two basal lineages, the moss Physcomitrella patens and the lycophyte Selaginella moellendorffii, will be sequenced this year (www.jgi.doe.gov/sequencing/cspseqplans.html). Thus, although more sparse than for metazoans and fungi, the Plantae branch of the eukaryotic tree is rapidly expanding in terms of genomic data. Agricultural interests will likely drive future choice of Plantae genomes to some degree, but decisions will also be influenced by phylogenetic implications as reflected in the recent choice of the P. patens and S. moellendorffii for genome sequencing.
With whole-genome data allowing reconstruction of more robust phylogenies for the major eukaryotic groups, new biological questions can now be addressed. Genomic and postgenomic data offer a new “global” view of the function of living systems across the tree of life. These new data suggest that biological systems (e.g., a cell) are composed of discrete “modules” of interacting components with different functions, and in turn these modules form biological networks that carry out the myriad functions of living systems (Hartwell et al., 1999). Multiple metabolic and regulatory networks are now being characterized in diverse organisms for which reasonably annotated genomes are available. Metabolites, be-