Life with 25,000 genes.

Plants make the earth a good place for humans to live. They produce the oxygen we breathe, the food we eat, fuel for our cars and factories, fiber for the clothes we wear, wood for the houses we live in, and chemicals that keep us healthy or help cure us when we get sick. Plus, they are pleasant to look at, fun to grow, and intellectually interesting. Given all of this, it is surprising that they remain so poorly understood. The completion of the Arabidopsis genome sequence will do much to change this (Arabidopsis Genome Initiative 2000; Lin et al. 1999; Mayer et al. 1999; Salanoubat et al. 2000; Tabata et al. 2000; Theologis et al. 2000). As the first plant genome to be sequenced, this is rightly heralded as a landmark event. With the array of molecular genetic tools available for Arabidopsis and the impetus provided by the 2010 project, it will not be long before we know the physiological and developmental function of every gene in this species (Chory et al. 2000; Somerville and Dangl 2000). It is easy to take these events for granted in the era of genomic sequencing and reverse genetics. However, none of this would have happened without the major change in plant biology that has taken place in the last 15 years (Fink 1998). For example, in the late 1970’s and early 1980’s, students in Ian Sussex’ plant biology laboratory completed Ph.D. theses on no less than 11 species, most of which were crop plants (my contribution was tobacco). At the time of Sussex’s retirement in 1997, all but one of the students in his lab were studying Arabidopsis (I. Sussex, pers. comm.). The recent explosion of interest in Arabidopsis—a weed of absolutely no economic importance—is unprecedented in the history of plant biology and provided this field with its first widely adopted model system. Arabidopsis is a small plant with a rapid life cycle and has been used in genetic studies for decades, but it was the discovery that Arabidopsis has a small genome with very little repeated DNA (Leutwiler et al. 1984; Pruitt and Meyerowitz 1986) that is primarily responsible for its recent popularity. The widespread adoption of Arabidopsis as an experimental system has resulted in rapid progress in many areas and has produced the international effort that led to the sequencing of the Arabidopsis genome. The Arabidopsis genome is 125 Mb and encodes ∼25,500 genes (Arabidopsis Genome Initiative 2000). Arabidopsis therefore has significantly more genes than yeast (Goffeau et al. 1996), Caenorhabditis elegans (C. elegans Sequencing Consortium 1998) or Drosophila (Adams et al. 2000). This is primarily because Arabidopsis genes often occur in more than one copy. Seventeen percent of the genes in Arabidopsis occur as tandem arrays of two or more closely related genes and ∼60% of the genome is segmentally duplicated, albeit in a highly rearranged fashion; the number of unique types of genes in Arabidopsis (12,000) is actually about equal to the number of gene types in worms (14,000) and flies (11, 000). The types of genes present in Arabidopsis reinforce what has been learned from previous sequencing projects about the evolution of eukaryotes. Genes required for eukaryotic cell function such as components of the cytoskeleton, or essential processes such as DNA replication, repair and recombination, cell division, protein synthesis, and vesicle trafficking, are largely conserved between Arabidopsis and other eukaryotes. In contrast, genes involved in regulatory processes such as signal transduction and transcriptional regulation are quite different in Arabidopsis, yeast, C. elegans, and Drosophila. For example, Arabidopsis has no genes similar to the components of major signaling pathways in animals, such as the Wingless/ Wnt, Hedgehog, Notch/lin12, JAK/STAT, TGF-b /SMADS, and receptor tyrosine kinase/Ras pathways. Instead, signaling in Arabidopsis depends largely on receptor Ser/Thr kinases, of which there are 340, and a novel family of receptors related to bacterial two-component histidine kinases. Plants have also evolved a diverse array of transcription factors not found in animals. Arabidopsis has ∼1500 transcription factors, 1.3 times as many as in Drosophila and 1.7 as many as C. elegans or yeast (Riechmann et al. 2000). Forty-five percent of the families of transcription factors found in Arabidopsis are unique to plants. These differences should not be surprising, given that multicellularity originated independently in plants and animals, and plants have cell walls and animals do not (Meyerowitz 1999). The important lesson is that plants are as different from other organisms as they are the same, and are interesting for both reasons. The fact that Arabidopsis has more genes than either C. elegans or Drosophila begs the question: Why does a structurally and behaviorally simple organism have more genes than organisms with a nervous system and cells that move? Although the answer to this question is unknown, there are some obvious possibiliE-MAIL spoethig@sas.upenn.edu; FAX (215)898-8780. Article and publication are at www.genome.org/cgi/doi/10.1101/gr. Commentary