4 The Arabidopsis Genome: A Foundation for Plant Research

Abstract

Arabidopsis thaliana was the first plant, and the third multicellular organism after Caenorhabditis elegans (The C. elegans Sequencing Consortium 1998) and Drosophila melanogaster (Adams et al. 2000), to be completely sequenced (The Arabidopsis Genome Initiative 2000). At the time, it was claimed that the Arabidopsis genome sequence “… creates the potential for direct and efficient access to a much deeper understanding of plant development and environmental responses, and permits the structure and dynamics of plant genomes to be assessed and understood.” Five years on, how justified was this claim? Furthermore, a vision for the Arabidopsis research community was articulated based on the promise of the genome sequence. A noteworthy aspiration was to “determine the function of all Arabidopsis genes by 2010.” What progress has been made toward this goal? This review takes a broad and necessarily shallow view of progress in Arabidopsis research and relates this to work in other reference organisms. Our analysis suggests that much of the extraordinary progress made in the past five years has drawn on the genome sequence, and shows that it has had a catalytic effect on the research community and on how plant science is conducted. However, the explosion of data has created unanticipated problems that the Arabidopsis and plant science community must address if it is to take successfully to the path of integrative biology.

PROGRESS IN SEQUENCING, REASSEMBLY, AND ANNOTATION OF THE GENOME
Since systematic sequencing was completed in late 2000, the genome sequence has undergone several rounds of reassembly, hole...