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Update on Comparative Genomics Beyond the Arabidopsis Genome Opportunities for Comparative Genomics1 Anne E Hall2 Aretha Fiebig2 and Daphne Preuss Howard Hughes Medical Institute The University of Chicago 1103 East 57th Street Chicago Illinois 60637 Like most higher eukaryotes flowering plants are believed to contain surprisingly similar numbers of genes Nevertheless angiosperm genome sizes vary over a wide range from 50 Mb to over 120 000 Mb Comparative mapping has shown that numerous alterations contribute to genomic diversity among plants Over time chromosomes are broken reassembled partially or wholly duplicated and even eliminated ultimately resulting in reproductive isolation and speciation However the mechanisms that create such variation and the evolutionary forces that fix these changes are not well understood Comparative analyses of plant genomes promise to clarify the selective pressures driving these changes such investigations will elucidate alterations at the level of whole genomes as well as those at the level of specific sequences including genes repetitive elements and other non coding regions Although low resolution genetic maps can identify gross chromosomal alterations a clear understanding of the mechanisms behind these changes requires multispecies sequence comparisons Such analyses reveal the composition organization and functional components of genomes and provide insight into regional differences in composition between related species In addition sequence comparisons elucidate evolutionary history for example the stepwise accumulation of nucleotide insertions deletions indels only becomes clear with the analysis of multiple species Comparative sequence analysis also aids in gene prediction and sequence annotation and facilitates the identification and definition of regulatory elements including promoters enhancers and transcription factor binding sites Kent and Zahler 2000 Koch et al 2001b The recent analysis of the sequence of the Arabidopsis genome highlighted unexpected aspects of its composition organization and function Arabidopsis Genome Initiative AGI 2000 The questions raised by these observations can best be approached through comparative genomics For example al1 This work was supported in part by the Howard Hughes Medical Institute and by the National Science Foundation grant no MCB 0077854 to A F 2 These authors contributed equally to the paper Corresponding author e mail dpreuss midway uchicago edu fax 773 702 6648 www plantphysiol org cgi doi 10 1104 pp 004051 though Arabidopsis is considered a true diploid its genome has undergone major duplication events followed by extensive rearrangements and chromosome fusion and loss hypothesized to have shifted the haploid chromosome number from 4 to 8 and then to 5 AGI 2000 Vision et al 2000 Interestingly however evidence of duplications was not found in the sequenced portions of the centromere regions All five centromeres contain tracts of unique DNA interspersed with similar types of transposable elements and interrupted by large tandem arrays of satellites Aside from the repetitive sequences pairwise comparisons of the centromere regions did not identify blocks of unique sequence indicative of ancient duplication events AGI 2000 In addition to large segmental duplications on the chromosome arms Arabidopsis also contains a prevalence of gene families many of which are the result of tandem duplications of individual genes rather than redundancy of entire chromosome segments Nearly 40 of the predicted genes in the Arabidopsis genome belong to families that contain more than five members AGI 2000 Through studies of related species it will become possible to discern the timing of genome duplications the types of DNA eliminated and the mechanisms responsible for rearrangements and deletions Moreover analysis of the genomes of related species will clarify how gene families expand contract and diversify Examination of relatives containing different types of genome duplications will also reveal the changes that occur after such events including mechanisms that are activated after large scale genomic perturbation Clearly comparative genomic approaches would provide enormous benefit toward understanding the origins of the Arabidopsis genome as well as other plant genomes Although previous comparisons with genes from yeast flies worms and mammals have provided functional clues for approximately 70 of Arabidopsis genes the vast evolutionary distances that separate these species restrict such comparisons to coding regions AGI 2000 Even the genomes of Arabidopsis and rice Oryza sativa which are separated by approximately 200 million years MY have substantially diverged Wolfe et al 1989 making the incremental stages of evolutionary change difficult to grasp Goff et al 2002 Yu et al 2002 In this Update we explore the utility of a comparative genomics approach that relies on Arabidopsis Plant Physiology August 2002 Vol 129 pp 1439 1447 www plantphysiol org 2002 American Society of Plant Biologists 1439 Hall et al and several other species within the Brassicaceae family We discuss discoveries made from prior comparisons within the family prospects for additional genomic studies and their potential for significantly improving our understanding of plant genomes Finally we discuss the community resources required to launch an effort with the necessary breadth to address a wide range of sequence based evolutionary questions and suggest a set of candidate species for genomic comparisons in the Brassicaceae THE BRASSICACEAE A USEFUL FAMILY FOR COMPARATIVE GENOMICS Arabidopsis is a member of the Brassicaceae family the wealth of information and resources provided by the community of Arabidopsis researchers consequently provides a well supported infrastructure that makes the Brassicaceae ideal for comparative studies of plant genomes The Brassicaceae family is large encompassing approximately 340 genera and more than 3350 species a few of which are shown in Figure 1 Al Shehbaz 1984 These species diverged from a common ancestor over a time period of approximately 40 to 50 MY as a result of numerous independent speciation events Koch et al 2001a Thus the thousands of extant species provide significant opportunities for investigating the genetic differences that lead to speciation In practical terms several species within the Brassicaceae have genomes sizes that are extremely small at 49 Mb the estimated genome size of


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