Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 10/1/2007
Publication Date: 6/1/2008
Citation: Cannon, S.B. 2008. Legume comparative genomics. In: Stacey, G. editor. Genetics and Genomics of Soybean. Series:Plant Genetics and Genomics:Crops and Models 2. New York, NY: Springer-Verlag. p. 35-54.
Technical Abstract: Comparisons among increasing numbers of plant genome sequences are uncovering features that seem likely to hold for most, if not all, higher plant genomes. Gene collinearity (synteny) is frequently conserved across long genomic regions and very long times, with limited synteny evident even between species from diverse plant families. Although synteny remains detectable for tens of millions of years, gene losses, local gene duplications, and transposon insertions occur frequently, often disrupting conservation for any given gene pair. Polyploidy, though infrequent, has occurred multiple times in most angiosperm lineages, complicating comparisons between genomes that have undergone independent WGD events. Enormous variations in genome size can occur over relatively short timeframes, without substantially disrupting synteny. Organization of genomes into gene-rich euchromatic and gene-poor heterochromatic regions (telomeres, centromeres, knobs) differs somewhat between plant lineages, but appears to follow a general pattern of relatively uniform gene density in euchromatic regions, with gene density falling off (and repetitive sequence increasing) towards pericentromeric regions. In the legumes, genome sequencing is well underway for Medicago truncatula, Lotus japonicus, and soybean. Sequence-based comparisons of the Medicago and Lotus genomes, and genetic marker-to-sequence comparisons between soybean and Medicago or Lotus, show a lack of large-scale genome duplications within the Lotus or Medicago ge-nomes following separation of those lineages approximately 40 mya, but do show evidence of a much older shared polyploidy event, as well as clear evidence of a more recent duplication in soybean. In short, comparative genomics has clear promise to provide a foundation for “translational genomics,” but researchers will need to be prepared to deal with the complicating consequences of polyploidy, local gene duplications and losses, rearrangements, and rapid turnover of repetitive elements.