Dimensions of Comparative Genomics 231 Comparative Genome Organization

Genomes of flowering plants are complex, containing varying degrees of repetitive elements and genes assembled into different sets of chromosomes (Bennett and Leitch 2003; Bennetzen et al. 2005). For example, the Arabidopsis genome size is 140 Mb assembled into five chromosomes, versus 4,900 Mb arranged in seven chromosomes for diploid wheat. Genes are not uniformly distributed across the genomes, either large or small, being generally rich in the terminal regions of chromosomes and generally poor but not absent in the centromeric regions (Nagaki et al. 2004).

In the well-studied grasses, the size of gene-rich regions in different genomes remains similar (Feuillet and Keller 1999). Detailed comparison of the rice sequence to a genetically-anchored sorghum physical map showed cytological-distinct euchro-matin versus heterochromatin to correlate closely with gene versus repeat abundance, patterns of rice-sorghum synteny, and the frequency of recombination (Bowers et al. 2005). Synteny is highest and retroelement abundance lowest in distal portions of the chromosomes, where recombination has generally been greatest per unit DNA. Preferential preservation of microsynteny in recombinogenic regions suggests that gene rearrangement is generally deleterious, an intuitive hypothesis that has previously lacked empirical support. 'Muller's ratchet' (Muller 1932) predicts that deleterious mutations may accumulate in, and contribute to degeneration of, non-recombinogenic regions, classical examples being mammalian Y chromosomes or incipient plant sex chromosomes (Liu et al. 2004). This is consistent with a strong negative correlation between repetitive DNA content and recombinational length of rice chromosomes, and with the much greater abundance of repetitive DNA than genes in the pericentromeric regions (Bowers et al. 2005). Accelerated gene loss in recombination-poor regions of wheat (Akhunov et al. 2003), and a propensity for small insertions in centromeric regions of mammalian genomes (Bailey et al. 2001), lend further support to this idea. Gene evolution can be particularly rapid in telomeric regions of wheat chromosomes (See et al. 2006) that yield new genes (Mefford and Trask 2002).

Genome size and gene number are not proportionate in the angiosperms. For example, the genome of papaya (372 Mb) is approximately three times larger than that of than Arabidopsis (125 Mb) but contains fewer genes (Ming et al. 2008). The Arabidopsis genome has incurred two whole-genome duplications that are absent from papaya - while most duplicated genes following each of these events were lost, enough persisted to account for its higher gene count. Comparison of the genome sequences of Arabidopsis, rice, poplar, grapevine and papaya elucidates 13,311 genes that appear to comprise a common set among these angiosperms (Ming et al. 2008).

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