Comparisons among the sequenced genomes of Arabidopsis, rice, poplar, grapevine, papaya and sorghum shed light on ancient gene orders. For example, most papaya segments correspond to three or four Arabidopsis segments, which shows that two genome duplications have affected the Arabidopsis lineage since its divergence from Carica (Ming et al. 2008). Individual Arabidopsis genome segments correspond to only one Carica segment, revealing that Carica has not experienced duplication since its divergence from Arabidopsis. Both Vitis and Carica share only one duplication event, g, with Arabidopsis, while a and b occurred within the Arabidopsis lineage (Tang et al. 2008a).
Large-scale (segmental or complete) genome duplication affects not only gene copy number but also substantially fractionates the ancestral gene linkages across multiple chromosomes. Recently, this problem was overcome using a robust computational framework that combines information from multiple orthologous and duplicated regions to construct local syntenic networks, which is instrumental in deducing the footprints of "paleo-hexaploid" before diverging from a common ancestor (Tang et al. 2008b). These findings will pave the way for approximating the number and arrangement of genes in the last universal common ancestor of angiosperms (Tang et al. 2008b).
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