Gene Order in Rosid Phylogeny, Inferred from Pairwise Syntenies among Extant Genomes

摘要

Based on the gene order of four core eudicot genomes (cacao, castor bean, papaya and grapevine) that have escaped any recent whole genome duplication (WGD) events, and two others (poplar and cucumber) that descend from independent WGDs, we infer the ancestral gene order of the rosid clade and those of its main subgroups, the fabids and malvids. We use the gene order evidence to evaluate the hypothesis that the order Malpighiales belongs to the malvids rather than as traditionally assigned to the fabids. Our input data are pairwise synteny blocks derived from all 15 pairs of genomes. Our method involves the heuristic solutions of two hard combinatorial optimization problems, neither of which invokes any arbitrary thresholds, weights or other parameters. The first problem, based on the conflation of the pairwise syntenies, is the inference of disjoint sets of orthologous genes, at most one copy for each genome, and the second problem is the inference of the gene order at all ancestors simultaneously, minimizing the total number of genomic rearrangements over a given phylogeny.