Universal processes of chromosomal rearrangement govern the evolution of the plant genome, but
recurrent and widespread polyploidization lends a distinctive characteristic this evolutionary domain. This
unusual pattern leads to new problems in the study of gene order-based phylogeny. One of these is the
inference of ancestral diploid gene order based on data from genomes of various ploidies. We investigate
this in the context of the hexaploidization event in the lineage leading to the modern core eudicots.
Other questions pertain to the mechanism of fractionation, the massive loss of genes in an interleaving manner from
pairs of identical homeologous chromosomes after polyploidization. Whether this loss proceeds gene by gene or through deletion of
multi-gene DNA segments of geometrically-distributed lengths is controversial, as is the question of fractionation bias, namely whether
one homeologous chromosome is more vulnerable to gene deletion than the other. We show how, using the
proportion of fractionated gene pairs as a proxy for time, to calculate a recurrence for the distribution of run length of single-copy genes,
allowing us to estimate the parameter of the geometric distribution, as well as the fractionation bias.
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