Gaps and Runs in Syntenic Alignments

Gene loss is the obverse of novel gene acquisition by a genome through a variety of evolutionary processes. It serves a number of functional and structural roles, compensating for the energy and material costs of gene complement expansion. A type of gene loss widespread in the lineages of plant genomes is “fractionation” after whole genome doubling or tripling, where one of a pair or triplet of paralogous genes in parallel syntenic contexts is discarded. The detailed syntenic mechanisms of gene loss, especially in fractionation, remain controversial. We focus on the the frequency distribution of gap lengths (number of deleted genes – not nucleotides) within syntenic blocks calculated during the comparison of chromosomes from two genomes. We mathematically characterize s simple model in some detail and show how it is an adequate description neither of the Coffea arabica subgenomes nor its two progenitor genomes. We find that a mixture of two models, a random, one-gene-at-a-time, model and a geometric-length distributed excision for removing a variable number of genes, fits well.