Fractionation in the Evolution of Syntenic Homology in Coffea Arabica

Abstract

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.

Based on previous mathematical work on the distribution of gap sizes caused by fractionation in synteny blocks, we studied fractionation in the evolutionary history of the allotetraploid Coffea arabica (CA) and its two diploid progenitors, C. canephora (CC) and C. eugenioides (CE), annotated genome assemblies being provided by the Arabica Coffee Genome Consortium. By taking advantage of synteny blocks produced by SynMap, we studied the fractionation process after speciation and tetraploidization events, including visualization and modelling the distribution of deletion segments, and mechanisms of deletion events. We also expanded the research to eight other plant species to verify the dominance of DNA excision over pseudigenization during the fractionation and other gene loss.