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The emergence of multigene families has been hypothesized as a major contributor to the evolution of complex traits and speciation. To help understand how such multigene families arose and diverged during plant evolution, we examined the phylogenetic relationships of  F-Box  ( FBX ) genes, one of the largest and most polymorphic superfamilies known in the plant kingdom. FBX proteins comprise the target recognition subunit of SCF-type ubiquitin-protein ligases, where they individually recruit specific substrates for ubiquitylation. Through the extensive analysis of 10,811  FBX  loci from 18 plant species, ranging from the alga  Chlamydomonas reinhardtii  to numerous monocots and eudicots, we discovered strikingly diverse evolutionary histories. The number of  FBX  loci varies widely and appears independent of the growth habit and life cycle of land plants, with a little as 198 predicted for  Carica papaya  to as many as 1350 predicted for  Arabidopsis lyrata . This number differs substantially even among closely related species, with evidence for extensive gains/losses. Despite this extraordinary inter-species variation, one subset of  FBX  genes was conserved among most species examined. Together with evidence of strong purifying selection and expression, the ligases synthesized from these conserved loci likely direct essential ubiquitylation events. Another subset was much more lineage specific, showed more relaxed purifying selection, and was enriched in loci with little or no evidence of expression, suggesting that they either control more limited, species-specific processes or arose from genomic drift and thus may provide reservoirs for evolutionary innovation. Numerous  FBX  loci were also predicted to be pseudogenes with their numbers tightly correlated with the total number of  FBX  genes in each species. Taken together, it appears that the  FBX  superfamily has independently undergone substantial birth/death in many plant lineages, with its size and rapid evolution potentially reflecting a central role for ubiquitylation in driving plant fitness.

Phylogenetic Comparison of F-Box (FBX) Gene Superfamily within the Plant Kingdom Reveals Divergent Evolutionary Histories Indicative of Genomic Drift