A systematic search for positive selection in higher plants (Embryophytes)

Background: Previously, a database characterizing examples of Embryophyte gene family lineages showing evidence of positive selection was reported. Of the gene family trees, 138 Embryophyte branches showed Ka/Ks >> 1 and are candidates for functional adaptation. The database and these examples have now been studied in further detail to better understand the molecular basis for plant genome evolution. Results: Neutral modeling showed an excess of positive and/or negative selection in the database over a neutral expectation centered on the mean Ka/Ks ratio. Out of 673 families with assigned structures, 490 have at least one branch with Ka/Ks >> 1 in a region of the protein, enabling a picture of selective pressures delineated by protein structure. Most gene families allowed reconstruction back to the last common ancestor of flowering plants (dMagnoliophytes) without saturation of 4-fold degenerate codon position. Positive selection occurred in a wide variety of gene families with different functions, including in the self incompatibility locus, in defense against pathogens, in embryogenesis, in cold acclimation, and in electrontransport. Structurally, selective pressures were similar between alpha-helices and beta-sheets, but were less negative and more variant on the surface and away from the hydrophobic core. Conclusion: Positive selection was detected statistically significantly in a small and nonrandom minority of gene families in a systematic analysis of embryophyte gene families. More sensitive methods increased the level of positive selection that was detected and presented a structural basis for the role of positive selection in plant genomes.