Molecular Evolution of Floral Homeotic B-class Genes in the Dogwood Genus Cornus (Cornaceae) - Gene Duplication, Selection, and Coevolution

Abstract

Comparative study of floral homeotic gene evolution through reconstructing gene genealogy is recognized as an important step toward understanding the molecular genetic basis of morphological evolution. The floral homeotic B-class genes, APETALA3 (AP3) and PISTILLATA (PI) encode MADS domain-containing transcription factors required to specify petal and stamen identities in Arabidopsis. My dissertation study investigates AP3- and PI- like gene evolution through genomic DNA in the dogwood genus Cornus (Cornaceae). Our studies show that ancient gene duplications occurred in CorPI genes but were lacking in the CorAP3 gene lineage during diversification of Cornus. Reconstruction of the PI genealogy in Cornus based on partial genomic DNA sequences reveals a dynamic history of gene duplication and loss at different phylogenetic levels. Ancient duplication events produced two ancient paralogs, named CorPI-A and CorPI-B, followed by the subsequent loss of gene copies in different subgroups during the early radiation of the genus. The AP3 genealogy of Cornus found no ancient gene duplication during diversification of the genus, while two divergent gene copies are found in Davidia, a close relative of Cornus. Multiple sequence types are observed for both CorPI and CorAP3 genes within the species of Cornus, suggesting that frequent, independent, and recent gene duplications occurred within species. Functional constraints of B-class genes in Cornus are generally relaxed compared to those observed in other plant groups. More relaxed functional constraints are found in CorPI than in CorAP3, and in AP3- than in PI-like genes in the outgroup genera Alangium and Davidia. Difference in the strength of selection on these paralog loci may be related to maintenance of ancient paralog gene copies in the CorPI gene lineage in Cornus, and also in the AP3-like gene lineage in Davidia. The four positively selected amino acid sites detected on the CorPI genes indicate that the relaxation of functional constraints in CorPI may be due to diversifying or positive selection. Moreover, positive selection acting on these sites may be related to gene duplication. For the CorAP3 loci, however, the relaxed functional constraint may be due to neutral evolution. I also discuss the divergence patterns of these two nuclear genes in Cornus and their potential use as phylogenetic markers.