OVATE FAMILY PROTEINS (OFP) gene family across Brassicaceae: Comparative genomic analysis uncovers evolutionary relationships, extensive sequence and structural variation with a potential for functional diversification

Abstract

Plant-specific Ovate Family Proteins (OFP), containing OVATE domain were identified as regulators of fruit shape. OFP homologs have been detected across plant kingdom as negative regulators of growth and adaptation, albeit with fragmentary information about evolutionary history, diversification, and functional significance. Phylogenetic position, evolutionary history, and availability of genome sequences from several species of Brassicaceae make them suitable for analysis of OFP gene family. Nineteen members of OFP gene family were previously identified from Arabidopsis thaliana. In the present study, we identified 390 homologs of 19 AtOFPs across thirteen Brassicaceae species and analysed their genomic distribution, organization, gene and protein structure, evolution, and possible mode of expansion. Comparative analysis of gene structure and protein architecture of 409 genes revealed conservation and variability in OVATE domain. This feature was used to classify OFPs as: i. OVATE-OFPs containing a canonical OVATE domain, ii. OVATE-like OFPs containing a partial or non-canonical OVATE domain, and, iii: OFP-Related which completely lacked OVATE domain. Two motifs that occur close to, or overlap with the OVATE domain were identified, and variations in amino acid composition that alter folding of OVATE domain were observed. Phylogenetic analysis showed that the paralogous pairs of OFPs found in A. thaliana were conserved across all species. Similar topologies of phylograms constructed from either full length protein, or only with OVATE domain indicate that the evolution of OFP gene family is driven by OVATE domain. A consequence of several post-polyploidization processes including sequence and structural variation among homeologs, and altered sub-cellular localization was observed. Analysis of selection pressure revealed purifying selection acting on seventeen out of nineteen OFPs, and positive selection on the remaining two OFPs. This present work thus lays the foundation for functional genomics of OFPs not only in agronomically important species of Brassicaceae but also in other multigene families to create a framework for future comparative functional genomics studies.