Genome-wide identification and in silico characterization of PEBP gene family in Avocado (Persea americana)

Abstract

As key regulators of plant architecture, phosphatidylethanolamine-binding proteins (PEBPs) integrate internal and environmental stimulus. That makes them interesting targets for biotechnological applications, especially in plant breeding. The six PEBP genes in Arabidopsis thaliana and a recently identified new member, gene AT5G01300, are considered as the model members, but there is a variable range of genes of the PEBP family in each species. Now at days, complete genome publications of non-model species like Persea americana have made it possible to explore the extension and function of this family. In this study, we aim to perform a manual curation of the PEBP genes in a variety and a cultivar of P. americana, place those genes in a phylogenetic context by comparison with different clades of the vegetal kingdom, and infer functionality. To do that, we performed a BLAST+ search against three P. Americana genomes, we characterized them in silico and reconstruct the phylogenetic relationships with other 13 species PEBP sequences in RAxML. We found 27 putative PEBP genes in P. americana classified in four sub-clades, FT-like, TFL-like, MFT-like, and a 4th sub-clade. The 4th sub-clade contains the most divergent sequences, including AT5G01300, with partial DPDxP and GHIR motifs, and was rarely found by other authors. Antecedents about the 4th clade show that the proteins from this clade are principally expressed in seed, bud, and flower, but functional characterization in Arabidopsis did not show any effect over flowering phenotype. On the other hand, characterization in silico of predicted PEBP proteins from P. americana, revealed a specific pattern in 4th clade proteins, meanwhile, the cis acting elements on the 2k bp up region, provided evidence of the functional 8 diversification between the 4th clade and the FT/TFL sub-clade and supported the closer relationship with the MFT-sub-clade found in the phylogeny. Based on our results we propose an HMM-based methodology to identify proteins from the PEBP family in plants. We also recognized a different group of PEBP genes with an unknown function, present in almost all the species we selected. Finally, this information could bring insights into the evolution of the flowering process in perennial species, contribute to the understanding of the role of the PEBP family in P. Americana and add information to the description of a new clade of PEBP proteins.