PharaohFUN: PHylogenomic Analysis foR plAnt prOtein History and FUNction elucidation

Abstract

AbstractMotivationSince DNA sequencing has turned commonplace, the development of efficient methods and tools to explore gene sequences has become indispensable. In particular, despite photosynthetic eukaryotes constituting the largest percentage of terrestrial biomass, computational functional characterization of gene sequences in these organisms still predominantly relies on comparisons withArabidopsis thalianaand other angiosperms. This paper introduces PharaohFUN, a web application designed for the evolutionary and functional analysis of protein sequences in photosynthetic eukaryotes, leveraging orthology relationships between them.ResultsPharaohFUN incorporates a homogeneous representative sampling of key species in this group, bridging clades that have traditionally been studied separately, thus establishing a comprehensive evolutionary framework to draw conclusions about sequence evolution and function. For this purpose, it incorporates modules for exploring gene tree evolutionary history, domain identification, multiple sequence alignments, and functional annotation. The study of the CCA1 protein exemplifies how PharaohFUN unifies results for both land plants and chlorophyte microalgae, accurately tracing the evolutionary history of this protein.Availability and ImplementationPharaohFUN web application is freely available athttps://greennetwork.us.es/AlgaeFUN/and its source code can be freely accessed athttps://github.com/fran-romero-campero/AlgaeFUN.Contactfran@us.es