PharaohFUN: phylogenomic analysis for plant protein history and function elucidation

Area of Science:

• Genomics
• Bioinformatics
• Evolutionary Biology

Background:

• Computational functional characterization of photosynthetic eukaryotes is limited, often relying on comparisons with angiosperms like Arabidopsis thaliana.
• Existing methods lack a comprehensive evolutionary framework for diverse photosynthetic eukaryotes.

Purpose of the Study:

• Introduce PharaohFUN, a web application for evolutionary and functional analysis of protein sequences in photosynthetic eukaryotes.
• Leverage orthology relationships to bridge traditionally separate clades within this group.
• Establish a unified evolutionary framework for sequence evolution and function studies.

Main Methods:

• PharaohFUN incorporates homogeneous representative sampling of key photosynthetic eukaryotic species.
• Includes modules for gene tree history, expansion/contraction events, ancestral states, domain identification, multiple sequence alignments, and functional annotation.
• Offers diverse search modes for user accessibility.

Main Results:

• PharaohFUN was tested on Arabidopsis thaliana transcription factors and CCA1 protein.
• Demonstrated accurate tracing of evolutionary histories across land plants, streptophyte, and chlorophyte microalgae.
• Successfully unified results from previously disparate clades.

Conclusions:

• PharaohFUN democratizes evolutionary and functional analysis of protein sequences in photosynthetic organisms.
• Provides a comprehensive framework for users regardless of bioinformatics expertise.
• Enhances understanding of sequence evolution and function across diverse photosynthetic eukaryotes.