Robust phylogenetic profile clustering for Saccharomyces cerevisiae proteins

Area of Science:

• Evolutionary Biology
• Genomics
• Bioinformatics

Background:

• Gene birth and death are fundamental processes in genome evolution.
• Gene origination may occur in specific evolutionary periods rather than uniformly.
• Identifying gene origination points traditionally uses common ancestors or heuristic thresholds, which can be problematic.

Purpose of the Study:

• To apply an alternative method for identifying gene origination epochs.
• To investigate epochal trends in gene origination within fungal evolution.
• To examine associations between gene age, sequence traits, and functional patterns.

Main Methods:

• Utilized phylogenetic profile clustering to analyze gene presence/absence across over 800 fungal species.
• Focused analysis on the budding yeast Saccharomyces cerevisiae.
• Compared phylogenetic profiles to identify patterns of gene occurrence and origination.

Main Results:

• Identified clear gene origination epochs linked to the last common ancestors of Saccharomycetaceae, Saccharomycetes, and earlier fungal lineages.
• Observed functional associations for gene clusters, including spore formation and chromosome segregation.
• Detected trends in intrinsic disorder, prion-like composition, and gene uniqueness correlating with gene age.

Conclusions:

• Phylogenetic profile clustering provides a robust method for studying gene origination epochs, independent of data quality.
• New proteins with prion-like domains arose consistently throughout evolution centered on S. cerevisiae.
• Recently formed genes are less likely to be single-copy, and intrinsic disorder is more prevalent in proteins from earlier epochs.