Computing prokaryotic gene ubiquity: rescuing the core from extinction.

Area of Science:

• Comparative genomics
• Evolutionary genomics
• Prokaryotic genomics

Background:

• The genomic core is defined as genes ubiquitous across a phylogenetic group.
• Core size diminishes with increased group size and phylogenetic diversity.
• Existing core definitions face challenges with expanding prokaryotic genome data.

Purpose of the Study:

• To investigate methods for defining the size and composition of the core gene set in prokaryotes (Bacteria and Archaea).
• To address the decreasing core size observed with increasing genome sequencing.
• To propose an alternative definition that preserves biological utility.

Main Methods:

• Analysis of gene content across 147 sequenced prokaryotic genomes.
• Evaluation of factors contributing to gene absence (sequencing errors, annotation errors, genuine gene loss).
• Development of the 'phylogenetically balanced core' concept.

Main Results:

• Few genes (<50) are shared by all 147 prokaryotic genomes analyzed.
• Sequencing/annotation errors and limited gene loss explain most apparent gene absences.
• Core size is expected to continue decreasing with more genome data.

Conclusions:

• The strict definition of a core genome is increasingly problematic with more sequenced genomes.
• A 'phylogenetically balanced core' offers a more biologically relevant alternative.
• Genomic cores are enriched for informational genes over operational genes, with a new hypothesis presented for this observation.