Systematic identification of gene families for use as markers for phylogenetic and phylogeny- driven ecological studies of bacteria and archaea and their major subgroups

TL;DR

This paper presents an automated method to identify marker gene families, called PhyEco markers, for robust phylogenetic and ecological studies of bacteria and archaea, enabling more detailed microbial community analyses.

Contribution

The authors develop a novel automated protocol to identify PhyEco markers based on criteria like universality and phylogenetic robustness, expanding available markers for microbial studies.

Findings

Identified 40 PhyEco markers for all bacteria and archaea.

Discovered 114 PhyEco markers specific to bacteria.

Enabled more detailed phylogenetic analyses of microbial groups.

Abstract

With the astonishing rate that the genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families that are particularly well suited for the tasks at hand. Such gene families have generally been referred to as marker genes. We are particularly interested in identifying and using such marker genes for phylogenetic and phylogeny-driven ecological studies of microbes and their communities. We therefore refer to these as PhyEco (for phylogenetic and phylogenetic ecology) markers. The dual use of these PhyEco markers means that we needed to develop and apply a set of somewhat novel criteria for identification of the best candidates for such markers. The criteria we focused on included universality across the taxa of interest, ability to be used to produce robust phylogenetic trees that reflect as much as possible the evolution of the species from which the genes come, and low variation in copy number across taxa. We describe here an automated protocol for identifying potential PhyEco markers from a set of complete genome sequences. The protocol combines rapid searching, clustering and phylogenetic tree building algorithms to generate protein families that meet the criteria listed above. We report here the identification of PhyEco markers for different taxonomic levels including 40 for all bacteria and archaea, 114 for all bacteria, and much more for some of the individual phyla of bacteria. This new list of PhyEco markers should allow much more detailed automated phylogenetic and phylogenetic ecology analyses of these groups than possible previously.