Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups - PubMed (original) (raw)

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

Dongying Wu et al. PLoS One. 2013.

Abstract

With the astonishing rate that 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 (e.g., construction of species trees, phylogenetic based assignment of metagenomic sequence reads to taxonomic groups, phylogeny-based assessment of alpha- and beta-diversity of microbial communities from metagenomic data). 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 (greatly expanding on the ∼30 commonly used), and 100 s to 1000 s 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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. Flow chart of the PhyEco marker identification pipeline.

Figure 2

Figure 2. The universality, evenness and monophyletic value of the 40 Bacterial/Archaeal PhyEco marker candidates in different taxonomic groups.

PhyEco marker genes for the taxonomic groups are highlighted with white boxes.

Figure 3

Figure 3. The universality, evenness and monophyletic value of the 74 Bacterial specific PhyEco marker candidates in different taxonomic groups.

PhyEco marker genes for the taxonomic groups are highlighted with white boxes.

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Grants and funding

Funding for this work was provided by the Gordon and Betty Moore Foundation (grant #1660 and #3300, website: http://www.moore.org/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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