Abstract
There is growing interest in reconstructing phylogenies from the copious amounts of genome sequencing projects that target related viral, bacterial or eukaryotic organisms. To facilitate the construction of standardized and robust phylogenies for disparate types of projects, we have developed a complete bioinformatic workflow, with a web-based component to perform phylogenetic and molecular evolutionary (PhaME) analysis from sequencing reads, draft assemblies or completed genomes of closely related organisms. Furthermore, the ability to incorporate raw data, including some metagenomic samples containing a target organism (e.g. from clinical samples with suspected infectious agents), shows promise for the rapid phylogenetic characterization of organisms within complex samples without the need for prior assembly.
Highlights
There is growing interest in reconstructing phylogenies from the copious amounts of genome sequencing projects that target related viral, bacterial or eukaryotic organisms
We present an open source workflow using a collection of existing bioinformatic tools for Phylogenetic and Molecular Evolutionary (PhaME) analysis that incorporates these additional features to allow more flexibility when studying the evolutionary relationships between closely related genomes
We further examined the robustness of how phylogenetic and molecular evolutionary (PhaME) handles raw reads, by comparing the placement of these datasets with the genome assemblies that resulted from these data, and have investigated how well PhaME performs when including metagenomic samples in the form of raw reads (Table 1)
Summary
There is growing interest in reconstructing phylogenies from the copious amounts of genome sequencing projects that target related viral, bacterial or eukaryotic organisms. The others are able to analyze raw reads to identify a core genome (the conserved portion among all genomes) and the SNPs within it, several of them cannot process assembled contigs or multiple complete genomes (e.g., CFSAN, SPANDx, Lyve-set), or will perform only a portion of the required functions to obtain a tree (e.g., Snippy), or identify SNPs from metagenomes (e.g. WG-FAST), and only few (CSI Phylogeny, REALPHY, SNVPhyl) can be accessed with a graphical user interface, limiting the user base to well-trained bioinformatics scientists Almost all these tools have been restricted in their testing to bacterial organisms, and have only been used with genomes from within a single species. We demonstrate PhaME’s ability to construct robust genus and species phylogenies using examples that span the tree of life, with up to thousands of genomes as input in the form of raw sequencing reads, draft assembled contigs, fully completed genomes, and even unassembled metagenomic reads
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