A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies

Alexis Criscuolo

doi:10.3897/rio.5.e36178

Abstract

This paper describes a novel alignment-free distance-based procedure for inferring phylogenetic trees from genome contig sequences using publicly available bioinformatics tools. For each pair of genomes, a dissimilarity measure is first computed and next transformed to obtain an estimation of the number of substitution events that have occurred during their evolution. These pairwise evolutionary distances are then used to infer a phylogenetic tree and assess a confidence support for each internal branch. Analyses of both simulated and real genome datasets show that this bioinformatics procedure allows accurate phylogenetic trees to be reconstructed with fast running times, especially when launched on multiple threads. Implemented in a publicly available script, named JolyTree, this procedure is a useful approach for quickly inferring species trees without the burden and potential biases of multiple sequence alignments.

Highlights

Evolutionary relationships between species are commonly represented by a phylogenetic tree inferred from multiple sequence alignments of orthologous genes
By analyzing simulated genome sequences, this procedure is shown to efficiently estimate the pairwise evolutionary distances between each pair of genomes, allowing the reconstruction of accurate phylogenetic trees. This expected accuracy is illustrated by the analysis of 187 real genome datasets, representative of different genera within the bacterial, archaeal and eukaryotic phyla. All these analyses show that this novel bioinformatics procedure, implemented in the script JolyTree, is an efficient approach to infer a phylogenetic tree from hundreds of genome assemblies in a few minutes
Several analyses from simulated and real datasets were performed to show that JolyTree allows accurate phylogenetic trees to be quickly inferred from genome sequences

Summary

Introduction

Evolutionary relationships between species are commonly represented by a phylogenetic tree inferred from multiple sequence alignments of orthologous genes. To infer a phylogenetic tree that represents the evolutionary relationships of a set of genomes, an alternative approach is to estimate a pairwise distance between each pair of unaligned genomes, and to build a phylogenetic tree with a fast distance-based reconstruction method. Such bioinformatics procedures are becoming popular because they allow dealing with thousands of assembled genomes, depend on few assumptions regarding their evolutionary process, and quickly lead to a phylogenetic tree with minimal manual intervention (Chan and Ragan 2013, Zielezinski et al 2017). A distance-based alignment-free phylogenetic inference from genome sequences could be decomposed in four main steps

Methods

Results

Conclusion