Abstract
BackgroundNext-generation sequencing technologies are rapidly generating whole-genome datasets for an increasing number of organisms. However, phylogenetic reconstruction of genomic data remains difficult because de novo assembly for non-model genomes and multi-genome alignment are challenging.ResultsTo greatly simplify the analysis, we present an Assembly and Alignment-Free (AAF) method (https://sourceforge.net/projects/aaf-phylogeny) that constructs phylogenies directly from unassembled genome sequence data, bypassing both genome assembly and alignment. Using mathematical calculations, models of sequence evolution, and simulated sequencing of published genomes, we address both evolutionary and sampling issues caused by direct reconstruction, including homoplasy, sequencing errors, and incomplete sequencing coverage. From these results, we calculate the statistical properties of the pairwise distances between genomes, allowing us to optimize parameter selection and perform bootstrapping. As a test case with real data, we successfully reconstructed the phylogeny of 12 mammals using raw sequencing reads. We also applied AAF to 21 tropical tree genome datasets with low coverage to demonstrate its effectiveness on non-model organisms.ConclusionOur AAF method opens up phylogenomics for species without an appropriate reference genome or high sequence coverage, and rapidly creates a phylogenetic framework for further analysis of genome structure and diversity among non-model organisms.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1647-5) contains supplementary material, which is available to authorized users.
Highlights
Next-generation sequencing technologies are rapidly generating whole-genome datasets for an increasing number of organisms
To provide a tool for researchers to assess their own AAF phylogenetic reconstructions, we developed a two-stage bootstrap that estimates the precision of our method when applied to novel genome data
The AAF approach first calculates pairwise genetic distances between each sample using the number of evolutionary changes between their genomes, which are represented by the number of k-mers that differ between genomes
Summary
Next-generation sequencing technologies are rapidly generating whole-genome datasets for an increasing number of organisms. Alignment-free methods were initially proposed to circumvent the issues of recombination and genetic shuffling that make alignment difficult [9], and they have attracted attention due to their computational efficiency [10] and accuracy [11]. Because they are not based on specific evolutionary models, they have been mainly used for comparing similarity between sequences [12, 13] and genomes [14]
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