Next-generation phylogenomics

Abstract

Thanks to advances in next-generation technologies, genome sequences are now being generated at breadth (e.g. across environments) and depth (thousands of closely related strains, individuals or samples) unimaginable only a few years ago. Phylogenomics--the study of evolutionary relationships based on comparative analysis of genome-scale data--has so far been developed as industrial-scale molecular phylogenetics, proceeding in the two classical steps: multiple alignment of homologous sequences, followed by inference of a tree (or multiple trees). However, the algorithms typically employed for these steps scale poorly with number of sequences, such that for an increasing number of problems, high-quality phylogenomic analysis is (or soon will be) computationally infeasible. Moreover, next-generation data are often incomplete and error-prone, and analysis may be further complicated by genome rearrangement, gene fusion and deletion, lateral genetic transfer, and transcript variation. Here we argue that next-generation data require next-generation phylogenomics, including so-called alignment-free approaches.

Figure 1

Simplified workflow of phylogenomic approaches. Workflow is shown for (A) the classical approach based on multiple sequence alignment, and (B) an alternative approach based on alignment-free methods, for a simple analysis example of homologous sequences 1, 2, 3 and 4, with a known phylogeny as a reference (shown on top). Sequence fragments that share the same ancestry across all four sequences (i.e. are highly similar among one another) are shown in the same colour (red, blue, yellow and orange regions in each sequence). In this example, the yellow and blue regions of sequences 2 and 4 have undergone rearrangement relative to 1 and 3. The dark yellow (in 1 and 2) and light yellow (in 3 and 4) regions are similar to each other. While the classical approach based on multiple sequence alignment (gaps introduced as dashed lines) yields an inaccurate phylogeny, the alternative alignment-free approach (grouping of sub-sequences) is not affected by the sequence rearrangement in 2 and 4, and yields the correct phylogeny. The difference between the two resulting phylogenetic trees is highlighted in red.