MinYS: mine your symbiont by targeted genome assembly in symbiotic communities

Abstract

Most metazoans are associated with symbionts. Characterizing the effect of a particular symbiont often requires getting access to its genome, which is usually done by sequencing the whole community. We present MinYS, a targeted assembly approach to assemble a particular genome of interest from such metagenomic data. First, taking advantage of a reference genome, a subset of the reads is assembled into a set of backbone contigs. Then, this draft assembly is completed using the whole metagenomic readset in a de novo manner. The resulting assembly is output as a genome graph, enabling different strains with potential structural variants coexisting in the sample to be distinguished. MinYS was applied to 50 pea aphid resequencing samples, with variable diversity in symbiont communities, in order to recover the genome sequence of its obligatory bacterial symbiont, Buchnera aphidicola. It was able to return high-quality assemblies (one contig assembly in 90% of the samples), even when using increasingly distant reference genomes, and to retrieve large structural variations in the samples. Because of its targeted essence, it outperformed standard metagenomic assemblers in terms of both time and assembly quality.

Figure 1.

Overview of MinYS approach, for targeted genome assembly. MinYS takes as input a reference genome and a set of metagenomic reads, and outputs the targeted genome assembly as a genome graph encompassing the potential strain diversity contained in the sample.

Figure 2.

Effect of the level of divergence of the reference genome on MinYS assembly statistics (assembly contiguity in the top plot, assembly completeness in the bottom left plot and running time in the bottom right plot) and on the relative contribution of the first backbone assembly step (in red) and of the gap-filling step (blue). The plots show the average values for the 32 individual samples.

Figure 3.

View of the genome graph generated by MinYS with a sample containing two coexisting strains of B. aphidicola differing by 20 structural variants. The graphical representation was obtained with the assembly graph visualization tool, Bandage, where each node is represented by a colored rectangle whose size is related to the node sequence size.