Send to

Choose Destination
G3 (Bethesda). 2014 May 22;4(7):1339-46. doi: 10.1534/g3.114.011825.

Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps.

Author information

Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5065.
Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5065


Microbial communities consist of mixed populations of organisms, including unknown species in unknown abundances. These communities are often studied through metagenomic shotgun sequencing, but standard library construction methods remove long-range contiguity information; thus, shotgun sequencing and de novo assembly of a metagenome typically yield a collection of contigs that cannot readily be grouped by species. Methods for generating chromatin-level contact probability maps, e.g., as generated by the Hi-C method, provide a signal of contiguity that is completely intracellular and contains both intrachromosomal and interchromosomal information. Here, we demonstrate how this signal can be exploited to reconstruct the individual genomes of microbial species present within a mixed sample. We apply this approach to two synthetic metagenome samples, successfully clustering the genome content of fungal, bacterial, and archaeal species with more than 99% agreement with published reference genomes. We also show that the Hi-C signal can secondarily be used to create scaffolded genome assemblies of individual eukaryotic species present within the microbial community, with higher levels of contiguity than some of the species' published reference genomes.


Hi-C; clustering algorithms; metagenome assembly; metagenomics

[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for HighWire Icon for PubMed Central
Loading ...
Support Center