A Rapid Method for End-to-End Assembly of Complex Genomes, Pathogen Discovery, and Metagenomic Deconvolution

Assembly of plant and animal genomes is inhibited by the lack of long-range contiguity information in short-read sequencing. This limitation also impedes metagenome assembly, since one cannot tell which sequences originate from the same species within a shotgun-sequenced population. We have overcome these bottlenecks by adapting a chromosome conformation capture technique (Hi-C) for the scaffolding of de novo assemblies of large complex genomes and the deconvolution of metagenomes.

Typically used for modelling the 3D structure of a genome, chromosome conformation capture techniques such as Hi-C measure long-range interactions of DNA molecules in physical space. These tools employ crosslinking of chromatin in intact cells followed by intra-molecular ligation, joining DNA fragments that were physically nearby at the time of crosslink. Subsequent deep sequencing of these DNA junctions generates a genome-wide contact probability map that allows the 3D modelling of genomic architecture within a cell. The strong enrichment in Hi-C signal between genetically neighboring loci allows the scaffolding of entire chromosomes from fragmented draft assemblies. Hi-C signal also preserves the cellular origin of each DNA fragment and its interacting partner, allowing for deconvolution and assembly of multi-chromosome genomes from a mixed population of organisms.

Our method (Proximity-Guided Assembly, PGA) allows rapid assembly of reference-quality, chromosome-scale genomes for plants and animals, regardless of genome size, repeat content, and without the need for isolating high-MW DNA. PGA also allows simultaneous decontamination of mixed draft assemblies (such as in the case of symbionts and pathogens) and metagenomic samples with low input requirements. The high quality of Hi-C-based assemblies allows the simultaneous closing of numerous unculturable genomes, placement of plasmids within host genomes, and microbial strain deconvolution in a way not possible with other methods.