Sequencing

11th Annual Sequencing, Finishing, and Analysis in the Future Meeting
ASSEMBLING WHOLE GENOMES FROM MIXED
MICROBIAL COMMUNITIES USING HI-C
Friday, 3rd June 10:10 La Fonda Ballroom Talk (OS‐7.03)
Ivan Liachko 1 , Joshua Burton 1 , Laura Sycuro 2 , Andrew Wiser 2 ,
David Fredricks 2 , Maitreya Dunham 1 , Jay Shendure 1
1 University of Washington, 2 Fred Hutchinson Cancer Research Institute
Assembly of whole genomes from next‐generation sequencing is inhibited by the lack of 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 population. We have
overcome these bottlenecks by adapting a chromosome conformation capture technique (Hi‐C) for
the deconvolution of metagenomes and the scaffolding of de novo assemblies of individual genomes.
In modeling the 3D structure of a genome, chromosome conformation capture techniques such as
Hi‐C are used to 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 modeling
of genomic conformation 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.
We have used Hi‐C to scaffold whole genomes of animals, plants, fungi, as well as prokaryotes and
archaea. We have also been able to use this data to annotate functional features of microbial
genomes, such as centromeres in many fungal species. Additionally, we have applied our technology
to diverse metagenomic populations such as craft beer, bacterial vaginosis infections, soil, and tree
endophyte samples to discover and assemble the genomes of novel strains of known species as well
as novel prokaryotes and eukaryotes.
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.
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