Post-holiday gift ideas: a draft genome

EVERYONE IS GETTING A GENOME!

What do you get the genomicist who has everything? How about a high-quality de novo genome of their favorite species?! How, you ask? Well, using Dovetail’s new Chicago library prep and analysis method.

This year, Ed Green and colleagues launched Dovetail Genomics with the promise of taking your organism’s purified high molecular weight DNA and turing it into a high-quality de novo genome assembly. To do so, they modified a chromosome conformation capture technique, Hi-C, so that it would work with naked DNA, thereby limiting the amount of inter-chromosomal cross-links (which are bad for genome assembly because you are build scaffolds that span multiple chromosomes).

Dovetail’s method, which is detailed in this preprint that generated a gator genome, takes your purified DNA, reconstitutes the chromatin in vitro, and then uses the Hi-C method to cross-link DNA and generate an Illumina sequencing library. The end results is essentially a mate-pair library on steroids. Where the typical mate-pair library gets you mate-pairs that are up to ~20Kb, in theory, the Chicago method can give you mate-pairs that are as long as the input DNA fragments, which should be millions of bases long. After sequencing your Chicago library (and a few other standard sequencing libraries), Dovetail uses their HiRise software pipeline to assemble a high quality de novo genome just for you.

So there you go — the post-holiday gift for that genomics researcher who is always hard to shop for. But it won’t be  cheap. It’ll run you at least $10,000 and potentially more than $40,000 depending on all of the bells and whistles you add to the genome. Happy shopping!

REFERENCES

Putnam NH, O’Connell B, Stites JC et al. (2015) Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.

 

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About Noah Snyder-Mackler

I'm a postdoctoral fellow in the department of Evolutionary Anthropology at Duke University. Broadly, I study non-human primate genetics and genomics. More specifically, I'm interested in the interaction between behavior, genotype, and gene expression in response to social stress.
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