Dovetail Genomics’ Prairie Chicken Genome Underpins Heath Hen De-extinction Efforts
The heath hen was a charismatic bird endemic to the grasslands of New England and surrounding regions. It was driven to extinction in large part due to over-hunting by humans. As a key mediator of biodiversity in its habitat, the “de-extinction” of the heath hen offers promise for restoring balance to that environment. Consequently, the Revive & Restore foundation has set out to understand the challenges and feasibility of reviving and reintroducing the heath hen, potentially creating the first community-backed de-extinction effort.
A critical component of the heath hen revival is the reconstruction of its original genome. Because no living heath hens remain, the genomic “scaffold” of this reconstruction effort had to be constructed from a close, living evolutionary relative. The greater prairie chicken was selected as an ideal candidate due its close evolutionary relationship to the heath hen. At the outset of this project only limited genomic sequence information had been collected for the greater prairie chicken, and no full genome assembly existed. Consequently, Revive & Restore partnered with Dovetail to produce a high quality greater prairie chicken genome assembly to lay the foundation for the heath hen reconstruction efforts.
To begin, members of the heath hen project provided Dovetail with tissue samples from two female greater prairie chickens, shipped frozen immediately after sampling. Dovetail extracted DNA from a number of the samples and selected the best extraction (that with highest yield and largest fragment size) for the full assembly effort. DNA from the chosen sample was used to prepare both conventional shotgun libraries and ChicagoTM libraries, the only two data types used in this project. The shotgun libraries were sequenced to a Q20 depth of ~95X, which corresponds to approximately 300 million read pairs at 2×150 bp. Dovetail then performed a Meraculous assembly with the collected shotgun data to yield a draft assembly with a scaffold N50 of 136 kbp.
Next, Dovetail produced and sequenced a Chicago library from the same source high molecular weight DNA. This library was sequenced to a physical coverage level of ~110X, corresponding to approximately 150 million read pairs at 2×100 bp. This library and the draft assembly were scaffolded by Dovetail’s HiRise™ pipeline to yield a final scaffold N50 of 12.2 Mbp, a nearly 90-fold increase in contiguity. The final genome totaled nearly 1 Gbp in size.
The entire duration of this process, from sample reception to genome delivery, took only 8 weeks. The greater prairie chicken’s genome is now in the hands of Revive & Restore’s scientists, who are hard at work leveraging it to reconstruct the heath hen’s genome.