NEXT GENERATION SEQUENCING CASE STUDY:

Kakapo Heading Towards World First

The kakapo is on track to become the first species where every individual within its population is genome sequenced. As of January 2016, there were 125 kakapo living. Just a few months later – thanks to a bumper breeding season – the population had grown by nearly a quarter, to 155 birds.

Conservation geneticist Associate Professor Bruce Robertson has worked with kakapo for 20 years. The University of Otago researcher says that, with 41 Kakapo already sequenced, the aim is to continue sequencing the remainder of the adult population.

World firsts aside, the comprehensive DNA dataset gives this preciously-rare bird the best possible chance of a successful future.

“The genomic information will add to helping us figure out who is related to whom, so we don’t have fathers mating daughters, etc. Currently, we use a combination of natural mating and attempted artificial insemination to ensure genetic diversity in this very small population. In the future, we will also identify lethal or detrimental genes and avoid mating those birds.”

NZGL is a key collaborator in this project and Associate Professor Robertson says the ability to carry out the sequencing within New Zealand has been invaluable.

“It’s been great for many reasons: the significance of the kakapo to iwi, avoiding the logistical challenges and longer timeframes involved with exporting samples overseas, and the people at NZGL are easy to work with. We can talk to them any time and it’s all very straightforward. We can do this genomic analysis here in New Zealand, so it makes sense to do so.”

Department of Conservation science advisor Dr Andrew Digby says the project will be of huge benefit to kakapo conservation. “Two of the biggest threats to the recovery of kakapo are high infertility – only about half of eggs hatch – and disease. The population genome data will help us understand whether there’s a genetic basis for these issues and how best to mitigate them. Plus we’ll learn so much more about kakapo from their genomes.”

This kakapo sequencing work has been part funded by two novel sources: crowd funding, via the Science Exchange Project; and an “adopt a genome” initiative whereby US$400 buys an artwork of a particular kakapo’s DNA sequence. The latter is facilitated by Genetic Rescue Foundation, a not-for-profit organisation focused on preserving global diversity.

NZGL Services: 12 lanes of HiSeq on 40 Kakapo

Dr Aaron Jeffs, Otago Genomics and Bioinformatics Facility

“For this project, Otago Genomics was able to personally interact with Associate Professor Robertson, to ensure safe hand-over and return of the 40 kakapo DNA samples. Library prep and sequencing was completed within six weeks, with the samples under our guardianship for as short a time as possible. Liaison with Dr Andrew Digby, Department of Conservation, allowed for the safeguarding of the culturally, nationally and internationally significant sequencing data by The Crown.”

 

 

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This juvenile bird on Whenua Hou/ Codfish Island is one of only 155 Kakapo remaining in the world. The species may be the first to have every individual within its population sequenced. Photo courtesy: Dr Andrew Digby, Department of Conservation

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