Scientists have used New Zealand's critically-endangered kākāpō to help build a blueprint for genetically mapping every extant vertebrate species on the planet. Photo / Peter Meecham
Scientists have used New Zealand's critically-endangered kākāpō to help build a blueprint for genetically mapping every extant vertebrate species on the planet. Photo / Peter Meecham
Scientists have used New Zealand's critically-endangered kākāpō to help build a blueprint for genetically mapping every extant vertebrate species on the planet.
Just over 200 kākāpō today remain, on two predator-free islands, and helping the bulky, flightless parrot to breed has proven a big challenge for conservationists.
Whether the last of the species have the genetic resilience to survive has long been unknown - and a question that only high-quality genomic analysis can answer.
After scientists sequenced the first kākāpō genome - or decoded its full genetic make-up - in 2015, Kākāpō Recovery and the Genetic Rescue Foundation launched the Kākāpō125+ project to map the genomes of all other surviving birds.
It marked the first time that the entire population of one animal had all been sequenced, and has since begun delivering a wealth of new information about crucial threats.
"Things like infertility is probably the biggest problem that we have for kākāpō are either infertile, or they suffer early embryo death," Department of Conservation kākāpō specialist Dr Andrew Digby said.
"And there's pretty strong indications from some earlier, much lower resolution genetic studies that that's related to inbreeding, both from a male and the female."
Last breeding season produced 252 eggs - an "incredible" number, Digby said - yet the programme only ended up with about 70 chicks.
"That's a lot of lost productivity, and any gains we can make is going to have a huge impact."
Another big barrier was disease - respiratory fungal infection Aspergillosis caused a major headache in 2019 - and Digby said it was possible genetic susceptibility could be a factor.
"That's the sort of thing that we want to try to understand. Because if we have a certain group of birds that are more susceptible, we can put them somewhere else."
In a just-published flagship study, scientists from the international Vertebrate Genomes Project picked kākāpō among 16 candidates from which to make a roadmap for assembling high-quality "reference" genomes.
These only exist for the celebrities of laboratory science, like mice, fruit flies, zebrafish, and, of course, humans.
Just over 200 kākāpō today remain, on two predator-free islands, and helping the bulky, flightless parrot to breed has proven a big challenge for conservationists. Photo / Peter Meecham
For less popular species, there is often no reference genome or, perhaps worse, messy genomes stitched together from sequences obtained via lower quality methods.
Compared to the new VGP genomes, up to 60 per cent of the genes in such genomes have missing sequences, are entirely missing, or incorrectly assembled, the researchers found.
It could take years to untangle the thousands of assembly errors per species.
In the new study, scientists found that extremely small populations of kākāpō have been able to survive their low numbers in the past since the last ice age more than 10,000 years ago, by purging "deleterious" mutations that cause disease from inbreeding.
As long as the population could be kept intact, the findings, published in major journal Nature, offered hope that kākāpō could survive even with fewer than 100 individuals.
Many false gene duplications were found among the 16 mapped species, which also included the world's rarest animal - the tiny vaquita porpoise, numbering only nine known individuals.
Most of the errors were caused by algorithms that didn't properly separate out maternal and paternal chromosome sequences, instead interpreted them as two separate sister genes.
"We have thousands of genes in the literature that are false duplications," said project chair Professor Erich Jarvis, of Rockefeller University in the US.
"The genes are not actually there. It is unconscionable to be working with some of these genomes."
The project arose from the frustrations of hundreds of scientists working in its parent organisation, the Genome 10K consortium, whose mission was to generate genome assemblies of 10,000 vertebrate species.
The initial genome assemblies that the G10K and other groups generated were based on short 35 to 200 base pair reads, but these assemblies were highly incomplete.
The VGP goal was to build a library of error-free reference genomes for all vertebrate species, which researchers and conservationists will be able to use readily, without dedicating months or years to fixing individual genes.
"We said, let's do some hard work on the front end, so that we can get high quality data on the back end," Jarvis said.
Many companies approached the project, promising a single sequencing technology that would solve every problem with messy reference genomes.
Respiratory fungal infection Aspergillosis caused a major headache for kākāpō conservation managers in 2019. Photo / Michael Craig
The project assembly team tested each method on a single hummingbird, chosen both for its relatively small genome and because of Jarvis's research interests in vocal learning among bird species, but every technology fell short.
"None had all of the necessary components to make a high-quality assembly," he said. "So we combined many tools into one pipeline."
Groups including Genomics Aotearoa, aiming to develop high-quality genomes of species of importance to New Zealand, were already using the most advanced version of the novel pipeline.
Reference genomes that once took years to generate were now rolling out in weeks and months — all without the false duplications and other errors endemic to previous assemblies.
Scientists are already using the new data to study genes that render bats immune to Covid-19, and question long-standing conventions in basic science, such as whether there are meaningful differences among oxytocin and its receptors found in humans, birds, reptiles, and fish.
All told, 20 studies and 25 high-quality vertebrate genomes accompany the rollout of the novel pipeline.
"The first high-quality genomes that we sequenced taught us so much about the technology and the biology that we decided to publish in these initial papers," Jarvis said.
