Video | Business Headlines | Internet | Science | Scientific Ethics | Technology | Search

 

New Zealand’s Most Devastating Predators’ Genomes Sequenced. DNA Codes Broken For Stoat And Ship Rat

The DNA secrets of the Predator Free 2050 programme’s most wanted species have been revealed.

The complete genome of the stoat is now available to researchers on the US-based National Center for Biotechnology Information genome database, hard on the heels of the ship rat genome.

The reference genomes were created by teams of Kiwi scientists working with international collaborators.

The genome sequencing of the stoat (Mustela erminea) was led by Dr Andrew Veale, a scientist based at Manaaki Whenua - Landcare Research.

“Stoats will be one of the trickiest pests to eradicate across Aotearoa, and this genome provides great opportunities to understand their biology, and to create tools to assist conservation”, says Dr Veale.

The assembled stoat genome is over 2.4 billion DNA bases long, with over 20,000 identified protein-coding genes. This new genome is one of the highest quality vertebrate genomes ever produced, with nearly gapless complete chromosomes assembled and annotated.

“This sets us up for the breakthrough research we will need to realise the Predator Free 2050 goal,” says Professor Dan Tompkins of Predator Free 2050 Limited, which co-funded the research as part of its Science Strategy. “Knowing the genetic code of these devastating predators is an important step towards finding their Achilles heel.”

The project was co-funded by the Biological Heritage Science Challenge and involved collaboration with scientists from the Vertebrate Genome Project, based at The Rockefeller Institute, and the Wellcome Sanger Institute.

Dr Fiona Carswell, Chief Scientist at Manaaki Whenua, says that the underpinning data provided by the genome will be invaluable in helping to achieve predator-free status for New Zealand. “This shared work in defining the stoat genome is a stepping-stone in our ongoing research into species-specific toxins, and a fantastic example of collaboration across the science sector.”

Biological Heritage Science Challenge co-director Dr Andrea Byrom says “the new genomes will build understanding of the origins and dispersal of predators, inform the development of novel control mechanisms such as species-specific toxins and help assess the potential of gene technologies.”

In March, sequencing of the ship rat (Rattus rattus) genome was completed through an Australia-New Zealand collaboration involving University of Auckland, Genomics Aotearoa and CSIRO, Australia’s national science agency.

The high-quality ship rat genome is similarly expected to become the international reference genome for the species.

Notes for editors

The completed stoat genome can be found here:

https://www.ncbi.nlm.nih.gov/genome/34548

What is a genome?

A genome is the complete set of an organism’s DNA, and ideally it is accurately assembled with no errors, deletions, duplications or gaps. Most published genomes are highly fragmented, but with recent advances in sequencing technology and assembly algorithms, ‘platinum quality’ genomes with accurate chromosome level assemblies are now possible.

Which stoat was sequenced and why?

The gene-sequenced stoat was live-trapped as part of pest control operations on private land in the Coromandel Ranges south of Thames. Importantly this stoat was a male, which means that he had both an X and a Y chromosome, giving him the full complete set of genes for the species. Most of the time trapped stoats are recovered a while after death and after they are beginning to decay, therefore they have poorly preserved DNA, but this was the perfect specimen to be immortalised as ‘The Stoat Genome’.

[The reference genome for the ship rat was created from a male rat trapped in Auckland’s Waitakere Ranges].

How was it sequenced?

Genomes are large and the genetic material they contain cannot be 'read out' in order (i.e., sequenced) end-to-end in a single step. This means that genomes have to be sequenced in smaller reads. Assembling a genome is like piecing together a massive jigsaw puzzle without a reference picture.

We used four different genetic sequencing technologies to produce the stoat genome assembly: PacBio, Chromium 10x, Bionano maps and Hi-C. Following the metaphor of a jigsaw puzzle, the PacBio reads are large – like large jigsaw pieces, so they provide a lot of information. It is unlikely that two regions of the genome will contain identical ‘pictures’ this large. The Chromium 10x reads consist of lots of little reads, but each one is labelled according to what row in the puzzle it goes. The Bionano map is like sticking big barcodes across the back of the pieces – so you can align the pieces to this reference. The Hi-C reads are small, but link together pairs of pieces that are physically near each other in the 3D folded chromatin structure. So to assemble the genome, first we assembled the long-read PacBio reads into contigs: a consensus DNA sequence of overlapping reads. We then used each of the other technologies to progressively scaffold (stick together and orient) each of these contigs together. After all of this assembly and scaffolding, all of the original reads are mapped back to ‘polish’ the genome (correcting errors) and to fill in any gaps.

How is it being used?

The stoat genome is already being used to assist conservation efforts in New Zealand, and there are many other projects on the horizon.

Dr Veale is currently mapping the connectivity of stoat populations across the landscape using spatial models, relying on novel genetic markers. “Once we have the precise relatedness of each individual and their location of capture, we can create models showing how the animals disperse across the New Zealand landscape. These models can then be used to optimise trapping networks, enabling traps to be placed to prevent reinvasion into areas cleared of stoats.” Dr Veale is also developing forensic genetic markers from the genome sequence to identify individual stoats from trace samples such as scat, saliva and hair. These markers can then be used in a CSI type setting. For instance, if a conservation program had a dead kiwi with a bite mark, and a dead stoat in a trap, we could ask “Was this the stoat that killed the kiwi, or is there another one out there?” Genetics can tell us the answer.

Dr Erica Hendrikse, a postdoctoral researcher at Manaaki Whenua working with Dr Veale and Dr Brian Hopkins, is currently using the stoat genome (along with the recently produced ship rat and possum genomes) to look for ways to develop species-specific toxins.

What about the ship rat genome?

The completed ship rat genome is available here:

https://www.ncbi.nlm.nih.gov/genome/13128

The story of the ship rat gene sequencing is here:
https://pf2050.co.nz/news/significant-milestone-in-new-zealands-predator-free-2050-research-reached-rattus-rattus-genome-sequenced/
[NOTE: This story went unreported by media in March because of the COVID-19 situation at the time]

Who are the funders?

The New Zealand government aims to remove three species of introduced rat, possums and mustelids from New Zealand by 2050 because of their devastating impact on native biodiversity. Predator Free 2050 Limited is a government-owned charitable company that provides co-funding for ambitious predator eradication operations and breakthrough science.

The BioHeritage National Science Challenge, Ngā Koiora Tuku Iko, aims to protect and manage Aotearoa New Zealand’s biodiversity, improve our biosecurity, and enhance our resilience to harmful organisms by focusing research happening across Aotearoa’s land-based and freshwater ecosystems, with the ultimate aim of reversing the decline of biological heritage.

© Scoop Media

 
 
 
Business Headlines | Sci-Tech Headlines

 

The Narrow Divide: New Poll Shows Tight Political Race For SME Votes

In a major turnaround following nearly a decade of MYOB election polls, Labour is currently the preferred political party of New Zealand’s SMEs, with 38% of SME owners and decision makers intending to vote red in the upcoming General Election, ... More>>

Reserve Bank: Further Easing In Monetary Policy Delivered

Tēnā koutou katoa, welcome all. The Monetary Policy Committee agreed to expand the Large Scale Asset Purchase (LSAP) programme up to $100 billion so as to further lower retail interest rates in order to achieve its remit. The eligible assets remain ... More>>

Retail: Post-Lockdown Retail Card Spending Picks Up

The rise in retail card spending was boosted by sales of furniture, hardware, and appliances, Stats NZ said today. “For a third consecutive month, card spending on the long-lasting goods (durables) remained at higher levels than last year, after ... More>>


Contact: Business Drops, New Generation On Hold

New Zealand’s second-largest energy company Contact Energy (‘Contact’) released its full year financial results for the 12 months to 30 June 2020 (‘FY20’) this morning. More>>

Mining: OceanaGold Announces Receipt Of WKP Mining Permit

MELBOURNE, Australia, Aug. 6, 2020 /CNW/ - OceanaGold Corporation (TSX: OGC) (ASX: OGC) (the 'Company') is pleased to announce it has received the mining permit for Wharekirauponga ('WKP') on the North Island of New Zealand. ... More>>

ALSO:

Economy: COVID-19 Lockdown Has Widespread Effects On Labour Market

In the June 2020 quarter, the seasonally adjusted unemployment rate fell to 4.0 percent, down from 4.2 percent last quarter, while underutilisation rose, Stats NZ said today. More>>

ALSO:

NZ Post: New Research By NZ Post Shows Online Shopping Grew 105% In Alert Level 3

New research by NZ Post into how the COVID-19 response has impacted the way Kiwis shop online, shows online shopping increased 105%* when the country moved into Alert Level 3, and may have changed the way Kiwis shop permanently. Online spend peaked ... More>>

ALSO:

Antarctica NZ: Ice-Olation

Antarctica New Zealand is gearing up for a much reduced season on the ice this year and a very different deployment to normal! Before they head to one of the remotest places on the planet, all personnel flying south with the New Zealand programme will ... More>>

ALSO:

QV Valuations: July House Price Index Illustrates Market Resilience

According to the July 2020 QV House Price Index (HPI) results out today , property values recorded a marginal increase, up 0.2% over the month. This is somewhat of a turnaround from June, after the national index edged 0.2% lower. More>>

ALSO:

Property: Queenstown Rents Experience Biggest Drop In Seven Years

Rental prices in the Queenstown-Lakes district saw the biggest annual percentage drop in seven years after falling 28 per cent on June last year, according to the latest Trade Me Rental Price Index. Trade Me Property spokesperson Aaron Clancy said ... More>>

Seismology: The Quiet Earth

As many daily activities came to a halt during lockdown, the Earth itself became quiet, probably quieter than it has been since humans developed the technology to listen in. Seismologists have analysed datasets from more than 300 international ... More>>

RNZ: James Shaw Says Kiwibank, Not Ministers Should Decide On Investors

Climate Change Minister James Shaw says Kiwibank's decision to stop doing business with companies dealing in fossil fuels is the right one. More>>

ALSO:

FMA: Kiwis Confident Financial Markets Will Recover From COVID-19, Plan To Increase Investments

Despite the majority (60%) of investors experiencing losses as a result of COVID-19, the outlook on investing remains positive, according to a Financial Markets Authority (FMA) survey. Most Kiwis (71%) were optimistic that the pandemic will pass eventually ... More>>

FIRST Union: Warehouse Using Covid For Cover As Extensive Restructure Makes Everyone Worse Off

(FIRST Union comments on The Warehouse consultation and proposed restructure) 'Unfortunately the Warehouse have done the disappointing thing and used Covid-19 to justify a bunch of operational business decisions that will leave hundreds of workers without jobs ... More>>

ALSO: