Genomic breakthrough in invasive species management

March 26th, 2020

A cross-Tasman collaboration involving our Synthetic Biology Future Science Platform and Managing Invasive Species and Diseases program has produced the first full genome sequence of the ship rat.


The ship rat, or black rat, is one of the most infamous invasive species in the world. They’re intelligent, adaptable, and they multiply like… well… ship rats.

A native to the Indian sub-continent, this pest has now spread to every corner of the globe and is an outstanding carrier for multiple zoonotic diseases – those which can be spread from animals to humans.

New Zealand is no stranger to the species. They first arrived in the country on European ships in the 19th century and quickly went about making a home for themselves. They can be found across the country in native forests, scrublands, and urban parklands.

They are one of the biggest threats to biodiversity in New Zealand. As well as spreading disease and affecting agricultural production , the ship rat also preys on bird eggs and chicks, and has been implicated in the extinction of:

  • The bush wren
  • Huia
  • Laughing owl
  • North Island and South Island piopio/ thrush
  • South Island kokako
  • South Island snipe, and
  • the greater short-tailed bat.

It’s no surprise then, that ship rat has been identified as a target for eradication by Predator Free 2050 (PF2050 Ltd), a New Zealand government mission aiming to remove three species of introduced rat, possums and mustelids from the country by 2050.

Knowledge is power

PF2050 Ltd provides co-funding for ambitious predator eradication operations and breakthrough science to inform future management and eradication plans for the targeted species.

So, a new genomic breakthrough with help from CSIRO and Genomics Aotearoa is something to be excited about – especially since 2020 is the Chinese Year of the Rat!

It’s in the genes

A collaboration with our Managing Invasive Species and Diseases program (Health and Biosecurity) and Synthetic Biology Future Science Platform has produced the first full genome sequence of the ship rat.

Genome sequences are the order of nucleotides, or bases, in an organism’s DNA. Knowing the order of these bases helps scientists understand the growth, development and maintenance of the organism.

This new reference genome – now available to international researchers – will empower scientists working on critical questions of conservation, evolution and disease prevention.

“Understanding the genetic makeup of Rattus rattus enables us to investigate how rats adapt to changing environments and what makes them so successful as invasive predators around the world,” said Dr Florian Pichlmüller from the University of Auckland, one of the lead researchers on the project.

The collaboration involved researchers from University of Auckland, University of Otago, and CSIRO.

Joining the dots

According to our scientist Dr Rahul Rane, who led the work from CSIRO, the result of the collaboration is one of the most complete mammalian genomes currently available, which  has enabled new techniques to be transferred to New Zealand researchers.

An initial assembly based on ‘short read’ technology was produced in late 2015 by Dr Florian Pichlmüller (who is now a research fellow with Genomics Aotearoa).

CSIRO was then brought on board to leverage its expertise in genome assembly and long read sequencing. While short read technologies break the DNA into small parts (often a few hundred nucleotides), long read sequencing captures larger fragments (often >10 – 100 times larger than the former). This allows the reconstruction of a more accurate genome.

Dr Rane described CSIRO’s long read genome assembly methods as creating highly accurate big lego blocks. The team then used established Hi-C techniques as bridges between the small and big lego blocks to assemble chromosomes and piece together the position of genes in the genome.

Cellular material and DNA strands that contain genes deteriorate with time, even in storage.

“The new techniques have optimised tissue harvesting and DNA extraction from older samples and further helped reduce research costs,” said Dr Rane.

Global interest

The next step of the project is leveraging the United States’  National Center for Biotechnology Information (NCBI) gene discovery service, RefSeq. This will help augment the existing studies and improve researchers’ ability to discover genes critical to genetic biocontrol.

The NCBI’s annotation has now been completed and is available online.

The new genome is also expected to attract international interest. The ship rat originated in South East Asia. Researchers have recently questioned the long-held view that ship rats carried the plague into Europe into the 14th Century. The role of intermediate reservoir species in the transfer of new infectious disease from mammal species to humans (such as Coronavirus COVID-19) is a topical research area.