Genomics Aotearoa

Genomic breakthrough in invasive species management - Genomics Aotearoa

Apr 15, 2020

Nick Kachel 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, … Read More

The importance of the humble blueberry - Genomics Aotearoa

Feb 26, 2020

Dr David Chagné New Zealand is involved in a US$12.8 million USDA grant to improve the quality of blueberry and cranberry. The four-year project, led by North Carolina State University, is part of the USDA’s National Institute of Food and Agriculture Specialty Crop Research Initiative, which funds multi-year, multi-institutional collaborative projects. Genomics Aotearoa and Plant and Food Research Ltd have just become part of this project, and we’re very excited about what that offers – for blueberry producers here, for the New Zealand economy, the consumer and for other genomics researchers. But what does this actually mean for us? As with all genome research, the solution is not in the sequencing itself, but in the opportunities it provides to use the genetic information for good. And for us, it’s not just the research results but also the potential to leverage … Read More

Finish what’s on your plate - Genomics Aotearoa

Nov 04, 2019

Murray Cox Do I have to finish my favourite genome? That’s an often-asked question. Geneticists generally strive to produce high-quality genomes that sequence every last gene, making full use of the state-of-the-art technologies coming on stream. Sequencing DNA means determining the order of the four chemical building blocks – called “bases” – that make up the DNA molecule. The sequence tells scientists the kind of genetic information that is carried in a particular DNA segment. For example, scientists can use sequence information to determine which stretches of DNA contain genes and which stretches carry regulatory instructions, turning genes on or off. Importantly, data from a genome sequence can highlight changes in a gene that may cause disease. Reference genomes are the cornerstone of modern genomics. These high-quality genomes are differentiated from draft genomes by their completeness – few gaps, low … Read More

Genomics, genetic persistence and the hihi - Genomics Aotearoa

Aug 20, 2019

Dr Anna Santure, University of Auckland How important is genetic diversity to species persistence? This is a question we’ve been puzzling over in New Zealand, and worldwide, for some decades. It has been difficult to address using ‘traditional’ approaches to determine genetic diversity, which sample just a handful of positions in the genome. However, in recent years, with much lower costs of DNA sequencing, we’ve been able to sample larger and larger amounts of the genome, and in some cases generate whole genome sequence data for individuals and even whole populations. This revolution in the affordability and accessibility in sequencing means we can finally assess, in a standardised way, how much genetic variation a species has, what this means for how responsive the species is to selection pressures, and hence how resilient it will be in the future. And that’s … Read More

The complexity of stick insect genomes and why it could help New Zealand conservation - Genomics Aotearoa

Jul 25, 2019

Dr Ann McCartney We have recently completed the first high-quality genome of a stick insect using link read technology, but what does this mean? And why is a gold standard reference genome important to New Zealand’s conservation efforts? Stick insects are actually biologically interesting. Firstly, in times of stress, they have the ability to become parthenogenic, meaning the females lay eggs without needing to mate with males to produce offspring. Secondly, they are dynamic in a range of temperatures and altitudes in New Zealand.  Better understanding of stick insect genomics will contribute much to global knowledge on the Phasmatodea species, including biogeographic origin, reproduction and temperature tolerance and its role in climate change. Furthermore, several New Zealand species are highly endangered, with one species occupying the highest Department of Conservation threatened species category. Stick insects are also interesting because … Read More

Don’t ignore the ‘omics - Genomics Aotearoa

Jul 23, 2019

Professor Cristin Print ‘Omics technologies are an advance that few health practitioners can ignore. The last five years has seen an expanding range of technological advances. Genomics and related ‘omic technologies are rapidly penetrating into the mainstream of primary and secondary care and transforming our knowledge of disease through research. Some of these new technologies are destined to be used by all health practitioners within the next five years, while others are research tools, used to build the evidence base for future medical practice. In fact, it has been said we are now experiencing the most transformative technological advance in biomedical science since the development of the optical microscope, thanks to the shift from sequencing one gene at a time, to easily sequencing the complete genomes of many people simultaneously. So what are ‘omic technologies? ‘Omic technologies generate masses of … Read More

A long read, and a tricky jigsaw puzzle - Genomics Aotearoa

Apr 05, 2019

Peter Dearden Sequencing is an essential part of creating a genome, be it human, stick insect, kākāpō or sheep (all genomes Genomics Aotearoa is currently working on). But what is sequencing, how does it work, and why does it take so long?  And why does it matter to us? Sequencing is a laboratory process where segments of DNA base pairs are put in order, so researchers know where genes are located on the chromosomes. Genomics Aotearoa is finding the best ways of new genomic technologies to assemble genomes of organisms important to NZ medicine, agriculture and conservation, and to make those into technology ‘pipelines’. That will streamline processes, and make the technology more readily available to other research projects. Current sequencing technology means the whole genome can’t be produced in one go. Researchers, therefore, cut DNA into pieces, then they … Read More

Why it’s important to have Māori-led capacity in genomics research - Genomics Aotearoa

Mar 06, 2019

Dr Phillip Wilcox Genomics research is an emerging frontier that will mean applications such as personalised medicine being developed for New Zealand-specific problems, and something that will see an increasing focus on the needs of Māori populations. However, Māori are significantly under-represented in genomic sciences. One successful way of building capability to improve understanding of genomics among Māori has been the Summer Internship of Native peoples in Genomics (SING) Aotearoa internship programme, an innovative initiative now co-sponsored by Genomics Aotearoa that we have been running since 2016. Phil Wilcox at SING Aotearoa 2019. This year, 20 SING interns spent a week in Palmerston North with some our best genomics researchers, the aim being for pākeke (Māori adults) and graduate-level Māori students to improve their understanding of the technologies, as well as the … Read More

A random bioinformatics career walk … and how Genomics Aotearoa is helping researchers be a little less scared of the “command line” - Genomics Aotearoa

Jan 30, 2019

Dr Alana Alexander A “random walk” is a mathsy term for a path strung together with a bunch of random steps (not unlike trying to walk my stubborn St. Bernard cross on a leash). Despite being a bioinformatician (which folks often think means “also a maths wiz”), my maths is (unfortunately) not great. Therefore, I mention random walks not because I’m about to drop a knowledge bomb about higher-dimensional Riemannian manifolds (thanks Wikipedia!), but because I think it is a great way to describe how I got into bioinformatics. Many researchers assume bioinformaticians have trained extensively to commune with processors, compilers, SLURM scripts, and core dumps. That’s definitely one way to become a bioinformatician, and probably a really smart one! Multiple universities in Aotearoa and internationally offer bioinformatics specialisations and/or degrees, and many of the other (brilliant) Genomics Aotearoa postdocs … Read More

How does epigenetics fit in? - Genomics Aotearoa

Dec 14, 2018

Greg Jones The study of epigenetics could well be a key tool in transforming valuable genomic information into useful health outcomes for New Zealanders. But what is epigenetics and why is it important? Epigenetics is the influence of genetic susceptibility combined with the complex interactions of each individual’s environment over their lifetime. An individual’s epigenome is a dynamic personalised profile of environmental stress exposures, influenced by things like diet, gut microbiota, toxin and drug exposure, psychological and physical stressors and levels of activity throughout life. The field of epigenetics could have an important role in precision medicine – an emerging approach for disease management that tailors treatment to the individual, based on their genes and environment. Measuring the epigenetic changes that occur in diseases, including cancer and heart disease, provides an understanding of the underlying mechanisms. This insight can then … Read More