Genomics Aotearoa

Containers for reproducible bioinformatics research - Genomics Aotearoa

Aug 12, 2020

By Aleksandra Pawlik, Ngoni Faya, Joseph Guhlin, Megan Guidry, Tom Harrop, Dinindu Senanayake Rapid development of computational bioinformatics tools mean we can more easily push research boundaries. However, it comes at a cost. The complexity of the software chain that needs to be installed and configured to run advanced workflows results in researchers spending hours, if not days, trying to set up and debug the computational environment before they can even start to analyse their data. Complex setups also hinder reproducibility, one of the core principles of science. Fortunately, there is a solution growing in popularity – containers. Simply put, containers allow wrapping up software packages in an executable environment which can be moved from one computer to another regardless of which operating system these computers run. You can think of it as a “computer inside a computer”, contained … Read More

Data analysis skills are in hot demand – what should we be doing about it? - Genomics Aotearoa

Jul 29, 2020

By Associate Professor Mik Black, Department of Biochemistry, University of Otago The increased availability of complex biological data sets means that analysis and computation are becoming critically important skills for New Zealand’s future scientists. Because of this, we need to be doing everything we can to help our students develop these skills, to better prepare them for large-scale data analysis across a range of fields. At present, students focusing on the biological sciences in New Zealand tend not to take the more “computational” subjects – statistics, mathematics, computer and/or information science – yet the growing importance of data manipulation and analysis in genomics make these important and sought-after skills. While there are now more students coming through biology-focused programmes like genetics and biochemistry who are starting to include computational/analytic training (great to see), those numbers need to grow. What is … Read More

Better understanding bacterial blooms in New Zealand waterways - Genomics Aotearoa

Jul 13, 2020

Dr Kim Handley, University of Auckland Just how do cyanobacteria live in their natural habitat, and how do they coexist with other bacteria and microbial life forms? And what difference will knowledge on this bacteria have on maintaining New Zealand’s water quality? One of the consequences of declining water quality is an increase in cyanobacteria – these are photosynthetic bacteria that live in a wide variety of aquatic or wet habitats. While they are integral to many aquatic systems, too many cyanobacteria are not a good thing – under favourable conditions cyanobacteria can multiply and form blooms, which can have a serious impact on the environment. Some cyanobacterial species produce natural toxins, which not only affect river ecosystems and aquatic life, but also threaten human and animal health – thick mats formed by Microcoleus for instance are well known for dog … Read More

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