Genome Graphs are a new international bioinformatics process used to construct pangenomes (the entire gene set of all strains of a species) to better detect gene variation.
Pangenome graphs are data structure used to represent and compare that genetic variation within a species or a population.
So why is this important to New Zealand?
Pangenomes are incredibly useful to detect and understand variants (genetic differences) in genome sequences of organisms, and in particular across microbial pathogen populations – pathogens being an organism that can produce disease.
Pangenomes have the ability to fill in the gaps of important information and provide much finer detail on the biology of each organism, which in turn offers a better understanding of pathogen origin, evolution and spread. Such genome sequencing techniques are now rapidly replacing traditional diagnostic detection tests.
It’s important we understand biological functions specifically in New Zealand populations. We need our own methods to test and analyse genetic variations to understand what pathogens are circulating, what are causing problems, what new ones are showing up, and if they are related to others globally or locally endemic.
Studying the pangenomes of microbial pathogens is essential for understanding their genetic diversity, virulence factors, antibiotic resistance mechanisms, and other traits relevant to public health and disease control.
Genomics Aotearoa is funding a Pangenome Graphs research project to come up with methods for improved variant detection in New Zealand across all organisms covering both large (human-scale) and small (microbial-scale) genomes.
Genome Graphs Post Doctoral researcher Zoe Yang, who is based at ESR in Wellington, explained improved variant detection will help to understand outbreaks and transmission of disease which has huge significance for improving infectious disease surveillance.
This will potentially improve the way Aotearoa New Zealand manages human disease, but also help with pathogen surveillance for plants and animals – for primary production and to help with conservation management.
“It’s like taking knowledge from one book to producing a series. Digital precision won’t resolve everything but better tools will give much better resolution on whatever issue is being looked at, and shed more light on how to prevent, manage or treat.”
“The Genomics Aotearoa project is starting at the beginning of this process - it’s making sure we have the capability so that we establish our own equipped and informed workforce and have the necessary resources within our research community.”
“I’m pleased to have an opportunity to build on my evolution research background, working in a team that is adapting brand new bioinformatics tools from overseas to expand evolutionary knowledge, and to answer our own research questions in more depth. Its exciting to be part of - I love that I’m working right at the beginning of something that has so much potential. It’s doing important work for human kind and I’m part of it.”
About Zoe
Zoe gained her B.A. in Agricultural Resources and Environment at the Northwest Agriculture & Forestry University, Yangling, China, then a PhD in Botany at the Institute of Botany, Chinese Academy of Science (IBCAS), Beijing, China
“My research has always been geared to maximise the health benefits of genomics through innovative use of sequencing technologies and analytical frameworks. I have worked with ‘omics’ data to understand the molecular underpinnings of health and disease, studying a wide variety of organisms and model systems such as cancer and infectious disease,” she said.
“During my PhD, the focus was molecular phylogeny and evolution. Then I worked on cancer genomics and evolution for five years before my family and I relocated from Beijing to Wellington. And since 2022 I have worked as a Senior Scientist at ESR, Porirua, overseeing both the pathogen and human genomics work for research.”
Her current work incudes developing the pangenome graph pipeline for Pan Genome construction and variant calling with a focus application on microbial pathogens, establishing pangenome graph based on system to undertake surveillance of plasmids in antibiotic-resistant pathogenic bacteria, and genomics diversity and population dynamics of Neisseria meningitidis, the causative agent for meningococcal disease. Zoe is also a Data Carpentries instructor.
Areas of expertise
- Multi omics data analysis such as whole genome, whole exome, epigenome, RNA-seq, and micro-RNA data
- Molecular phylogeny and evolution
- Cancer genomics and evolution
- Pathogen genomics.
Read more about Genome Graphs here