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Environment projects

Current projects

Environmental microbiomes

NZ river landscape

Led by Dr Kim Handley, University of Auckland

The metagenomics approach is rapidly transitioning into a mainstream tool in microbial ecology. However, there is a need for approaches to reconstruct and analyse challenging mixtures of prokaryotic (bacterial and archaeal) community sequence data along with the genomes of other understudied organisms (viruses and microeukaryotes). The Environmental Microbiomes project looks to meet this need by providing clear methods and guidelines.

High Quality Genomes and Population Genomics


Photo: Kākāpō by Andrew Digby

Led by Thomas Buckley, Manaaki Whenua - Landcare Research, Shannon Clarke, AgResearch, David Chagné, Plant & Food Research, Anna Santure, University of Auckland

This project, which spans both Environment and Primary production themes, is a merged workstream of previous Genomics Aotearoa projects - High Quality Genomes and Better Breeding Values. It aims to develop gold standard high quality assemblies, building on the progress already made in developing and benchmarking new technologies and bioinformatics tools on species unique to New Zealand. The project will also utilise these high-quality genome assemblies as a basis to generate and analyse population genomic sequence data. Knowledge of genomic variation within species will lead to better prediction of traits of economic importance, and informed prioritisation of functionally important variation in threatened species.


Led by Manpreet Dhami, Manaaki Whenua Landcare Research and Angela McGaughran, University of Waikato.

The Invasomics project aims to address key knowledge gaps in how to predict inherent invasibility by building a generalisable tool that characterises and compares invasive and non-invasive populations and species to identify the genome, microbiome, and phenome traits that define successful invaders.

Completed projects

Environmental Metagenomics

Led by Kim Handley, University of Auckland

A powerful way of studying microorganisms is by direct sampling of their collective genomes from the environment. This helps determine the role of organisms and their impact on environmental health. This project will generate a high quality database of mixed genomes from DNA collected from a stream to determine its health and genetic potential. The aim is to develop national capabilities and contribute to improved environmental monitoring approaches using genomics.

High Quality Genomes

Stick insect

Photo: Birgit Rhode

Led by David Chagné, Plant & Food Research, and Thomas Buckley, Manaaki Whenua - Landcare Research

High quality genome (sets of DNA) sequences of organisms that are important to New Zealand are needed for conservation purposes and breeding within our primary industries. Assembling high quality genomes is a challenge as many genomes are large, variable or very complex. This project developed the capability and distributed tools needed to routinely generate high quality genome assemblies. These tools will accelerate protection of our threatened species and improve knowledge for primary production species.