High quality genomes and population genomics

Technology that helps to analyse genomes will play a major part in the future of managing conservation and primary production species in New Zealand.

High quality genomes help researchers in the conservation and primary production sectors to better predict the biology, appearance, behaviour, disease status and economic value of an organism. This critical information can then inform breeding and management decisions for threatened native species, and will assist primary industry industry stakeholders to incorporate valuable genetic traits into breeding programmes.

Photo: Hihi by Abi Low

High Quality Genomes and Population Genomics 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.

The team are developing optimal combinations of data, methods, tools and pipelines to assemble and analyse some of the more difficult genomes to deploy to the wider New Zealand science community. This will involve evaluating the tools needed to assemble high quality genomes for population genomics analyses, focusing on models of biological, ecological, agronomical and cultural importance, including some taonga species.

This three-year project involves approximately 30 researchers across New Zealand, ranging from early career researchers to senior scientists, from institutions including Victoria University of Wellington, University of Otago and Massey University. It is co-led by Thomas Buckley (Manaaki Whenua - Landcare Research), Shannon Clarke (AgResearch), David Chagné (Plant and Food Research) and Anna Santure (University of Auckland).

Photo: Blue Cod by Stephen Wing, University of Otago

Outcomes

Effective pipelines to generate high quality genomes of strategic importance to Aotearoa New Zealand
Effective pipelines to obtain information on genome variation in a range of species with different biological features
Improved understanding of the uniqueness of Aotearoa, taking into account Māori worldviews and aspirations
Enhanced New Zealand capability in genome assembly and analysis
Effective cooperation between Genomics Aotearoa partners and stakeholders
Information rich, high quality genomes, methods and tools that will be curated and shared appropriately, and that will underpin environmental protection and primary industries
Leveraging proven methods and emerging ideas into new technologies in genome assembly
Tools to link whole genome population genomics to older genotyping datasets
Tools to manage populations in agriculture, fisheries and conservation using population genomics.