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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.

Hihi, photo by Abi Low

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).

Blue Cod

Photo: Blue Cod by Stephen Wing, University of Otago


  • 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.


  • Thomas Buckley (Manaaki Whenua - Landcare Research) - Co-lead researcher
  • Shannon Clarke (AgResearch) - Co-lead researcher
  • David Chagné (Plant and Food Research) - Co-lead researcher
  • Anna Santure (University of Auckland) - Co-lead researcher
  • Rudiger Brauning (AgResearch)
  • Chris Couldrey (LIC)
  • Susan Thomson (Plant and Food Research)
  • Elena Hilario (Plant and Food Research)
  • Amali Thrimawithana (Plant and Food Research)
  • Chen Wu (Plant and Food Research)
  • Roy Storey (Plant and Food Research)
  • Duckchul Park (Manaaki Whenua - Landcare Research)
  • Natalie Forsdick (Manaaki Whenua - Landcare Research)
  • Joseph Guhlin (University of Otago)
  • Abdul Batten (AgResearch)
  • Rachel Ashby (AgResearch)
  • Jeanne Jacobs (AgResearch)
  • Libby Liggins (Massey University)
  • Peter Dearden (University of Otago)
  • Neil Gemmell (University of Otago)
  • Alana Alexander (University of Otago)
  • Michael Lee (University of Otago)
  • Andrew Hess (AgResearch)
  • Annabel Whibley (University of Auckland)
  • Peter Ritchie (Victoria University Wellington - Te Herenga Waka)
  • Tom Oosting (Victoria University Wellington - Te Herenga Waka)
  • Tammy Steeves (University of Canterbury)
  • Maren Wellenreuther (Plant and Food Research)
  • Jessie Prebble (Manaaki Whenua - Landcare Research)
  • Manpreet Dhami (Manaaki Whenua - Landcare Research)
  • Jana Wold (University of Canterbury)
  • Vanessa Arranz-Martinez (Massey University)
  • Ali Saei (Plant and Food Research)
  • Ross Crowhurst (Plant and Food Research)
  • Levi Collier-Robinson (University of Canterbury)  
  • Lara Urban (University of Otago)
  • Seung-Sub Choi (Manaaki Whenua - Landcare Research)
  • Cecilia Deng (Plant and Food Research)



Insights into the effect of human civilization on Malus evolution and domestication
Chen et al 
Plant Biotechnology Journal

An exploration of assembly strategies and quality metrics on the accuracy of the rewarewa (Knightia excelsa) genome.                
McCartney et al.               
Molecular Ecology Resources

Polygenic basis for adaptive morphological variation in a threatened Aotearoa | New Zealand bird, the hihi (Notiomystis cincta)      
Duntsch et al.     
Proceedings of the Royal Society B: Biological Sciences

The potential for a CRISPR gene drive to eradicate or suppress globally invasive social wasps
Lester et al.         
Scientific Reports

High-quality assemblies for three invasive social wasps from the Vespula genus    
Harrop et al.       
G3: Genes, Genomes, Genetics

Building genomic infrastructure: Sequencing platinum-standard reference-quality genomes of all cetacean species.                
Morin et al.         
Marine Mammal Science

The Gillenia trifoliata genome reveals dynamics correlated with growth and reproduction in Rosaceae.  
Ireland H, Wu C, Deng C, Hilario E, Saei A, Erasmuson S, Crowhurst R, David K, Schaffer R, Chagné D.
Horticulture Research. DOI