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High quality genomes

Genome sequencing, or determining the complete DNA sequence of an organism, has become hugely important for understanding the biology of entire populations of a species in relation to key aspects such as its ability to adapt to its environment or its economic value.

kaki

Photo: Kaki by Stephanie Galla

High quality genomes of New Zealand species will support conservation and selective breeding within our primary industries – the higher quality the genomes, the greater the potential impact for research in conservation and our primary industries.  The barrier is that many are large, very complex, repetitive, or highly variable which make these genomes ‘difficult’ to sequence and assemble.

New sequencing technologies have allowed us to develop and adapt informatics methods and capability, enabling high quality genomes to be produced from some of New Zealand's key primary production and conservation species. These complex target genomes are of high importance to stakeholders and Māori entities.

Outcomes

  • High quality genomes of strategic importance to Aotearoa New Zealand - plants (bilberry, Gillenia, rewarewa, ryegrass), birds (hihi, kaki), insects (stick insect, giant weta, wasps) and mammals (rat, dolphin)

  • Enhanced New Zealand capability in genome assembly and analysis

  • Effective cooperation between Genomics Aotearoa partners and Māori stakeholders, including for the genome analysis of birds (hihi, kaki), invertebrates (giant weta, peripatus) and plants (rewarewa)

  • Distribution of methods and tools for generating high quality genomes; these include bioinformatics solutions using long read sequencing, linked-reads technologies and long range Hi-C scaffolding.

See our new project, High quality genomes and population genomics

Our team

  • Associate Professor Thomas Buckley (Manaaki Whenua - Landcare Research) – Co-lead researcher
  • Dr David Chagné (Plant & Food Research) – Co-lead researcher
  • Dr Jeanne Jacobs (AgResearch)
  • Professor Murray Cox (Massey University)
  • Associate Professor Patrick Biggs (Massey University)
  • Professor Neil Gemmell (University of Otago)
  • Professor Peter Dearden (University of Otago)
  • Dr Anna Santure (University of Auckland)
  • Associate Professor Maren Wellenreuther (University of Auckland and Plant & Food Research)
  • Dr Chen Wu (Plant & Food Research)
  • Dr Ross Crowhurst (Plant & Food Research)
  • Ms Cecilia Deng (Plant & Food Research)
  • Dr Susan Thomson (Plant & Food Research)
  • Dr Elena Hilario (Plant & Food Research)
  • Mr Roy Storey (Plant & Food Research)
  • Professor Richard Newcomb (University of Auckland and Plant & Food Research)
  • Dr Gary Houliston (Manaaki Whenua - Landcare Research)
  • Dr Ann McCartney (Manaaki Whenua - Landcare Research)
  • Associate Professor Tammy Steeves (University of Canterbury)
  • Duckchul Park (Manaaki Whenua - Landcare Research)
  • Dr Jessie Prebble (Manaaki Whenua - Landcare Research)
  • Dr Florian Pichlmueller (University of Otago)
  • Dr Joseph Guhlin (University of Otago)
  • Roger Moraga (Tea Break Bioinformatics Ltd)
  • Talia Brav-Cubitt (Manaaki Whenua - Landcare Research)
  • Dr Manpreet Dhami (Manaaki Whenua - Landcare Research)

  • Dr Chris Smith (Manaaki Whenua - Landcare Research)

  • Caroline Mitchell (Manaaki Whenua - Landcare Research)

  • Dr Emily Koot (Plant & Food Research)

  • Dr Sara Montanari (Plant & Food Research)

  • Seung-Sub (Shane) Choi (University of Auckland)

Murray Cox blog, Finish what’s on your plate: How important is it to finish a genome? When and why are finished genomes useful?

More Genomics Aotearoa blogs

Publications

Genome architecture facilitates phenotypic plasticity in the honeybee (Apis mellifera)
EJ Duncan, MP Leask, PK Dearden
Molecular Biology and Evolution, 37(7), 1964-1978, 2020, https://doi.org/10.1093/molbev/msaa057

Sawfly genomes reveal evolutionary acquisitions that fostered the mega-radiation of Parasitoid and Eusocial Hymenoptera
JP Oeyen et al.
Genome Biology and Evolution, 12(7), 1099–1188, 2020, https://doi.org/10.1093/gbe/evaa106

Genetic diversity in invasive populations of Argentine stem weevil associated with adaptation to biocontrol
TWR Harrop et al.
Insects, 11(7), 441, 2020, https://doi.org/10.3390/insects11070441

Opportunities for modern genetic technologies to maintain and enhance Aotearoa New Zealand’s bioheritage
SN Inwood, GM McLaughlin, TR Buckley, MP Cox, KA Handley, TE Steeves, TJ Strabala, R McDougal, PK Dearden
New Zealand Journal of Ecology, 44(2), 2020, https://www.jstor.org/stable/26931313

Genotyping-by-sequencing of pooled drone DNA for the management of living honeybee (Apis mellifera) queens in commercial beekeeping operations in New Zealand
GEL Petersen, PF Fenessy, TC Van Stijn, S Clarke, KG Dodds, PK Dearden
Apidologie, 51, 545–556, 2020, https://doi.org/10.1007/s13592-020-00741-w

Phylogenetic determinants of toxin gene distribution in genomes of Brevibacillus laterosporus
TR Glare, A Durrant, C Berry, L Palma, MM Ormskirk, MP Cox
Genomics, 112(1), 1042-1053, 2020, doi.org/10.1016/j.ygeno.2019.06.020

Designing and implementing a genetic improvement program in commercial beekeeping operations
GEL Petersen, PF Fennessy, PR Amer, PK Dearden
Journal of Apicultural Research, 59(4), 2020, https://doi.org/10.1080/00218839.2020.1715583

The Pacific Biosciences de novo assembled genome dataset from a parthenogenetic New Zealand wild population of the longhorned tick, Haemaphysalis longicornis Neumann, 1901
FD Guerrero et al.
Data in Brief, 27, 2019, https://doi.org/10.1016/j.dib.2019.104602

Pseudo-chromosome-length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.)
G Linsmith et al.
GigaScience, 8(12), 2019, https://doi.org/10.1093/gigascience/giz138

Ancestral hymenopteran queen pheromones do not share the broad phylogenetic repressive effects of honeybee queen mandibular pheromone
 MR Lovegrove, PK Dearden, EJ Duncan
Journal of Insect Physiology, 119, 2019, https://doi.org/10.1016/j.jinsphys.2019.103968

TCR- or cytokine-activated CD8+ mucosal-associated invariant T cells are rapid polyfunctional effectors that can coordinate immune responses
R Lamichhane et al.
Cell Reports, 28(12), 3061-3076, 2019, https://doi.org/10.1016/j.celrep.2019.08.054

Invasive insects: Management methods explored
G McLaughlin, PK Dearden
Journal of Insect Science, 19(5), 17, 2019, https://doi.org/10.1093/jisesa/iez085

Comparative transcriptomic analysis of a wing-dimorphic stonefly reveals candidate wing loss genes
G McCulloch, A Oliphant, PK Dearden, AJ Veale, CW Ellen, JM Waters
Evo Devo, 10(21), 2019, https://doi.org/10.1186/s13227-019-0135-4

The torso-like gene functions to maintain the structure of the vitelline membrane in Nasonia vitripennis, implying its co-option into Drosophila axis formation
SE Taylor, J Tuffery, D Bakopoulos, S Lequeux, C Warr, TK Johnson, PK Dearden
Biology Open, 8: 2019, doi:10.1242/bio.046284

Ecological gradients drive insect wing loss and speciation: The role of the alpine treeline
G McCulloch, B Foster, L Dutoit, T Ingram, E Hay, A Veale, PK Dearden, J Waters
Molecular Ecology, 28(13), 3141-3150, 2019, https://doi.org/10.1111/mec.15114

The complete mitogenome sequence of the agricultural pest, clover root weevil: The key to its own demise?
RA Al-Jiab, J Gillum, A Alexander, DM Tompkins, CB Phillips, PK Dearden, NJ Gemmell
Mitochondrial DNA Part B, 4(1), 878-879, 2019, https://doi.org/10.1080/23802359.2018.1561218

First complete mitochondrial genome of a Gripopterygid stonefly from the sub-order Antarctoperlaria: Zelandoperla fenestrate
AJ Veale, PK Dearden, JM Waters
Mitochondrial DNA Part B, 4(1), 886-888, 2019, https://doi.org/10.1080/23802359.2018.1546130

Science at the intersection of cultures – Māori, Pākehā and mānuka
ER Morgan, NB Perry, D Chagné
NZ Journal of Crop & Horticultural Science, 47(4), 2019, https://doi.org/10.1080/01140671.2019.1691610

Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome
KA Panfilio et al.
Genome Biology, 20(1), 64, 2019, https://doi.org/10.1186/s13059-019-1660-0

Evolution of the Torso activation cassette, a pathway required for terminal patterning and moulting
J Skelly, C Pushparajan, EJ Duncan, PK Dearden
Insect Molecular Biology, 28(3), 2019, doi.org/10.1111/imb.12560

Data

Rattus rattus chromosomal assembly (New Zealand strain), https://data.csiro.au/collections/collection/CIcsiro:43176v2/DItrue

See also Data