Genome Alliance in Australasia (GAIA)

CRICOS code 00025B
Genome Alliance in Australasia (GAiA)
Professor David W. Burt (Director UQ Genomics Initiative)
Chair - GAiA Steering Committee
E-mail: dburt@uq.edu.au
Australian BioCommons/EMBL-ABR/ARDC Webinar, October 30, 2019
@GenomeinANZ

CRICOS code 00025BCRICOS code 00025B
PROPOSAL
Create a Community of Practice (Launched at GSA July 1, currently 150+ members) with diverse interests
in the genomes, biodiversity and evolution of the plant, animal, fungal and microbial species of Australia
and New Zealand.
AIMS OF THE GENOME ALLIANCE
• Create an infrastructure based on Comparative Genomics and Evolutionary Approaches to understand
the biodiversity and evolution of our diverse ecosystems.
• Collaborate with similar international initiatives to build a global “Network of Networks”.
• Data-mine genome-scale information to reveal new knowledge and create new opportunities on the
Evolution of Traits and applications in Conservation of Ecosystems, Health and Agriculture.
2

Sustainable Development Goals – United Nations
3

Genome Assembly
• Genome assembly.
• Comparative genomics.
• 1st, 2nd, 3rd generation sequencing technologies.

Genome Assembly Timeline

Comparative Genomics

CRICOS code 00025B
Second (Next) Generation Sequencing
7
www.illumina.com

B10K Project: Sequence Genomes of all 10,500 Bird Species
Zhang et al 2015 Nature

CRICOS code 00025B
Assoc. Prof. Parwinder Kaur
Director- DNA Zoo Australia (DZA)
Faculty of Science • UWA School of Agriculture and Environment (SAgE) • The University of Western Australia
DNA Zoo
Tracking Genomes in Space for Fast, Inexpensive,
and Accurate Chromosome-Length Scaffold
Assemblies

CRICOS code 00025B
DNA
Zoo-
Houston
HQ
Founder & Director
Erez Aiden Lieberman
Zookeeper
Olga Dudchenko
Baylor College of Medicine
Rice University
DNA Zoo Australia
Director
Parwinder Kaur
Faculty of Science
UWA School of Agriculture and Environment (SAgE)
The University of Western Australia
DNA Zoo China
DNA Zoo Data HQ
UWA & Pawsey Supercomputing
Centre Partnership
DNA Zoo Global Labs

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3D-DNA SUITE INCLUDES SOFTWARE FOR
ASSEMBLING GENOMES INTERACTIVELY…
Unpublished Parwinder Kaur
Draft assembly: Moll et al. BMC Genomics (Aug 2017) (PacBio DNA-Seq + Bionano + Dovetail)

CRICOS code 00025B https://www.dnazoo.org
Within 10 months of project announcement >100
mammalian genomes made available with annotations
at chromosome-length!

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◉ parwinder.kaur@uwa.edu.au
◉ @Dr_Parwinder
◉ @thednazoo
◉ Subscribe www.dnazoo.org
DNA Zoo Australia
A gift of genome empowerment for unique Australian biodiversity

• Missing genes or parts of genes.
• Incorrectly assembled genes.
• Biological meaningful repetitive regions mis-assembled or not all.
• Causes many months/gene to clone, correct gene structure and sequence.
• Unknowingly work with artefactual gene structure and sequence.
• Unknowingly make false conclusions about the biology.
• Etc…
Limitations of 1st and 2nd Generation Sequencing

Third-Generation Sequencing
15

Assembly Pipeline for High Quality Reference
https://vertebrategenomesproject.org

Genome/Gene Annotation
• Gene organisation.
• Protein coding genes.
• Non-coding RNAs.
• Regulatory elements.

Short Reads and the RNA-SEQ Method

Long Reads and the ISO-SEQ Method
5’Cap and normalised > full transcriptome

Realistic Transcript Complexity
Elongation Factor 1-alpha 1 (EEF1A1): ENSGAL00000015917

Genome Assembly/Annotation Solved?
21

CRICOS code 00025B
• Evolution of Genomes, Species and
Traits.
• Conservation of Species and
Ecosystems.
• Agriculture and Food Security.
• Medicine and Healthy Lives.
Comparative Genomics – Solving Problems
22

CRICOS code 00025B
Vision
• A network of capability that has the capacity
to complete projects of a scale that no
single existing group could.
• A network that would propose projects that
go beyond the self-interest of any single
research group.
• An organization that has the backing, the
skills and, increasingly over time, the track
record to successfully lobby for major
funding support from governments,
philanthropists and industry.
The NEED for a Genome Alliance
[Entity Name]
[Presentation Title] | [Date] 23
https://www.slideshare.net/KTNUK/gillian-whitworth-policy-officer-
bioeconomy-and-plastics-beis
An Alliance Inspired by Nature

PROPOSAL
and New Zealand.
24

PROPOSAL
and New Zealand.
25

PROPOSAL
and New Zealand.
26

PROPOSAL
and New Zealand.
27

Evolution of Genomes, Species and Traits
• Phylogenomics and genome evolution.
• Phylogenetics and the Tree of Life.
• Clarify and discover new species.
• Increased understanding of evolutionary processes that drive
speciation and adaptive traits.

Evolution of Genomes, Species and Traits
• Phylogenomics and genome evolution.
• Phylogenetics and the Tree of Life.
• Clarify and discover new species.
• Increased understanding of evolutionary processes that drive
speciation and adaptive traits.
• e.g. Avian Phylogenomics Consortium.

CRICOS code 00025B
Collected + sequenced genomes of
48 avian species representing nearly
all avian orders.

Avian Phylogenomics Consortium

CRICOS code 00025B
Avian Phylogenomics Consortium
• Sex chromosome evolution
• Fast Z Chromosome evolution
• Paleo viral invasions
• Hepatitis B virus invasions
• Avian ancestor genome
• Positive selection & body mass
• GC-bias gene conversion
• Genes missing in bird genomes
• Penguin genome adaptations
• ncRNAs in birds
• Manakin speciation
• Parrot genomes
• Pigeon; Duck; & Falcon genomes
Flagship Papers
• Comparative genomics
• Avian family tree
Trait evolution
• Tooth gene loss evolution in birds
• Keratin evolution - feathers, skin, claws
• Hedgehog gene family evolution
• Bones genes & evolution of flight
• Stable globin blood genes
• Blood gene hemostasis
• Olfactory receptor subgenomes
• Visual opsins & plumage co-evolution
Methodology & Data
• Phylogenomes data
• Comparative genomes data
• Avianbase: ENSEMBL resource
• Coalescent gene-species tree method
• Concatenate whole genome tree method
• Multi-processors in phylogenetics
• Ultra-large alignments
• Crocodile slow genome evolution
• MHC immune genes
• CR1 retroposons
• Ancient endogenous retroviruses
Commentaries
• Flock of genomes
• Birds of G10K
• G10K Community of Scientist
Jarvis lab lead/co-lead
Jarvis collaboration
Other
• Convergent genes & brains, humans &
song learning birds
• The singing genome
• Axon guidance genes in vocal learners
• Parrot core & shell song system
• Songbird unique genes
• Proteome convergence vocal learners
• Natural vs artificial selection
Neurogenetics
Conservation
• Genomes of endangered species
Reptiles
Genome Evolution
https://www.sciencemag.org/content/346/6215.toc

CRICOS code 00025B
• Total evidence genome-scale tree (exons, introns,
UCEs) ~30MB.
• 2 to 3 independent gains of vocal learning, predatory
and water-bird traits.
• Common ancestor of core land birds an apex
predator.
• Rapid radiation of Neoves between 66-50 MYA.
• All modern orders formed by 50 MYA.
48-Bird Phylogenetic Tree
Jarvis et al 2014 Science

• General assumption: things that are functional are maintained/improved.
• Genome sequences are changing due to random mutations.
• Consequences are that mutations which hit functional regions are:
- Eliminated, if function disrupted → no change in sequence.
- Fixed, if function improved → change in sequence.
• Most changes which gets fixed are close to neutral.
• Changes become “visual” when we compare genomes of different species.
Genome Constraints

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• Changes in nucleotide sequence over
millions of years.
• Tree topology resolved.
• Rate of nucleotide change can be estimated.
Pre-requisite Information …
Jarvis et al., Science, 2014

• Changes become “visual” when we compare genomes of different species.
• Built an EPO low-coverage alignment for 48 birds and anole Lizard.
• Mutation rate was estimated at 4-fold sites for genes having 1-to-1 orthologs between
chicken and zebra finch.
49-way Alignment and Constraint

Constrained Elements
• Used GERP++ to call selectively constrained blocks.
• Thresholding on rate of rejected substitutions and elements length.
• Classified highly conserved elements (HCEs).
• Alignment depth >= 45 species.
• Rate of rejected substitutions = 1 (i.e. no change).

Genome Constraints
38

Genome Constraints
39

Conservation of Species and Ecosystems
• Role of climate change on biodiversity.
• Clarify how human activities affect biodiversity.
• Develop plans to conserve rare and endangered species.
• Metagenomics studies of complex interacting ecosystems.

Conservation of Species and Ecosystems
• Role of climate change on biodiversity.
• Clarify how human activities affect biodiversity.
• Develop plans to conserve rare and endangered species.
• Metagenomics studies of complex interacting ecosystems.
• e.g. Great Barrier Reef.

CRICOS code 00025B
Great Barrier Reef – Economics & Resilience
Great Barrier Reef Foundation & Deloitte (2017) Peter Mumby et al (2017)

Great Barrier Reef - Metagenomics
Raúl González-Pech (UQ)

Interactions between members of the Coral Holobiont

Agriculture and Food Security
• Consumer needs: taste, health, sustainability …
• New species/varieties, tolerance/pathogen, drought, heat …
• Non-food products: biomass/biofuels, biomaterials, natural
insecticides and fungicides …

Agriculture and Food Security
• Consumer needs: taste, health, sustainability …
• New species/varieties, tolerance/pathogen, drought, heat …
• Non-food products: biomass/biofuels, biomaterials, natural
insecticides and fungicides …
• e.g. Wild Crop Relatives as a Genetic Resource.

Crop Wild Relatives – A Genetic Resource
Robert Henry (QAAFI)

CRICOS code 00025B
Collecting Hotspots for Wild Crop Relatives
SOTWP RBG2017
Given that no major domesticated food plants originated in the
country, Australia’s native flora of crop wild relatives is surprisingly
rich, including potentially valuable cousins of banana, egg-plant,
melon, mung bean, pigeon-pea, rice, sorghum, sweet-potato,
soybean and yam. Species richness of the wild relatives of major
food crops is concentrated in the northern and north-eastern
tropical regions, in the Northern Territory, Western Australia, and
Queensland.

CRICOS code 00025B
Rice (Oryza) Genomes

CRICOS code 00025B
Ancient Relatives of Domesticated Rice in Australia
Rice in Cape York Peninsula
• Inter-fertile with domesticated rice.
• Resistance to Australian pests and diseases.
• Novel health and nutrition traits.

Medicine and Healthy Lives
• Enhance control of pandemics (Avian Influenza and other infectious
diseases).
• Discover new medicines for human and non-human health (“One
Health”).

Medicine and Healthy Lives
• Enhance control of pandemics (Avian Influenza and other infectious
diseases).
• Discover new medicines for human and non-human health (“One
Health”).
• e.g. from Venomous species.

About 15% of all animals on Earth are venomous!
Glenn King (UQ)

CRICOS code 00025BCRICOS code 00025BInstitute for Molecular Bioscience | The University of Queensland
Venomous animals around for over 0.5 billion years!
Glenn King (UQ)

Venom-derived drugs — Captopril
Captopril, the world's first
blockbuster antihypertensive
drug was derived from the
venom of a deadly Brazilian pit
viper. Approved in 1981.
Glenn King (UQ)

The analgesic drug ziconotide
(Prialt®) was isolated from the venom
of a marine cone snail. Used to treat
intractable chronic pain. Approved in
2004.
Venom-derived drugs — Prialt
Glenn King (UQ)

Venom-derived drugs — Byetta
The anti-diabetic drug
exenatide (ByettaTM) was
isolated from the Gila
monster, a venomous lizard.
Approved in 2005.
Glenn King (UQ)

Venom-derived drugs — Hi1a, disulfide-rich venom peptide
PNAS (2017) vol 114: 3750-3755;
https://doi.org/10.1073/pnas.1614728114
Australian funnel-web spider Hadronyche infensa

PROPOSAL
and New Zealand.
• Aim is not to rule but to facilitate the creation of such consortia and provide support through the actions
of the working groups.
60

CRICOS code 00025B
Linkage to Other Organisations & Initiatives/Taxonomic Communities
Parwinder Kaur, University of Western Australia, WA
E: parwinder.kaur@uwa.edu.au
Donald Hobern, International Barcode of Life, Canberra, ACT
E: dhobern@gmail.com
Wildlife Collections, Herbariums & Museums
Andrew Young, National Collections, CSIRO, ACT
E: andrew.young@csiro.au
Technologies (Genomes & Transcriptomes)
Tony Papenfuss, WEHI, VIC
E: papenfuss@wehi.edu.au
Cheong Xin Chan (CX), University of Queensland, QLD
E: c.chan1@uq.edu.au
Data Management & Bioinformatics
Jeff Christiansen, QCIF, Australian BioCommons, QLD
E: jeff.christiansen@qcif.edu.au
Andrew Lonie, University of Melbourne, EMBL-ABR, Australian BioCommons, VIC
E: andrew.lonie@gmail.com
Training & Capacity Building
Mark Crowe, Training Coordinator at QCIF, QLD
E: mark.crowe@qcif.edu.au
Craig Moritz, Australian National University, ACT
E: craig.moritz@anu.edu.au
Engagement with Public, Government & Industry
Peter Dearden, University of Otago, NZ
E: peter.dearden@otago.ac.nz
Michelle Butterfield, CSIRO, ACT
E: michelle.butterfield@csiro.au
Ethical, Legal, Social Implications & Indigenous Rights
Nicole Makoviney, University of Queensland, QLD
E: director.ethics@research.uq.edu.au
Maui Hudson, University of Waikato, NZ
E: maui.hudson@waikato.ac.nz
Please contact the co-chairs to register your interest in joining a Working
Group (Include: name, affiliation, email, specific interest and further
comments).
The GAiA Working Groups on Shared Needs
[Entity Name]
61

CRICOS code 00025B
Linkage to Other Organisations & Initiatives/Taxonomic Communities
Parwinder Kaur, University of Western Australia, WA
E: parwinder.kaur@uwa.edu.au
Donald Hobern, International Barcode of Life, Canberra, ACT
E: dhobern@gmail.com
Wildlife Collections, Herbariums & Museums
Andrew Young, National Collections, CSIRO, ACT
E: andrew.young@csiro.au
Technologies (Genomes & Transcriptomes)
Tony Papenfuss, WEHI, VIC
E: papenfuss@wehi.edu.au
Cheong Xin Chan (CX), University of Queensland, QLD
E: c.chan1@uq.edu.au
Data Management & Bioinformatics
Jeff Christiansen, QCIF, Australian BioCommons, QLD
E: jeff.christiansen@qcif.edu.au
Andrew Lonie, University of Melbourne, EMBL-ABR, Australian BioCommons, VIC
E: andrew.lonie@gmail.com
Training & Capacity Building
Mark Crowe, Training Coordinator at QCIF, QLD
E: mark.crowe@qcif.edu.au
Craig Moritz, Australian National University, ACT
E: craig.moritz@anu.edu.au
Engagement with Public, Government & Industry
Peter Dearden, University of Otago, NZ
E: peter.dearden@otago.ac.nz
Michelle Butterfield, CSIRO, ACT
E: michelle.butterfield@csiro.au
Ethical, Legal, Social Implications & Indigenous Rights
Nicole Makoviney, University of Queensland, QLD
E: director.ethics@research.uq.edu.au
Maui Hudson, University of Waikato, NZ
E: maui.hudson@waikato.ac.nz
Please contact the co-chairs to register your interest in joining a Working
Group (Include: name, affiliation, email, specific interest and further
comments).
The GAiA Working Groups on Shared Needs
[Entity Name]
62

Professor David W. Burt
Director UQ Genomics
Chair - GAiA Steering Committee
E-mail: d.burt@uq.edu.au
@GenomeinANZ
Thank you

Genome Alliance in Australasia (GAIA)

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