David W Burt

David W Burt
The University of Queensland | UQ

Professor

About

450
Publications
61,567
Reads
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20,457
Citations
Introduction
Major research interests • Comparative genomics and analysis of vertebrate genomes. • Avian genomes: genes, transcripts, conserved elements, regulatory elements, etc. • Seasonal control of gene expression. • Crop and livestock genomics. • Genomics of the Great Barrier Reef and other ecosystems. • Translation of medical genomics into clinical practice.
Additional affiliations
September 2020 - present
The University of Queensland
Position
  • Professor (Associate)
April 2017 - August 2020
The University of Queensland
Position
  • Managing Director
Description
  • Director of the UQ Genomics (2017 to date), responsible for integration and coordination of genomics research and innovation across the University of Queensland, in crops and livestock, medicine and the environment. The Director will develop and implement a cost-effective, virtual network that co-ordinates, leverages and promotes UQ’s genomics capacity and initiatives through: - • Development of novel, collaborative and cross disciplinary initiative. • Advice on national and international policy
October 2014 - June 2016
The University of Edinburgh
Position
  • Managing Director
Education
September 1999 - June 2002
The University of Manchester
Field of study
  • MSc Modules: C for Bioinformatics (Distinction), Biocomputing (Distinction), Introduction to Bioinformatics (Distinction)
September 1977 - September 1980
University of Leicester
Field of study
  • Molecular Genetics
September 1973 - June 1977
The University of Edinburgh
Field of study
  • Molecular Biology

Publications

Publications (450)
Article
The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long‐read transcriptome of an Australian‐sourced European starling (S. vulgaris vAU), and a second, North American, short‐read genome assem...
Preprint
Full-text available
The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related Northern Hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious disease, notably infectious diseases from which Austr...
Preprint
Full-text available
Background Appreciable Linkage Disequilibrium (LD) is commonly found between pairs of loci close to one another, decreasing rapidly with distance between the loci. This provides the basis studies to map Quantitative Trait Loci Regions (QTLRs), where it is custom to assume that the closest sites to a significant markers are the prime candidate to be...
Preprint
Full-text available
A species' success during the invasion of new areas hinges on an interplay between demographic processes and the outcome of localized selection. Invasive European Starlings (Sturnus vulgaris) established populations in Australia and North America in the 19th century. Here, we compare whole-genome sequences among native and independently introduced...
Article
Full-text available
A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03473-8.
Article
Full-text available
Background Dinoflagellates in the family Symbiodiniaceae are important photosynthetic symbionts in cnidarians (such as corals) and other coral reef organisms. Breakdown of the coral-dinoflagellate symbiosis due to environmental stress (i.e. coral bleaching) can lead to coral death and the potential collapse of reef ecosystems. However, evolution of...
Preprint
Full-text available
The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second North American genome (S. vulgaris vNA),...
Article
Full-text available
Avian Leukosis Virus subgroup E (ALVE) integrations are endogenous retroviral elements found in the chicken genome. The presence of ALVE has been reported to have negative impacts on multiple traits, including egg production and body weight. The recent development of rapid, inexpensive and specific ALVE detection methods has facilitated their chara...
Article
Full-text available
Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1,2,3,4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic...
Article
Full-text available
Marek’s disease (MD) represents a significant global economic and animal welfare issue. Marek’s disease virus (MDV) is a highly contagious oncogenic and highly immune-suppressive α-herpes virus, which infects chickens, causing neurological effects and tumour formation. Though partially controlled by vaccination, MD continues to have a profound impa...
Article
Full-text available
The annual photoperiod cycle provides the critical environmental cue synchronizing rhythms of life in seasonal habitats. In 1936, Bünning proposed a circadian-based coincidence timer for photoperiodic synchronization in plants. Formal studies support the universality of this so-called coincidence timer, but we lack understanding of the mechanisms i...
Preprint
Full-text available
Marek’s Disease (MD) represents a significant global economic and animal welfare issue. Marek’s Disease Virus (MDV) is a highly contagious oncogenic and highly immune-suppressive alpha-herpes virus, which infects chickens, causing neurological effects and tumour formation. Though partially controlled by vaccination, MD continues to have a profound...
Article
Full-text available
Background: Endogenous retroviruses (ERVs) are the remnants of retroviral infections which can elicit prolonged genomic and immunological stress on their host organism. In chickens, endogenous Avian Leukosis Virus subgroup E (ALVE) expression has been associated with reductions in muscle growth rate and egg production, as well as providing the pot...
Article
Full-text available
Background: Dinoflagellates are taxonomically diverse and ecologically important phytoplankton that are ubiquitously present in marine and freshwater environments. Mostly photosynthetic, dinoflagellates provide the basis of aquatic primary production; most taxa are free-living, while some can form symbiotic and parasitic associations with other or...
Preprint
Full-text available
The annual photoperiod cycle provides the critical environmental cue synchronizing rhythms of life in seasonal habitats. In 1936, Bunning proposed a circadian-basis for photoperiodic synchronization. Here, light-dark cycles entrain a circadian rhythm of photosensitivity, and the expression of summer or winter biology depends on whether light coinci...
Preprint
Full-text available
Background The human transcriptome annotation is regarded as one of the most complete of any eukaryotic species. However, limitations in sequencing technologies have biased the annotation toward multi-exonic protein coding genes. Accurate high-throughput long read transcript sequencing can now provide stronger evidence for genes that were previousl...
Preprint
Full-text available
Background: The human transcriptome annotation is regarded as one of the most complete of any eukaryotic species. However, limitations in sequencing technologies have biased the annotation toward multi-exonic protein coding genes. Accurate high-throughput long read transcript sequencing can now provide stronger evidence for rare transcripts and gen...
Preprint
Full-text available
Background: The human transcriptome annotation is regarded as one of the most complete of any eukaryotic species. However, limitations in sequencing technologies have biased the annotation toward multi-exonic protein coding genes. Accurate high-throughput long read transcript sequencing can now provide additional evidence for rare transcripts and g...
Article
Full-text available
Background: The Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research. Results: We have produced a high-quality quail genome sequence, spanning 0.93 Gb assigned to 33 chromosomes. In terms of contiguity, assembly statistics,...
Article
Full-text available
Significance In the fields of conservation biology and sustainable agriculture, the ability to cryopreserve and revive animal species is paramount to efforts to preserve genetic diversity. An innovative approach is to use sterile surrogate host animals for the transplantation of reproductive germ cells from rare/endangered animals. This technology...
Preprint
Full-text available
Symbiodiniaceae are predominantly symbiotic dinoflagellates critical to corals and other reef organisms. Symbiodinium is a basal symbiodiniacean lineage and includes symbiotic and free-living taxa. However, the molecular mechanisms underpinning these distinct lifestyles remain little known. Here, we present high-quality de novo genome assemblies fo...
Preprint
Full-text available
The human transcriptome is one of the most well-annotated of the eukaryotic species. However, limitations in technology biased discovery toward protein coding spliced genes. Accurate high throughput long read RNA sequencing now has the potential to investigate genes that were previously undetectable. Using our Transcriptome Annotation by Modular Al...
Conference Paper
Since 2005 various swans (Cygnus spp.) have been affected by highly pathogenic avain influenza (HPAI) viruses. Australian black swans (Cygnus atratus) are particularly suceptible to HPAI. Specifically, following infection with A/whooper swan/Mongolia/244/05(H5N1), 100% of black swans succumbed to disease within 2-3 days. Death was often so rapid th...
Preprint
Full-text available
The Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research. We have produced a high-quality quail genome sequence, spanning 0.93 Gb assigned to 33 chromosomes. In terms of contiguity, assembly statistics, gene content and chromos...
Article
Full-text available
Missing in Metastasis (MIM), or Metastasis Suppressor 1 (MTSS1), is a highly conserved protein, which links the plasma membrane to the actin cytoskeleton. MIM has been implicated in various cancers, however, its modes of action remain largely enigmatic. Here, we performed an extensive in silico characterisation of MIM to gain better understanding o...
Article
Full-text available
Toll-like receptors (TLRs) are key sensor molecules in vertebrates triggering initial phases of immune responses to pathogens. The avian TLR family typically consists of ten receptors, each adapted to distinct ligands. To understand the complex evolutionary history of each avian TLR, we analysed all members of the TLR family in the whole genome ass...
Article
Full-text available
Background Japanese quail (Coturnix japonica), a recently domesticated poultry species, is important not only as an agricultural product, but also as a model bird species for genetic research. However, most of the biological questions concerning genomics, phylogenetics and genetics of some important economic traits have not been answered. It is thu...
Article
Full-text available
Chicken anaemia virus (CAV) is a lymphotropic virus that causes anaemia and immunosuppression in chickens. Previously, we proposed that CAV evades host antiviral responses in vivo by disrupting T-cell signalling, but the precise cellular targets and modes of action remain elusive. In this study, we examined gene expression in Marek's disease virus-...
Article
As one of the most economically important species and a unique model organism for biological and medical research, the chicken represents the first non-mammalian amniotic species to have its genome sequenced; and so far, the chicken reference genome represents the best assembled and annotated avian genome. Since the release of the first draft genom...
Article
Full-text available
Background Misidentification of the chicken leptin gene has hampered research of leptin signaling in this species for almost two decades. Recently, the genuine leptin gene with a GC-rich (~70%) repetitive-sequence content was identified in the chicken genome but without indicating its genomic position. This suggests that such GC-rich sequences are...
Article
Full-text available
Correction: After the publication of this work [1] an error was noticed in one of the author surnames. The author name Leif Anderson should be spelt as Leif Andersson.
Article
Full-text available
Increased TSHβ expression in the pars tuberalis is thought to be an early step in the neuroendocrine mechanism transducing photoperiodic information. This study aimed to determine the relationship between long-photoperiods (LP) and diurnal TSHβ gene expression in the juvenile chicken by comparing LP-photostimulated birds with groups kept on short p...
Article
Full-text available
Background Despite the significance of chicken as a model organism, our understanding of the chicken transcriptome is limited compared to human. This issue is common to all non-human vertebrate annotations due to the difficulty in transcript identification from short read RNAseq data. While previous studies have used single molecule long read seque...
Article
Full-text available
With the recent exploration of how we may improve livestock production and meet growing demand for animal protein products using genome editing technology, we argue that exemplary genome references will be required to ensure that the proposed edits are specific and carefully evaluated for any potentially harmful side effects. We explore in this sho...
Article
Full-text available
The importance of the Gallus gallus (chicken) as a model organism and agricultural animal merits a continuation of sequence assembly improvement efforts. We present a new version of the chicken genome assembly (Gallus_gallus-5.0; GCA_000002315.3) built from combined long single molecule sequencing technology, finished BACs, and improved physical ma...
Article
Full-text available
Organizers are regions of the embryo that can both induce new fates and impart pattern on other regions. So far, surprisingly few organizers have been discovered, considering the number of patterned tissue types generated during development. This may be because their discovery has relied on transplantation and ablation experiments. Here we describe...
Article
Full-text available
Background: LTR retrotransposons contribute approximately 10 % of the mammalian genome, but it has been previously reported that there is a deficit of these elements in the chicken relative to both mammals and other birds. A novel LTR retrotransposon classification pipeline, LocaTR, was developed and subsequently utilised to re-examine the chicken...
Data
Supplementary Figures 1-12, Supplementary Tables 1-6
Data
Spontaneous beating in explants of #3-mesoderm after 48 hours of in vitro co-culture with AIP.