A5029229427- Genomics and Phylogenetic Studies
- Molecular Biology Techniques and Applications
- Plant and Fungal Interactions Research
- CRISPR and Genetic Engineering
- Genetic diversity and population structure
- Bacteriophages and microbial interactions
- Chromosomal and Genetic Variations
- Genetic and phenotypic traits in livestock
- Plant Virus Research Studies
- Wildlife Ecology and Conservation
- Animal Virus Infections Studies
- Indigenous Studies and Ecology
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Epigenetics and DNA Methylation
- Viral gastroenteritis research and epidemiology
- Respiratory viral infections research
- Polyomavirus and related diseases
- Viral Infections and Immunology Research
- Animal Disease Management and Epidemiology
- Archaeology and ancient environmental studies
- Forensic and Genetic Research
- Virus-based gene therapy research
- Vector-Borne Animal Diseases
- Virology and Viral Diseases
- Plant tissue culture and regeneration
Australian Museum
2018-2024
Leibniz Institute for Zoo and Wildlife Research
2015-2021
Natural History Museum Aarhus
2012-2019
University of Copenhagen
2013-2019
Natural History Museum of Denmark
2012-2013
The koala, the only extant species of marsupial family Phascolarctidae, is classified as 'vulnerable' due to habitat loss and widespread disease. We sequenced koala genome, producing a complete contiguous reference including centromeres. reveal that koala's ability detoxify eucalypt foliage may be expansions within cytochrome P450 gene family, its smell, taste moderate ingestion plant secondary metabolites in vomeronasal receptors. characterized novel lactation proteins protect young pouch...
Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly partial plastome sequences from herbarium specimens feasible, total DNA extracts and up 146 years old. use genome skimming an automated pipeline, Iterative Organelle Genome Assembly, assembles paired-end reads into a series candidate assemblies, best one which selected based on likelihood estimation. used 93...
ObjectivesSample preparation for high-throughput sequencing (HTS) includes treatment with various laboratory components, potentially carrying viral nucleic acids, the extent of which has not been thoroughly investigated. Our aim was to systematically examine a diverse repertoire components used prepare samples HTS in order identify contaminating sequences.MethodsA total 322 mainly human origin were analysed using eight protocols, applying wide variety components. Several (60% specimens)...
Significance Endogenous retroviruses (ERVs) are proviral sequences that result from host germ-line invasion by exogenous retroviruses. The majority of ERVs degraded. Using the koala retrovirus (KoRV) as a model system, we demonstrate recombination with an ancient retroelement disables KoRV, and occurs frequently early in process. Recombinant KoRVs (recKoRVs) then able to proliferate germ line. This may part explain generally degraded nature vertebrate genomes suggests degradation via is one...
Abstract Repeated retroviral infections of vertebrate germlines have made endogenous retroviruses ubiquitous features mammalian genomes. However, millions years evolution obscure many the immediate repercussions endogenisation on host health. Here we examine during its earliest stages in koala ( Phascolarctos cinereus ), a species undergoing germline invasion by retrovirus (KoRV) and affected high cancer prevalence. We characterise KoRV integration sites (IS) tumour healthy tissues from 10...
The characterization of biomolecules from ancient samples can shed otherwise unobtainable insights into the past. Despite fundamental role transcriptomal change in evolution, potential RNA remains unexploited – perhaps due to dogma associated with fragility RNA. We hypothesize that seeds offer a plausible refuge for long-term survival, during seed germination. Using RNA-Seq on cDNA synthesized nucleic acid extracts, we validate this hypothesis through demonstration partial recovery two...
Climatic and evolutionary processes are inextricably linked to conservation. Avoiding extinction in rapidly changing environments often depends upon a species' capacity adapt the face of extreme selective pressures. Here, we employed exon capture high-throughput next-generation sequencing investigate mechanisms underlying population structure adaptive genetic variation koala (Phascolarctos cinereus), an iconic Australian marsupial that represents unique conservation challenge because it is...
Molecular detection of viruses has been aided by high-throughput sequencing, permitting the genomic characterization emerging strains. In this study, we comprehensively screened 500 respiratory secretions from children with upper and/or lower tract infections for viral pathogens. The detected are described, including a divergent human parainfluenza virus type 4 GS FLX pyrosequencing 92 specimens. Complete full-genome followed, using Single Molecule, Real-Time (SMRT®) sequencing. Subsequent...
Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis KoRV patterns modern koalas demonstrate that they share sites primarily if are related, indicating process driven by vertical transmission rather than infection. However, due to methodological challenges,...
Outbreaks of zoonotic diseases in humans and livestock are not uncommon, an important component containment such emerging viral is rapid reliable diagnostics. Such methods often PCR-based hence require the availability sequence data from pathogen. Rattus norvegicus (R. norvegicus) a known reservoir for pathogens. Transmission may be direct via contact with animal, example, through exposure to its faecal matter, or indirectly mediated by arthropod vectors. Here we investigated content rat...
Abstract There are few available tools to comprehensively and economically identify uncharacterized flanking regions that not extremely labour intensive which exploit the advantages of emerging long‐read sequencing platforms. We describe SIP; a sonication‐based inverse PCR high‐throughput strategy investigate region sequences, including those mobile DNA. SIP combines unbiased fragmentation by sonication target enrichment coupling outward facing priming with technologies. demonstrate...
Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies virus-cancer associations have mainly focused on transcriptome data.In this study, we applied a diverse selection presequencing enrichment methods targeting all major viral groups, to characterize the viruses present in 197 samples from 18 sample types cancerous origin. Using high-throughput sequencing, generated 710 datasets constituting 57 billion sequencing...
Virus discovery from high throughput sequencing data often follows a bottom-up approach where taxonomic annotation takes place prior to association disease. Albeit effective in some cases, the fails detect novel pathogens and remote variants not present reference databases. We have developed species independent pipeline that utilises sequence clustering for identification of nucleotide sequences co-occur across multiple instances. applied workflow 686 libraries 252 cancer samples different...
X chromosome inactivation (XCI) mediated by differential DNA methylation between sexes is an iconic example of epigenetic regulation. Although XCI shared eutherians and marsupials, the role in marsupial remains contested. Here, we examine genome-wide signatures across fives tissues from a male female koala ( Phascolarctos cinereus ), present first whole-genome, multi-tissue ‘methylome atlas’. Using these novel data, elucidate divergent versus common features representative eutherian...
Transcriptome analysis of polar bear (Ursus maritimus) tissues identified sequences with similarity to Porcine Endogenous Retroviruses (PERV). Based on these sequences, four proviral copies and 15 solo long terminal repeats (LTRs) a newly described endogenous retrovirus were characterized from the draft genome sequence. Closely related by PCR brown arctos) black americanus) but absent in non-Ursinae species. The virus was therefore designated UrsusERV. Two distinct groups LTRs observed...
In recent years, the availability of reduced representation library (RRL) methods has catalysed an expansion genome-scale studies to characterize both model and non-model organisms. Most these rely on use restriction enzymes obtain DNA sequences at a genome-wide level. These approaches have been widely used sequence thousands markers across individuals for many organisms reasonable cost, revolutionizing field population genomics. However, there are still some limitations associated with...
Abstract Maintenance of genetic diversity within species is a key objective biodiversity conservation, and small, isolated populations are particularly vulnerable to erosion. Conservation management actions such as predator removal, captive breeding reintroduction can facilitate numerical recovery population, but often remain at risk from depleted inbreeding. We investigated dispersal, bottlenecks population structuring in the island‐dwelling Lord Howe woodhen, that came perilously close...
Abstract Genetic management is a critical component of threatened species conservation. Understanding spatial patterns genetic diversity essential for evaluating the resilience fragmented populations to accelerating anthropogenic threats. Nowhere this more relevant than on Australian continent, which experiencing an ongoing loss biodiversity that exceeds any other developed nation. Using proprietary genome complexity reduction‐based method (DArTSeq), we generated data set 3239 high quality...
This document represents a synthesis of discussions held online at the Second Koala Retrovirus Workshop in 2021. The three days were based on workshop presentations and comprise: KoRV foundational science (Day 1); applied management koalas zoo populations 2); wild 3). Each these gathers current knowledge, explores points consensus disagreement, identifies important knowledge gaps. Recommendations arise regarding research strategy, interim measures for management, support via initiation...
Abstract As the global biodiversity crisis deepens, with increasing habitat fragmentation and a changing climate, innovative options for conserving species are being explored. One such conservation action is genetic rescue: introduction of new alleles to promote population fitness. However, critically endangered where only one viable remains, introducing limited. Interspecies hybridization offers potential solution but requires resolution evolutionary relationships, sound understanding...
Virus discovery from high throughput sequencing data often follows a bottom-up approach where taxonomic annotation takes place prior to association disease. Albeit effective in some cases, the fails detect novel pathogens and remote variants not present reference databases. We have developed species independent pipeline that utilises sequence clustering for identification of nucleotide sequences co-occur across multiple instances. applied workflow 686 libraries 252 cancer samples different...