A5045020036- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Machine Learning in Bioinformatics
- Marine and coastal plant biology
- Microbial Community Ecology and Physiology
- Coral and Marine Ecosystems Studies
- Wheat and Barley Genetics and Pathology
- Genetic Mapping and Diversity in Plants and Animals
- Plant Disease Resistance and Genetics
- Genetics and Plant Breeding
- RNA and protein synthesis mechanisms
- Fractal and DNA sequence analysis
- Aquaculture disease management and microbiota
- Legume Nitrogen Fixing Symbiosis
- Coastal wetland ecosystem dynamics
- Invertebrate Immune Response Mechanisms
- Genetic and Environmental Crop Studies
- Biofuel production and bioconversion
- Echinoderm biology and ecology
- Plant Virus Research Studies
- Gene expression and cancer classification
- Agricultural pest management studies
- RNA modifications and cancer
- Bioinformatics and Genomic Networks
- Photosynthetic Processes and Mechanisms
Australian Genome Research Facility
2018-2022
Victorian Comprehensive Cancer Centre
2021-2022
The University of Western Australia
2015-2021
The University of Queensland
2014-2017
Agriculture and Food
2014-2017
The University of Melbourne
2007-2015
Hong Kong Polytechnic University
2002
Abstract There is an increasing awareness that as a result of structural variation, reference sequence representing genome single individual unable to capture all the gene repertoire found in species. A large number genes affected by presence/absence and copy variation suggest it may contribute phenotypic agronomic trait diversity. Here we show analysis Brassica oleracea pangenome nearly 20% are variation. Several displaying annotated with functions related major traits, including disease...
There is an increasing understanding that variation in gene presence-absence plays important role the heritability of agronomic traits; however, there have been relatively few studies on crop species. Hexaploid wheat one most food crops world and intensive breeding has reduced genetic diversity elite cultivars. Major efforts produced draft genome assemblies for cultivar Chinese Spring, but it unknown how well this represents found current modern In study we build improved reference Spring...
Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation (PAV) is also major contributor genetic diversity. In this study, we show that there an association between these two events, particularly recent Brassica napus synthetic accessions, represent source diversity, which can be captured for the improvement important crop By assembling pangenome B. napus, 38% genes display PAV behaviour,...
Summary As an increasing number of plant genome sequences become available, it is clear that gene content varies between individuals, and the challenge arises to predict a species. However, comparison often confounded by variation in assembly annotation. Differentiating true absence or annotation essential for accurate identification conserved variable genes Here, we present de novo B. napus cultivar Tapidor with improved Brassica Darmor ‐bzh . Both cultivars were annotated using same method...
Brassica oleracea is an important agricultural species encompassing many vegetable crops including cabbage, cauliflower, broccoli and kale; however, it can be susceptible to a variety of fungal diseases such as clubroot, blackleg, leaf spot downy mildew. Resistance these meditated by specific disease resistance genes analogs (RGAs) which are differently distributed across B. lines. The sequenced reference cultivar does not contain all due gene presence/absence variation between individuals,...
Tropical reef-building coral stress levels will intensify with the predicted rising atmospheric CO2 resulting in ocean temperature and acidification increase. Most studies to date have focused on destabilization of coral-dinoflagellate symbioses due warming oceans, or declining calcification acidification. In our study, pH conditions consistent end-of-century scenarios Intergovernmental Panel Climate Change (IPCC) caused major changes photosynthesis respiration, addition decreased rates...
Changes to the environment as a result of human activities can in range impacts on reef building corals that include coral bleaching (reduced concentrations algal symbionts), decreased growth and calcification, increased incidence diseases mortality. Understanding how elevated temperatures nutrient concentration affect early transcriptional changes their endosymbionts is critically important for evaluating responses reefs global happening environment. Here, we investigated expression genes...
Seagrasses are marine angiosperms that evolved from land plants but returned to the sea around 140 million years ago during early evolution of monocotyledonous plants. They successfully adapted abiotic stresses associated with growth in environment, and today, seagrasses distributed coastal waters worldwide. Seagrass meadows an important oceanic carbon sink provide food breeding grounds for diverse species. Here, we report assembly characterization Zostera muelleri genome, a southern...
Abstract Background In metagenomic studies, a process called binning is necessary to assign contigs that belong multiple species their respective phylogenetic groups. Most of the current methods binning, such as BLAST, k -mer and PhyloPythia, involve assigning sequence fragments by comparing similarity or composition with already-sequenced genomes are still far from comprehensive. We propose semi-supervised seeding method for does not depend on knowledge completed genomes. Instead, it...
Summary With the expansion of next‐generation sequencing technology and advanced bioinformatics, there has been a rapid growth genome projects. However, while this enables cost‐effective assembly draft genomes, quality these assemblies usually falls short gold standard produced using more traditional BAC by Sanger approaches. Assembly validation is often performed physical anchoring genetically mapped markers, but prone to errors resolution low, especially towards centromeric regions where...
Seagrasses are flowering plants which grow fully submerged in the marine environment. They have evolved a range of adaptations to environmental challenges including light attenuation through water, physical stress wave action and tidal currents, high concentrations salt, oxygen deficiency sediment, water-borne pollination. Although, seagrasses key stone species costal ecosystems, many questions regarding seagrass biology evolution remain unanswered. Genome sequence data for widespread...
Summary Despite being a major international crop, our understanding of the wheat genome is relatively poor due to its large size and complexity. To gain greater diversity, we have identified single nucleotide polymorphisms between 16 Australian bread varieties. Whole‐genome shotgun Illumina paired read sequence data were mapped draft assemblies chromosomes 7A, 7B 7D identify more than 4 million intervarietal SNP s. density varied three genomes, with much observed on A B genomes D genome....
Metagenomic projects using whole-genome shotgun (WGS) sequencing produces many unassembled DNA sequences and small contigs. The step of clustering these sequences, based on biological molecular features, is called binning. A reported strategy for binning that combines oligonucleotide frequency self-organising maps (SOM) shows high potential. We improve this by identifying suitable training implementing a better algorithm, defining quantitative measures assessing results. investigated the...
Seagrasses are marine angiosperms that live fully submerged in the sea. They evolved from land plant ancestors, with multiple species representing at least three independent return-to-the-sea events. This raises question of whether these followed same adaptation pathway to allow them and reproduce under hostile conditions. To compare basis between seagrass lineages, we generated genomic data for Halophila ovalis compared this recently published genomes two members Zosteraceae, as well five...
Summary Advances in sequencing technology have led to a rapid rise the genomic data available for plants, driving new insights into evolution, domestication and improvement of crops. Single nucleotide polymorphisms ( SNP s) are major component crop diversity, invaluable as genetic markers research breeding programs. High‐throughput arrays, or ‘ chips’, can generate reproducible sets informative been broadly adopted. Although there many public repositories data, which routinely uploaded, no...
Abstract Shrimp are a valuable aquaculture species globally; however, disease remains major hindrance to shrimp sustainability and growth. Mechanisms mediated by endogenous viral elements have been proposed as means which that encounter new virus start accommodate rather than succumb infection over time. However, evidence on the nature of such how they mediate accommodation is limited. More extensive genomic data Penaeid from different geographical locations should assist in exposing...
There has been an exponential growth in the number of genome sequencing projects since introduction next generation DNA technologies. Genome have increasingly involved assembly whole data which produces inferior assemblies compared to traditional Sanger genomic fragments cloned into bacterial artificial chromosomes (BACs). While shotgun using (NGS) is relatively fast and inexpensive, this method extremely challenging for highly complex genomes, where polyploidy or high repeat content...
The way we refer to a place can often differ from official titles assigned by authorities, especially when referenced in informal settings. This results collection of vernacular and alternative names shared used among the general public but hidden current gazetteers name databases. A common source these is large-scale social events occur established host sites geographical region begins take on identity event. limitation databases creates conflict efforts reconcile unofficial label with...
Reference genome assemblies are valuable, as they provide insights into gene content, genetic evolution and domestication. The higher the quality of a reference assembly more accurate downstream analysis will be. During last few years, major efforts have been made towards improving assemblies. However, erroneous incomplete still common. Complementary to DNA sequencing technologies, optical mapping has advanced genomic studies by facilitating production scaffolds assessing structural...