A5088211647- Genetic and phenotypic traits in livestock
- Genomics and Phylogenetic Studies
- Genetic Mapping and Diversity in Plants and Animals
- Cancer-related molecular mechanisms research
- Virology and Viral Diseases
- Gut microbiota and health
- Genomics and Chromatin Dynamics
- Animal Genetics and Reproduction
- Animal Virus Infections Studies
- Antibiotic Resistance in Bacteria
- Chromosomal and Genetic Variations
- Microbial infections and disease research
- Livestock Farming and Management
- Bacterial Identification and Susceptibility Testing
- Molecular Biology Techniques and Applications
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Genetic diversity and population structure
- Pharmaceutical and Antibiotic Environmental Impacts
- Probiotics and Fermented Foods
- Antimicrobial Resistance in Staphylococcus
- Sperm and Testicular Function
- Livestock and Poultry Management
- Genomics, phytochemicals, and oxidative stress
- Scientific Computing and Data Management
- Viral Infections and Vectors
The University of Adelaide
2017-2024
Perdana University
2017-2020
Roman L. Hruska U.S. Meat Animal Research Center
2020
Universiti Putra Malaysia
2017
Malaysian Agricultural Research and Development Institute
2017
Monash University
2012-2017
The University of Melbourne
2007-2010
Cedars-Sinai Medical Center
1969
Major advances in selection progress for cattle have been made following the introduction of genomic tools over past 10-12 years. These depend upon Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety deficiencies inaccuracies. We present new cattle, ARS-UCD1.2, based on same animal as original to facilitate transfer interpretation results obtained from earlier version, but applying combination modern de novo assembly increase...
Rapid innovation in sequencing technologies and improvement assembly algorithms have enabled the creation of highly contiguous mammalian genomes. Here we report a chromosome-level water buffalo (Bubalus bubalis) genome using single-molecule chromatin conformation capture data. PacBio Sequel reads, with mean length 11.5 kb, helped to resolve repetitive elements generate sequence contiguity. All five B. bubalis sub-metacentric chromosomes were correctly scaffolded centromeres spanned. Although...
Inbred animals were historically chosen for genome analysis to circumvent assembly issues caused by haplotype variation but this resulted in a composite of the two genomes. Here we report haplotype-aware scaffolding and polishing pipeline which was used create haplotype-resolved, chromosome-level assemblies Angus (taurine) Brahman (indicine) cattle subspecies from contigs generated trio binning method. These reveal structural copy number variants that differentiate variant detection is...
Abstract Haplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. To date, these have been best created with complex protocols, such as cultured cells that contain a single-haplotype (haploid) genome, single where haplotypes separated, or co-sequencing parental genomes in trio-based approach. These approaches impractical most situations. address this issue, we present FALCON-Phase, phasing tool uses ultra-long-range Hi-C chromatin...
As classical phase II detoxification enzymes, glutathione S-transferases (GSTs) have been implicated in insecticide resistance and may evolved response to toxins the niche-defining feeding substrates of Drosophila species. We annotated GST genes 12 species with recently sequenced genomes analyzed their molecular evolution. Gene copy number variation is attributable mainly unequal crossing-over events large delta epsilon clusters. Within these gene clusters there are also slowly diverging...
Abstract More people globally depend on the water buffalo than any other domesticated species, and as most closely related species to cattle they can provide important insights into shared evolutionary basis of domestication. Here, we sequence genomes 79 across seven breeds compare patterns between breed selective sweeps with those seen for 294 representing 13 global breeds. The genomic regions under selection significantly overlap linked stature in human genetic studies, a disproportionate...
Abstract Water buffalo is a globally important species for agriculture and local economies. A de novo assembled, well-annotated reference sequence the water an prerequisite studying biology of this species, necessary to manage genetic diversity use modern breeding genomic selection techniques. However, no such genome assembly has been previously reported. There are 2 domestic buffalo, river (2n = 50) swamp 48) buffalo. Here we describe draft quality created from Illumina GA Roche 454 short...
<title>Abstract</title> The cattle genome is crucial for understanding ruminant biology, but it remains incomplete. first telomere-to-telomere haplotype-resolved X chromosome and four autosomes of are presented in a near-complete assembly that 431 Mb (16%) longer than the current reference genome. UOA_Wagyu_1 identified 738 new protein-coding genes supported characterization centromeric repeats transposable elements while revealing 49,610 structural variants. centromere natural neocentromere...
Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y smaller, have undergone substantial evolutionary changes accumulated male specific genes involved in sex determination. The pseudoautosomal region (PAR) is conserved on the pair during meiosis. structure, evolution function of mammalian chromosomes, particularly chromsome, still poorly understood because few high quality chromosome assemblies.Here we report first bovine assemblies that...
Abstract Background Water buffalo is one of the most important livestock species in world. Two types water exist: river ( Bubalus bubalis ) and swamp carabanensis ). The genome has been recently sequenced, thus a new 90 K single nucleotide polymorphism (SNP) bead chip developed. In this study, we investigated genomic population structure level inbreeding 185 153 buffaloes using runs homozygosity (ROH). Analyses were carried out jointly separately for two types. Results SNP detected about...
Large cytoplasmic ribonucleoprotein germ granule complexes are a common feature in cells. In C. elegans these called P granules and for much of the life-cycle they associate with nuclear pore rich proteins that function diverse RNA pathways. Here we report homologue eIF4E-transporter IFET-1 is required oogenesis but not spermatogenesis. We show translational repression several maternal mRNAs distal gonad functions conjunction broad-scale regulators CGH-1, CAR-1 PATR-1 to regulate cell sex...
This study investigated the antimicrobial resistance (AMR) profile of fecal Escherichia coli isolates from beef cattle (n = 150) at entry and exit an Australian feedlot. Sample plating on MacConkey agar Brilliance ESBL differentiated generic extended-spectrum β-lactamase (ESBL)-producing E. coli, respectively. Resistance profiles were determined by minimum inhibitory concentration (MIC) testing further analyzed whole-genome sequencing (WGS). At entry, prevalence to amoxicillin/clavulanic...
Abstract The publication of the first complete, haploid telomere-to-telomere (T2T) human genome revealed new insights into structure and function heretofore “invisible” parts including centromeres, tandem repeat arrays, segmental duplications. Refinement T2T processes now enables comparative analyses complete genomes across entire clades to gain a broader understanding evolution chromosome function. project involved unique ad hoc effort involving many researchers laboratories, serving as...
Abstract More people in the world depend on water buffalo for their livelihoods than any other domesticated animals, but its genetics is still not extensively explored. The 1000 Buffalo Genomes Project (1000BGP) provides genetic resources global population study and tools to breed more sustainable productive buffaloes. Here we report most contiguous swamp genome assembly (PCC_UOA_SB_1v2) with substantial resolution of telomeric centromeric repeats, ∼4-fold existing reference river exceeding...
The rise of nature-based ecotourism in the past decade has introduced unprecedented challenges managing increasing interaction between humans and animals. potential transmission antibiotic resistant microbes non-human primate populations is a concern due to their genetic similarity. Malaysia well known for hotspots wildlife diversity where primates like monkeys orangutans have become popular tourist attractions. In this study, we assessed prevalence antimicrobial Staphylococcus aureus,...
Glutathione S-Transferases (GSTs) are phase II detoxification enzymes that may have evolved in response to changes of environmental substrates. GST genes formed a multigene family and mammals, there six classes known as Alpha, Mu, Omega, Pi, Theta, Zeta. Recent studies I system specifically the cytochrome P450s provided general explanation on why from common origin such those both phylogenetically stable unstable genes. Genes participate core functions organisms development physiology...
Cis-regulatory elements (CREs) are non-coding parts of the genome that play a critical role in gene expression regulation. Enhancers, as an important example CREs, interact with genes to influence complex traits like disease, heat tolerance and growth rate. Much what is known about enhancers come from studies humans few model organisms mouse, little other mammalian species. Previous have attempted identify less studied mammals using comparative genomics but limited success. Recently, Machine...
Abstract Newcastle disease virus (NDV) has caused significant outbreaks in South-East Asia, particularly Indonesia recent years. Recently emerged genotype VII NDVs (NDV-GVII) have shifted their tropism from gastrointestinal/respiratory to a lymphotropic virus, invading lymphoid organs including spleen and bursa of Fabricius cause profound depletion. In this study, we aimed identify candidate genes biological pathways that contribute the by velogenic NDV-GVII. A transcriptomic analysis based...
Abstract Background The gaur ( Bos gaurus ) is the largest extant wild bovine species, native to South and Southeast Asia, with unique traits, listed as vulnerable by International Union for Conservation of Nature (IUCN). Results We report first reference genome identify three biological pathways including lysozyme activity, proton transmembrane transporter oxygen transport significant changes in gene copy number compared other mammals. These may reflect adaptation challenges related climate...