Terrier: a deep learning repeat classifier.

Repetitive DNA sequences underpin genome architecture and evolutionary processes, yet they remain challenging to classify accurately. Terrier is a deep learning model designed to overcome these challenges by classifying repetitive DNA sequences using a publicly available, curated repeat sequence library trained under the RepeatMasker schema. Poor representation of taxa within repeat databases often limits the classification accuracy and reproducibility of current repeat annotation methods, limiting our understanding of repeat evolution and function.

Population structure, gene flow and genetic diversity of sheep blowfly (Lucilia cuprina dorsalis) in Australia.

Background: Flystrike (cutaneous myiasis) is caused by blowfly larvae of the genus Lucilia. This disease is a major obstacle to sustainable global sheep and wool production. Flystrike control relies primarily on breech modification surgery (mulesing) and insecticidal treatment; however, control is constantly compromised by the emergence and spread of insecticide-resistance.

Mitochondrial Genomes of the Blood Flukes and (Trematoda: Aporocotylidae).

Parasitic diseases can be a significant constraint on aquaculture industries, which continue to develop in response to the rise in global demand for sustainable protein sources. Blood flukes, and , are economically significant parasites of Southern bluefin tuna (Australia), Pacific bluefin tuna (Japan), and Atlantic bluefin tuna (Mediterranean) as they are responsible for blood vessel obstruction in the gills leading to branchitis and mortalities when untreated. Here, we have defined the mitochondrial genomes for these species-the first for any aporocotylids.

Chromosome-Contiguous Reference Genome for to Underpin Future Discovery Research.

Sparganosis is a neglected food- and water-borne zoonotic disease caused by members of the tapeworm genus . More than 1600 human cases have been reported in the literature, primarily in Korea and China; however, the clinical significance of sparganosis is likely underestimated. The control of this disease is challenging in endemic regions because of the complexity of its lifecycle and the involvement of many animal host species, and treatment of clinical disease in humans and animals with selected drugs (e.

Mechanisms of vaccine protection in chickens against challenge with virulent Mycoplasma synoviae.

The Vaxsafe MS vaccine is used globally to control infections with Mycoplasma synoviae (MS) in commercial poultry. It provides long-term protective immunity against airsacculitis and tracheitis caused by M. synoviae.

Chromosome-Contiguous Reference Genome from a Single Archived Specimen Elucidates Human Hookworm Biology and Host-Parasite Interactions.

Soil-transmitted helminths (STHs) are parasitic nematodes that infect humans, particularly in tropical and subtropical regions, where they contribute substantially to neglected tropical diseases (NTDs). Among them, hookworms (, and ) cause substantial morbidity, leading to anaemia, malnutrition, and developmental impairment. Despite the global impact of hookworm disease, genomic research on has lagged behind that of other hookworms, limiting comparative and molecular biological investigations.

Comparative genomic analysis of necrophagous and parasitic subspecies of Lucilia cuprina (Diptera: Calliphoridae) provides important insight into their divergent biologies.

Lucilia cuprina, a species of blowfly, consists of two recognized subspecies: L. cuprina cuprina and L. cuprina dorsalis.

Dirofilaria asiatica sp. nov. (Spirurida: Onchocercidae) - Defined using a combined morphological-molecular approach.

Parasitic nematodes of the family Onchocercidae (superfamily Filarioidea) have evolved alongside vertebrate hosts for millions of years. While morphological methods have played a central role in identifying species, many taxa remain cryptic and are challenging to differentiate, complicating diagnosis and the understanding of their epidemiology. Among the clinically relevant genera are Onchocerca and Dirofilaria, the latter being responsible for illnesses such as heartworm disease in canines and rare zoonotic infections in humans.

Systems biology of Haemonchus contortus - Advancing biotechnology for parasitic nematode control.

Parasitic nematodes represent a substantial global burden, impacting animal health, agriculture and economies worldwide. Of these worms, Haemonchus contortus - a blood-feeding nematode of ruminants - is a major pathogen and a model for molecular and applied parasitology research. This review synthesises some key advances in understanding the molecular biology, genetic diversity and host-parasite interactions of H.

Comparative analysis of amphibian genomes: An emerging resource for basic and applied research.

Amphibians are the most threatened group of vertebrates and are in dire need of conservation intervention to ensure their continued survival. They exhibit unique features including a high diversity of reproductive strategies, permeable and specialized skin capable of producing toxins and antimicrobial compounds, multiple genetic mechanisms of sex determination and in some lineages, the ability to regenerate limbs and organs. Although genomic approaches would shed light on these unique traits and aid conservation, sequencing and assembly of amphibian genomes has lagged behind other taxa due to their comparatively large genome sizes.

Inference of essential genes in and by machine learning and the implications for discovering new interventions.

Detailed explorations of the model organisms (elegant worm) and (vinegar fly) have substantially improved our knowledge and understanding of biological processes and pathways in metazoan organisms. Extensive functional genomic and multi-omic data sets have enabled the discovery and characterisation of 'essential' genes that are critical for the survival of these organisms. Recently, we showed that a machine learning (ML)-based pipeline could be utilised to predict essential genes in both and using features from DNA, RNA, protein and/or cellular data or associated information.

Chromosome-contiguous genome for the Haecon-5 strain of Haemonchus contortus reveals marked genetic variability and enables the discovery of essential gene candidates.

Millions of livestock animals worldwide are infected with the haematophagous barber's pole worm, Haemonchus contortus, the aetiological agent of haemonchosis. Despite the major significance of this parasite worldwide and its widespread resistance to current treatments, the lack of a high-quality genome for the well-defined strain of this parasite from Australia, called Haecon-5, has constrained research in a number of areas including host-parasite interactions, drug discovery and population genetics. To enable research in these areas, we report here a chromosome-contiguous genome (∼280 Mb) for Haecon-5 with high-quality models for 19,234 protein-coding genes.

Enhanced Genomic and Transcriptomic Resources for and to Underpin the Discovery of Molecular Differences between Stages and Species.

Nematodes of the genus are important pathogens of humans and animals. This study aimed to enhance the genomic and transcriptomic resources for (non-encapsulated phenotype) and (encapsulated phenotype) and to explore transcriptional profiles. First, we improved the assemblies of the genomes of (code ISS13) and (code ISS534), achieving genome sizes of 56.

Inference of Essential Genes of the Parasite via Machine Learning.

Over the years, comprehensive explorations of the model organisms (elegant worm) and (vinegar fly) have contributed substantially to our understanding of complex biological processes and pathways in multicellular organisms generally. Extensive functional genomic-phenomic, genomic, transcriptomic, and proteomic data sets have enabled the discovery and characterisation of genes that are crucial for life, called 'essential genes'. Recently, we investigated the feasibility of inferring essential genes from such data sets using advanced bioinformatics and showed that a machine learning (ML)-based workflow could be used to extract or engineer features from DNA, RNA, protein, and/or cellular data/information to underpin the reliable prediction of essential genes both within and between and .

Mitochondrial genome of the fluke pond snail, Austropeplea cf. brazieri (Gastropoda: Lymnaeidae).

Background: Lymnaeid snails of the genus Austropeplea are an important vector of the liver fluke (Fasciola hepatica), contributing to livestock production losses in Australia and New Zealand. However, the species status within Austropeplea is ambiguous due to heavy reliance on morphological analysis and a relative lack of genetic data. This study aimed to characterise the mitochondrial genome of A.

Characterisation of the tracheal transcriptional response of chickens to chronic infection with Mycoplasma synoviae.

Mycoplasma synoviae causes infectious synovitis and respiratory tract infections in chickens and is responsible for significant economic losses in the poultry industry. Effective attachment and colonisation of the trachea is critical for the persistence of the organism and progression of the disease it causes. The respiratory tract infection is usually sub-clinical, but concurrent infection with infectious bronchitis virus (IBV) is known to enhance the pathogenicity of M.

Analysis of embryos at single cell resolution identifies two eukaryotic elongation factors as intervention target candidates.

Advances in single cell technologies are allowing investigations of a wide range of biological processes and pathways in animals, such as the multicellular model organism - a free-living nematode. However, there has been limited application of such technology to related parasitic nematodes which cause major diseases of humans and animals worldwide. With no vaccines against the vast majority of parasitic nematodes and treatment failures due to drug resistance or inefficacy, new intervention targets are urgently needed, preferably informed by a deep understanding of these nematodes' cellular and molecular biology - which is presently lacking for most worms.

Transcriptomic analysis of the effects of tylosin on the protective immunity provided by the Mycoplasma gallisepticum vaccine Vaxsafe MG ts-304.

The antimicrobial tylosin is commonly used to control mycoplasma infections, sometimes in combination with vaccination. However, the efficacy of a live mycoplasma vaccine, when combined with subsequent antimicrobial treatment, against the effects of subsequent infection with a virulent strain is unknown. This study employed differential gene expression analysis to evaluate the effects of tylosin on the protection provided by the live attenuated Vaxsafe MG ts-304 vaccine, which has been shown to be safe and to provide long-term protective immunity against infection with Mycoplasma gallisepticum.

Structure-activity relationship and target investigation of 2-aryl quinolines with nematocidal activity.

Within the context of our anthelmintic discovery program, we recently identified and evaluated a quinoline derivative, called ABX464 or obefazimod, as a nematocidal candidate; synthesised a series of analogues which were assessed for activity against the free-living nematode Caenorhabditis elegans; and predicted compound-target relationships by thermal proteome profiling (TPP) and in silico docking. Here, we logically extended this work and critically evaluated the anthelmintic activity of ABX464 analogues on Haemonchus contortus (barber's pole worm) - a highly pathogenic nematode of ruminant livestock. First, we tested a series of 44 analogues on H.

Development and validation of a long-read metabarcoding platform for the detection of filarial worm pathogens of animals and humans.

Background: Filarial worms are important vector-borne pathogens of a large range of animal hosts, including humans, and are responsible for numerous debilitating neglected tropical diseases such as, lymphatic filariasis caused by Wuchereria bancrofti and Brugia spp., as well as loiasis caused by Loa loa. Moreover, some emerging or difficult-to-eliminate filarioid pathogens are zoonotic using animals like canines as reservoir hosts, for example Dirofilaria sp.

'Bingo'-a large language model- and graph neural network-based workflow for the prediction of essential genes from protein data.

The identification and characterization of essential genes are central to our understanding of the core biological functions in eukaryotic organisms, and has important implications for the treatment of diseases caused by, for example, cancers and pathogens. Given the major constraints in testing the functions of genes of many organisms in the laboratory, due to the absence of in vitro cultures and/or gene perturbation assays for most metazoan species, there has been a need to develop in silico tools for the accurate prediction or inference of essential genes to underpin systems biological investigations. Major advances in machine learning approaches provide unprecedented opportunities to overcome these limitations and accelerate the discovery of essential genes on a genome-wide scale.

Structure activity relationship and target prediction for ABX464 analogues in Caenorhabditis elegans.

Global challenges with treatment failures and/or widespread resistance in parasitic worms against commercially available anthelmintics lend impetus to the development of new anthelmintics with novel mechanism(s) of action. The free-living nematode Caenorhabditis elegans is an important model organism used for drug discovery, including the screening and structure-activity investigation of new compounds, and target deconvolution. Previously, we conducted a whole-organism phenotypic screen of the 'Pandemic Response Box' (from Medicines for Malaria Venture, MMV) and identified a hit compound, called ABX464, with activity against C.

Metabarcoding using nanopore long-read sequencing for the unbiased characterization of apicomplexan haemoparasites.

Apicomplexan haemoparasites generate significant morbidity and mortality in humans and other animals, particularly in many low-to-middle income countries. Malaria caused by Plasmodium remains responsible for some of the highest numbers of annual deaths of any human pathogen, whilst piroplasmids, such as Babesia and Theileria can have immense negative economic effects through livestock loss. Diagnosing haemoparasites via traditional methods like microscopy is challenging due to low-level and transient parasitaemia.

Mitochondrial genomic investigation reveals a clear association between species and genotypes of Lucilia and geographic origin in Australia.

Background: Lucilia cuprina and L. sericata (family Calliphoridae) are globally significant ectoparasites of sheep. Current literature suggests that only one of these blowfly subspecies, L.