Pangenomes are collections of annotated genome sequences of multiple individuals of a species¹. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants². Here we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that are rich in gene copy number variation. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that allelic diversity at structurally complex loci may have helped crop plants to adapt to new selective regimes in agricultural ecosystems.

The quality and maturation of an oocyte not only play decisive roles in fertilization and embryo success, but also have long-term impacts on the later growth and development of the fetus. Female fertility declines with age, reflecting a decline in oocyte quantity. However, the meiosis of oocytes involves a complex and orderly regulatory process whose mechanisms have not yet been fully elucidated. This review therefore mainly focuses on the regulation mechanism of oocyte maturation, including folliculogenesis, oogenesis, and the interactions between granulosa cells and oocytes, plus in vitro technology and nuclear/cytoplasm maturation in oocytes. Additionally, we have reviewed advances made in the single-cell mRNA sequencing technology related to oocyte maturation in order to improve our understanding of the mechanism of oocyte maturation and to provide a theoretical basis for subsequent research into oocyte maturation.

The insecticidal activities of essential oils obtained from black pepper, eucalyptus, rosemary, and tea tree and their binary combinations were investigated against the green peach aphid, Myzus persicae (Aphididae: Hemiptera), under laboratory and glasshouse conditions. All the tested essential oils significantly reduced and controlled the green peach aphid population and caused higher mortality. In this study, black pepper and tea tree pure essential oils were found to be an effective insecticide, with 80% mortality when used through contact application. However, for combinations of essential oils from black pepper + tea tree (BT) and rosemary + tea tree (RT) tested as contact treatment, the mortality was 98.33%. The essential oil combinations exhibited synergistic and additive interactions for insecticidal activities. The combination of black pepper + tea tree, eucalyptus + tea tree (ET), and tea tree + rosemary showed enhanced activity, with synergy rates of 3.24, 2.65, and 2.74, respectively. Essential oils formulation was effective on the mortality of aphids. Fourier Transform Infrared Spectroscopy (FTIR) analysis showed that stability of a mixture of essential oils was not affected by store temperature (15, 25, and 35 °C) and the functional groups were not changed during storage. Based on our results, the essential oils can be used as a commercial insecticide against M. persicae.

Non-typhoidal Salmonella is a major zoonotic pathogen that plays a significant role in foodborne human salmonellosis worldwide through the consumption of contaminated foods, particularly those of animal origin. Despite a considerable reduction in human salmonellosis outbreaks in developed countries, Australia is experiencing a continuous rise of such outbreaks in humans. This review of the literature highlights the reported non-typhoidal Salmonella outbreaks in humans as well as the occurrence of the pathogen in foods from animal sources throughout Australia. Non-typhoidal Salmonella infections from food animals are more often associated with at-risk people, such as immunocompromised and aged people or children. Although several animal-sourced foods were recognised as the catalysts for salmonellosis outbreaks in Australia, egg and egg-based products remained the most implicated foods in the reported outbreaks. This review further highlights the antimicrobial resistance trends of non-typhoidal Salmonella isolates at the human–food interface, with a focus on clinically important antimicrobials in humans, by collating evidence from previous investigations in Australia. The rise in antimicrobial-resistant Salmonella, especially to antimicrobials commonly prescribed to treat human salmonellosis, has become a significant global public health concern. However, the overall prevalence of antimicrobial resistance in Australia is considerably lower than in other parts of the world, particularly in terms of critically important antimicrobials for the treatment of human salmonellosis. The present review adds to our understanding of the global epidemiology of non-typhoidal Salmonella with emphasis on the past few decades in Australia.

Non-typhoidal Salmonella serovars are recognized as zoonotic pathogens. Although human salmonellosis is frequently associated with ingestion of contaminated foods of animal origin, contact with animals may also be a significant source of Salmonella infection, especially contact with turtles, which have shown to be an important reservoir of Salmonella, specifically through their intestinal tracts. Turtles are among the most common reptiles kept as house pets that may pose a public health risk associated with Salmonella exposure, especially among infants and young children. This review discusses the literature reporting the link between turtles and Salmonella as well as turtle-associated human salmonellosis in the last ten years. In most outbreaks, a high proportion of patients are children under five years of age, which indicates that children are at the greatest risk of turtle-associated salmonellosis. Therefore, turtles should not be preferred as recommended pets for children under five years of age. Reducing turtle stress to minimise Salmonella shedding as well as providing client education handouts at the points of sale of these animals may reduce the risk of transmitting such significant pathogen to humans. Further studies are required to investigate the role of both direct contact with turtles as well as indirect contact through cross-contamination in the transmission of turtles-associated Salmonella to humans.

Estrogen-related receptor α (ERRα) is a member of the nuclear receptor superfamily controlling energy homeostasis; however, its precise role in regulating antiviral innate immunity remains to be clarified. Here, we showed that ERRα deficiency conferred resistance to viral infection both in vivo and in vitro. Mechanistically, ERRα inhibited the production of type-I interferon (IFN-I) and the expression of multiple interferon-stimulated genes (ISGs). Furthermore, we found that viral infection induced TBK1-dependent ERRα stabilization, which in turn associated with TBK1 and IRF3 to impede the formation of TBK1-IRF3, IRF3 phosphorylation, IRF3 dimerization, and the DNA binding affinity of IRF3. The effect of ERRα on IFN-I production was independent of its transcriptional activity and PCG-1α. Notably, ERRα chemical inhibitor XCT790 has broad antiviral potency. This work not only identifies ERRα as a critical negative regulator of antiviral signaling, but also provides a potential target for future antiviral therapy. As a member of the nuclear receptor superfamily involved in metabolism signaling, the precise role of ERRα in antiviral innate immunity remains to be clarified. Here, we showed that ERRα deficiency led to increased interferon production, resulting in enhanced resistance to viral infection both in vivo and in vitro. Mechanistically, viral infection induced TBK1-dependent ERRα stabilization, which in turn increased its binding to TBK1 and IRF3 to prevent the formation of a functional TBK1-IRF3 complex. The effect of ERRα on IFN-I production was independent of its transcriptional activity and PCG-1α. Notably, ERRα chemical inhibitor XCT790 has broad antiviral potency. Taken together, our results identified ERRα as an important negative downstream regulator of TBK1 in RLRs-TLRs signaling pathways and suggested a potential therapeutic target for viral infection.