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Global climate change will probably exacerbate crop losses from insect pests, reducing agricultural production, and threatening food security. To predict where crop losses will occur, scientists have mainly used correlative models of species' distributions, but such models are unreliable when extrapolated to future environments. To minimize extrapolation, we developed mechanistic and hybrid models that explicitly capture range‐limiting processes, and we explored how incorporating mechanisms altered the projected impacts of climate change for an agricultural pest, the South American locust (Schistocerca cancellata). Because locusts are generalist herbivores surrounded by food, their population growth may be limited by thermal effects on digestion more than food availability. To incorporate this mechanism into a distribution model, we measured the thermal effects on the consumption and defecation of field‐captured locusts and used these data to model energy gain in current and future climates. We then created hybrid models by using outputs of the mechanistic model as predictor variables in correlative models, estimating the potential distribution of gregarious outbreaking locusts based on multiple predictor sets, modeling algorithms, and climate scenarios. Based on the mechanistic model, locusts can assimilate relatively high amounts of energy throughout temperate and tropical South America; however, correlative and hybrid modeling revealed that most tropical areas are unsuitable for locusts. When estimating current distributions, the top‐ranked model was always the one fit with mechanistic predictors (i.e., the hybrid model). When projected to future climates, top‐ranked hybrid models projected range expansions that were 23%–30% points smaller than those projected by correlative models. Therefore, a combination of the correlative and mechanistic approaches bracketed the potential outcomes of climate change and enhanced confidence where model projections agreed. Because all models projected a poleward range expansion under climate change, agriculturists should consider enhanced monitoring and the management of locusts near the southern margin of the range.

 

Previously, sugarcane mosaic virus (SCMV) was developed as a vector for transient expression of heterologous genes inZea mays(maize). Here, we show that SCMV can also be applied for virus‐induced gene silencing (VIGS) of endogenous maize genes. Comparison of sense and antisense VIGS constructs targeting maizephytoene desaturase(PDS) showed that antisense constructs resulted in a greater reduction in gene expression. In a time course of gene expression after infection with VIGS constructs targetingPDS,lesion mimic 22(Les22), andIodent japonica 1(Ij1), efficient expression silencing was observed 2, 3, and 4 weeks after infection with SCMV. However, at Week 5, expression ofLes22andIj1was no longer significantly reduced compared with control plants. The defense signaling molecule jasmonate‐isoleucine (JA‐Ile) can be inactivated by 12C‐hydroxylation and hydrolysis, and knockout of these genes leads to herbivore resistance. JA‐Ile hydroxylases and hydrolases have been investigated in Arabidopsis, rice, andNicotiana attenuata. To determine whether the maize homologs of these genes function in plant defense, we silenced expression ofZmCYP94B1(predicted JA‐Ile hydroxylase) andZmJIH1(predicted JA‐Ile hydrolase) by VIGS with SCMV, which resulted in elevated expression of two defense‐related genes,Maize Proteinase Inhibitor(MPI) andRibosome Inactivating Protein 2(RIP2). AlthoughZmCYP94B1andZmJIH1gene expression silencing increased resistance toSpodoptera frugiperda(fall armyworm),Schistocerca americana(American birdwing grasshopper), andRhopalosiphum maidis(corn leaf aphid), there was no additive effect from silencing the expression of both genes. Further work will be required to determine the more precise functions of these enzymes in regulating maize defenses.

 

Abstract Background Gastrointestinal (GIT) helminthiasis is a global problem that affects livestock health, especially in small ruminants. One of the major helminth parasites of sheep and goats, Teladorsagia circumcincta , infects the abomasum and causes production losses, reductions in weight gain, diarrhoea and, in some cases, death in young animals. Control strategies have relied heavily on the use of anthelmintic medication but, unfortunately, T. circumcincta has developed resistance, as have many helminths. Vaccination offers a sustainable and practical solution, but there is no commercially available vaccine to prevent Teladorsagiosis. The discovery of new strategies for controlling T. circumcincta , such as novel vaccine targets and drug candidates, would be greatly accelerated by the availability of better quality, chromosome-length, genome assembly because it would allow the identification of key genetic determinants of the pathophysiology of infection and host-parasite interaction. The available draft genome assembly of T. circumcincta (GCA_002352805.1) is highly fragmented and thus impedes large-scale investigations of population and functional genomics. Results We have constructed a high-quality reference genome, with chromosome-length scaffolds, by purging alternative haplotypes from the existing draft genome assembly and scaffolding the result using chromosome conformation, capture-based, in situ Hi-C technique. The improved (Hi-C) assembly resulted in six chromosome-length scaffolds with length ranging from 66.6 Mbp to 49.6 Mbp, 35% fewer sequences and reduction in size. Substantial improvements were also achieved in both the values for N50 (57.1 Mbp) and L50 (5 Mbp). A higher and comparable level of genome and proteome completeness was achieved for Hi-C assembly on BUSCO parameters. The Hi-C assembly had a greater synteny and number of orthologs with a closely related nematode, Haemonchus contortus. Conclusion This improved genomic resource is suitable as a foundation for the identification of potential targets for vaccine and drug development. 

Abstract We use data-driven physical simulations to study the three-dimensional architecture of the Aedes aegypti genome. Hi-C maps exhibit both a broad diagonal and compartmentalization with telomeres and centromeres clustering together. Physical modeling reveals that these observations correspond to an ensemble of 3D chromosomal structures that are folded over and partially condensed. Clustering of the centromeres and telomeres near the nuclear lamina appears to be a necessary condition for the formation of the observed structures. Further analysis of the mechanical properties of the genome reveals that the chromosomes of Aedes aegypti , by virtue of their atypical structural organization, are highly sensitive to the deformation of the nuclei. This last finding provides a possible physical mechanism linking mechanical cues to gene regulation. 

Abstract Background The Australian black swan ( Cygnus atratus ) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan ( Cygnus olor ), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. Results Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan. Conclusion Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril. 

Abstract We present a chromosome-length genome assembly and annotation of the Black Petaltail dragonfly (Tanypteryx hageni). This habitat specialist diverged from its sister species over 70 million years ago, and separated from the most closely related Odonata with a reference genome 150 million years ago. Using PacBio HiFi reads and Hi-C data for scaffolding we produce one of the most high-quality Odonata genomes to date. A scaffold N50 of 206.6 Mb and a single copy BUSCO score of 96.2% indicate high contiguity and completeness. 

Synapses are crucial structures that mediate signal transmission between neurons in complex neural circuits and display considerable morphological and electrophysiological heterogeneity. So far we still lack a high-throughput method to profile the molecular heterogeneity among individual synapses. In the present study, we develop a droplet-based single-cell (sc) total-RNA-sequencing platform, called Multiple-Annealing-and-Tailing-based Quantitative scRNA-seq in Droplets, for transcriptome profiling of individual neurites, primarily composed of synaptosomes. In the synaptosome transcriptome, or ‘synaptome’, profiling of both mouse and human brain samples, we detect subclusters among synaptosomes that are associated with neuronal subtypes and characterize the landscape of transcript splicing that occurs within synapses. We extend synaptome profiling to synaptopathy in an Alzheimer’s disease (AD) mouse model and discover AD-associated synaptic gene expression changes that cannot be detected by single-nucleus transcriptome profiling. Overall, our results show that this platform provides a high-throughput, single-synaptosome transcriptome profiling tool that will facilitate future discoveries in neuroscience.