Summary: Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface. BLAST comparisons between multiple genomic regions, ranging from single genes to whole prokaryote chromosomes, can be generated, visualized and interactively coloured, enabling a rapid transition between analysis and the preparation of publication quality figures.Availability: Easyfig is freely available (under a GPL license) for download (for Mac OS X, Unix and Microsoft Windows) from the SourceForge web site: http://easyfig.sourceforge.net/.Contact: s.beatson@uq.edu.au

New York City (NYC) has emerged as one of the epicenters of the current SARS-CoV-2 pandemic. To identify the early transmission events underlying the rapid spread of the virus in the NYC metropolitan area, we sequenced the virus causing COVID-19 in patients seeking care at the Mount Sinai Health System. Phylogenetic analysis of 84 distinct SARS-CoV2 genomes indicates multiple, independent but isolated introductions mainly from Europe and other parts of the United States. Moreover, we find evidence for community transmission of SARS-CoV-2 as suggested by clusters of related viruses found in patients living in different neighborhoods of the city.

Cannabis sativa is widely cultivated for medicinal, food, industrial, and recreational use, but much remains unknown regarding its genetics, including the molecular determinants of cannabinoid content. Here, we describe a combined physical and genetic map derived from a cross between the drug-type strain Purple Kush and the hemp variety "Finola." The map reveals that cannabinoid biosynthesis genes are generally unlinked but that aromatic prenyltransferase (AP), which produces the substrate for THCA and CBDA synthases (THCAS and CBDAS), is tightly linked to a known marker for total cannabinoid content. We further identify the gene encoding CBCA synthase (CBCAS) and characterize its catalytic activity, providing insight into how cannabinoid diversity arises in cannabis. THCAS and CBDAS (which determine the drug vs. hemp chemotype) are contained within large (>250 kb) retrotransposon-rich regions that are highly nonhomologous between drug-and hemp-type alleles and are furthermore embedded within ∼40 Mb of minimally recombining repetitive DNA. The chromosome structures are similar to those in grains such as wheat, with recombination focused in gene-rich, repeat-depleted regions near chromosome ends. The physical and genetic map should facilitate further dissection of genetic and molecular mechanisms in this commercially and medically important plant.

Cattle production plays a significant role in terms of world food production. Nearly 82% of the world's 1.2 billion cattle can be found in developing countries. An increasing demand for meat in developing countries has seen an increase in intensification of animal industries, and a move to cross-bred animals. Heat tolerance is considered to be one of the most important adaptive aspects for cattle, and the lack of thermally-tolerant breeds is a major constraint on cattle production in many countries. There is a need to not only identify heat tolerant breeds, but also heat tolerant animals within a non-tolerant breed. Identification of heat tolerant animals is not easy under field conditions. In this study, panting score (0 to 4.5 scale where 0 = no stress and 4.5 = extreme stress) and the heat load index (HLI) [HLI(BG<25°C) = 10.66 + 0.28 × rh + 1.30 × BG - WS; and, HLI (BG> 25°C) = 8.62 + 0.38 × rh + 1.55 × BG - 0.5 × WS + e((2.4 - WS)), where BG = black globe temperature ((o)C), rh = relative humidity (decimal form), WS = wind speed (m/s) and e is the base of the natural logarithm] were used to assess the heat tolerance of 17 genotypes (12,757 steers) within 13 Australian feedlots over three summers. The cattle were assessed under natural climatic conditions in which HLI ranged from thermonuetral (HLI < 70) to extreme (HLI > 96; black globe temperature = 40.2°C, relative humidity = 64%, wind speed = 1.58 m/s). When HLI > 96 a greater number (P < 0.001) of pure bred Bos taurus and crosses of Bos taurus cattle had a panting score ≥ 2 compared to Brahman cattle, and Brahman-cross cattle. The heat tolerance of the assessed breeds was verified using panting scores and the HLI. Heat tolerance of cattle can be assessed under field conditions by using panting score and HLI.

Most strains of the widespread endosymbiotic bacterium Wolbachia pipientis are benign or behave as reproductive parasites. The pathogenic strain wMelPop is a striking exception, however: it overreplicates in its insect hosts and causes severe life shortening. The mechanism of this pathogenesis is currently unknown. We have sequenced the genomes of three variants of wMelPop and of the closely related nonpathogenic strain wMelCS. We show that the genomes of wMelCS and wMelPop appear to be identical in the nonrepeat regions of the genome and differ detectably only by the triplication of a 19-kb region that is unlikely to be associated with life shortening, demonstrating that dramatic differences in the host phenotype caused by this endosymbiont may be the result of only minor genetic changes. We also compare the genomes of the original wMelPop strain from Drosophila melanogaster and two sequential derivatives, wMelPop-CLA and wMelPop-PGYP. To develop wMelPop as a novel biocontrol agent, it was first transinfected into and passaged in mosquito cell lines for approximately 3.5 years, generating wMelPop-CLA. This cell line-passaged strain was then transinfected into Aedes aegypti mosquitoes, creating wMelPop-PGYP, which was sequenced after 4 years in the insect host. We observe a rapid burst of genomic changes during cell line passaging, but no further mutations were detected after transinfection into mosquitoes, indicating either that host preadaptation had occurred in cell lines, that cell lines are a more selectively permissive environment than animal hosts, or both. Our results provide valuable data on the rates of genomic and phenotypic change in Wolbachia associated with host shifts over short time scales.

One hundred twenty-six Black Angus yearling heifers were used in a 119-d study to assess the effect of shade allocation (0, 2.0, 3.3, or 4.7 m(2)/animal) on the performance and welfare of feedlot cattle. Shade treatments were replicated 4 times and the no-shade treatment was replicated twice. Shade was provided by 70% solar block shade cloth, attached to a 4-m-high frame with a north-south orientation. Cattle were randomly allocated to a pen (9/pen; 19.2 m(2)/animal) within treatment. Performance was assessed using DMI, G:F, ADG, HCW, dressing percentage, and rump fat depth. Climatic data (ambient and black globe temperature, solar radiation, wind speed, relative humidity, and rainfall) were recorded. From these data, the heat load index (HLI) was calculated. When the daily maximum HLI (HLI(Max)) was <86, individual panting score (0 = no panting; 4 = open mouth, tongue extended), animal location (eating, drinking, under shade), and animal posture (standing or lying) were collected at 0600, 1200, and 1800 h. When HLI(Max) was ≥ 86, these data were collected every 2 h between 0600 and 1800 h. Feed intake was recorded weekly and water intake was recorded daily on a pen basis. When HLI(Max) was ≥ 86, mean panting score (MPS: mean of animals within treatment) was greatest (1.02; P < 0.001) for unshaded cattle compared with cattle in the shade treatments, which were similar (0.82; P = 0.81). During heat waves, the MPS of unshaded cattle was greater (2.66; P < 0.001) than that for shaded cattle. The MPS of cattle in the 2.0 m(2)/animal treatment (2.43 ± 0.13) was greater (P < 0.001) than that of cattle in the 3.3 (2.11 ± 0.13) and 4.7 m(2)/animal (2.03 ± 0.13) treatments. The MPS of cattle in the 3.3 and 4.7 m(2)/animal treatments were similar (P = 0.09). Number standing was similar (P = 0.98) between unshaded and shaded at 2.0 m(2)/animal treatments with 4.75 and 4.76 animals/pen, respectively. Fewer (P < 0.0001) were standing in the 3.3 (4.19 animals/pen) and 4.7 m(2)/animal (4.06 animals/pen) treatments. Fewer (P = 0.004) cattle were under the shade at 2.0 m(2)/animal (47.1%) compared with the number under the shade at 3.3 (53.7%) and 4.7 m(2)/animal (53.6%). Unshaded cattle had the smallest (0.085 ± 0.006) G:F ratio (P = 0.01), followed by cattle shaded at 4.7 m(2)/animal (0.104 ± 0.006; P ≤ 0.001). There was no difference (P = 0.12) between the 2.0 and 3.3 m(2)/animal treatments. There were no differences (P > 0.10) for final BW, HCW, dressing percentage, and rump fat depth. Cattle with access to shade had smaller panting scores, which suggests improved welfare, and had better feed efficiency. Shade reduced the intensity of the heat load but did not fully remove the effect of heat.

bChlamydia pecorum is an important global pathogen of livestock, and it is also a significant threat to the long-term survival of Australia's koala populations. This study employed a culture-independent DNA capture approach to sequence C. pecorum genomes directly from clinical swab samples collected from koalas with chlamydial disease as well as from sheep with arthritis and conjunctivitis. Investigations into single-nucleotide polymorphisms within each of the swab samples revealed that a portion of the reads in each sample belonged to separate C. pecorum strains, suggesting that all of the clinical samples analyzed contained mixed populations of genetically distinct C. pecorum isolates. This observation was independent of the anatomical site sampled and the host species. Using the genomes of strains identified in each of these samples, whole-genome phylogenetic analysis revealed that a clade containing a bovine and a koala isolate is distinct from other clades comprised of livestock or koala C. pecorum strains. Providing additional evidence to support exposure of koalas to Australian livestock strains, two minor strains assembled from the koala swab samples clustered with livestock strains rather than koala strains. Culture-independent probebased genome capture and sequencing of clinical samples provides the strongest evidence yet to suggest that naturally occurring chlamydial infections are comprised of multiple genetically distinct strains. Chlamydia pecorum is a widespread pathogen of economically important livestock species, such as cattle and sheep. In cattle, C. pecorum is associated with sporadic bovine encephalomyelitis (SBE), which presents as a fever followed by limb stiffness and staggering (1). In sheep, C. pecorum infections commonly are linked to polyarthritis and conjunctivitis, which can spread rapidly in a flock (2, 3). While these infections are economically relevant to producers, most C. pecorum infections in ruminants appear to be asymptomatic or subclinical, characterized by a consistent presence in the gastrointestinal tract (4, 5). While questions remain over the impact of these infections in livestock globally, the best example of the pathogenic potential of this obligate intracellular bacterium actually is found in koalas, a native Australian marsupial that continues to experience localized extinctions. C. pecorum infections in koalas can cause debilitating ocular and urogenital tract diseases (6, 7). Epidemiological questions have been raised about the relationships between C. pecorum strains infecting domesticated animals and the koala, with a recent C. pecorum multilocus sequence typing (MLST) study revealing the presence of identical sequence types in samples collected from each host (8). As a follow-up to these studies, we recently sequenced the genomes of several cultured koala C. pecorum isolates, revealing a high degree of synteny and sequence identity (98.5 to 98.8%) with C. pecorum genomes from European and U.S. cattle and sheep (9).High-throughput comparative genome sequencin...

The pathogen Staphylococcus aureus colonizes and infects a variety of different sites within the human body. To adapt to these different environments, S. aureus relies on a complex and finely tuned regulatory network. While some of these networks have been well-elucidated, the functions of more than 50% of the transcriptional regulators in S. aureus remain unexplored. Here, we assess the contribution of the LacI family of metabolic regulators to staphylococcal virulence. We found that inactivating the purine biosynthesis regulator purR resulted in a strain that was acutely virulent in bloodstream infection models in mice and in ex vivo models using primary human neutrophils. Remarkably, these enhanced pathogenic traits are independent of purine biosynthesis, as the purR mutant was still highly virulent in the presence of mutations that disrupt PurR’s canonical role. Through the use of transcriptomics coupled with proteomics, we revealed that a number of virulence factors are differentially regulated in the absence of purR. Indeed, we demonstrate that PurR directly binds to the promoters of genes encoding virulence factors and to master regulators of virulence. These results guided us into further ex vivo and in vivo studies, where we discovered that S. aureus toxins drive the death of human phagocytes and mice, whereas the surface adhesin FnbA contributes to the increased bacterial burden observed in the purR mutant. Thus, S. aureus repurposes a metabolic regulator to directly control the expression of virulence factors, and by doing so, tempers its pathogenesis.