Haplotype-based inference of the distribution of fitness effects

Recent genome sequencing studies with large sample sizes in humans have discovered a vast quantity of low-frequency variants, providing an important source of information to analyze how selection is acting on human genetic variation. In order to estimate the strength of natural selection acting on low-frequency variants, we have developed a likelihood-based method that uses the lengths of pairwise identity-by-state between haplotypes carrying low-frequency variants. We show that in some non-equilibrium populations (such as those that have had recent population expansions) it is possible to distinguish between positive or negative selection acting on a set of variants. With our new framework, one can infer a fixed selection intensity acting on a set of variants at a particular frequency, or a distribution of selection coefficients for standing variants and new mutations. We show an application of our method to the UK10K phased haplotype dataset of individuals.

Identification and expression of odorant binding proteins in the egg-parasitoid Trissolcus basalis (Wollaston) (Hymenoptera, Scelionidae, Telenominae)

Trissolcus basalis (Wollaston) (Hymenoptera, Scelionidae) is an egg-parasitoid of the southern green stink bug, Nezara viridula (Linneaus) (Hemiptera, Pentatomidae). Many behaviors associated with female T. basalis host-finding and acceptance are mediated by chemosensory pathways, for which olfactory, gustatory and ionotropic receptors have been previously identified. Odorant binding proteins (OBPs) are small, globular proteins, one of the functions of which is the transport of odorant ligands through the aqueous lymph of chemosensory sensilla to these receptors. We identified 18 classical OBP sequences in the T. basalis genome and transcriptomes sharing an average 26.8% pairwise identity. Gene tree analyses suggest very limited lineage-specific expansion and identify potential orthologs among other scelionids and Hymenoptera. Transcriptome mapping and qPCR comparison of expression levels in antennae and bodies of both sexes determine that at least five TbOBPs are preferentially expressed in the female antennae. These are, therefore, prime candidates for further study to determine their role in detecting host-produced semiochemicals.

Identification of Theileria spp. in sheep and goats from Jeddah, Saudi Arabia, using molecular techniques

Background Thileriosis is a tick -born disease caused by hemoprotozoan parasites which has global veterinary and economic implications. Methods Blood samples were collected from 216 sheep and 83 goats from Jeddah, Saudi Arabia, were analyzed to determine whether the animals were infected with Theileria spp. parasites. The parasites were detected using a polymerase chain reaction (PCR) targeting the gene of 18S rRNA followed by sequencing. Results According to obtained findings, Theileria spp. were detected in sheep (57.8%, 48/83) and goats (51.9%, 112/216). Phylogenetic analysis to sequence data showed that T. ovis identified in this study were found to be closely connected to an isolate from Turkey, with 84.4–99.8% pairwise identity and 52.35–99.79% coverage.

Xanthobacter dioxanivorans sp. nov., a 1,4-dioxane-degrading bacterium

A Gram-stain-negative bacterium, designated as YN2T, that is capable of degrading 1,4-dioxane, was isolated from active sludge collected from a wastewater treatment plant in Harbin, PR China. Cells of strain YN2T were aerobic, motile, pleomorphic rods, mostly twisted, and contained the water-insoluble yellow zeaxanthin dirhamnoside. Strain YN2T grew at 10–40 °C (optimum, 30 °C), pH 5.0–8.0 (pH 7.0) and with 0–1 % (w/v) NaCl (0.1 %). It also could grow chemolithoautotrophically and fix N2 when no ammonium or nitrate was supplied. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YN2T belongs to the genus Xanthobacter and shares the highest pairwise identity with Xanthobacter autotrophicus 7cT (98.6 %) and Xanthobacter flavus 301T (98.4 %). The major respiratory quinone was ubiquinone-10. Chemotaxonomic analysis revealed that the strain possesses C16 : 0, C19 : 0 cyclo ω8c and C18 : 1 ω7c as the major fatty acids. The DNA G+C content was 67.95 mol%. Based on genome sequences, the DNA–DNA hybridization estimate values between strain YN2T and X. autotrophicus 7cT, X. flavus 301T and X. tagetidis TagT2CT (the only three species of Xanthobacter with currently available genomes) were 31.70, 31.30 and 28.50 %; average nucleotide identity values were 85.23, 84.84 and 83.59 %; average amino acid identity values were 81.24, 80.23 and 73.57 %. Based on its phylogenetic, phenotypic, and physiological characteristics, strain YN2T is considered to represent a novel species of the genus Xanthobacter , for which the name Xanthobacter dioxanivorans sp. nov. is proposed. The type strain is YN2T (=CGMCC 1.19031T=JCM 34666T).

Near Chromosome-Level Genome Assembly and Annotation of Rhodotorula babjevae Strains Reveals High Intraspecific Divergence

The genus Rhodotorula includes basidiomycetous oleaginous yeast species. R. babjevae can produce compounds of biotechnological interest such as lipids, carotenoids and biosurfactants from low value substrates such as lignocellulose hydrolysate. High-quality genome assemblies are needed to develop genetic tools and to understand fungal evolution and genetics. Here, we combined short- and long-read sequencing to resolve the genomes of two R. babjevae strains, CBS 7808 (type strain) and DBVPG 8058 at chromosomal level. Both genomes have a size of 21 Mbp and a GC content of 68.2%. Allele frequency analysis indicated tetraploidy in both strains. They harbor 21 putative chromosomes with sizes ranging from 0.4 to 2.4 Mb. In both assemblies, the mitochondrial genome was recovered in a single contig, which shared 97% pairwise identity. The pairwise identity between the majority of chromosomes ranges from 82% to 87%. We found indications for strain-specific extrachromosomal endogenous DNA. 7,591 protein-coding genes and 7,607 associated transcripts were annotated in CBS 7808 and 7,481 protein-coding genes and 7,516 associated transcripts in DBVPG 8058. CBS 7808 has accumulated a higher number of tandem duplications than DBVPG 8058. We identified large translocation events between putative chromosomes and a high genetic divergence between the two strains.

Screening of Bacterial Isolates with Probiotic Potential of Tiger Nut Drink, Ogi and Palm Wine

Probiotics are live microorganisms that are very beneficial to human health when consumed in a sufficient amount. Screening and fingerprinting of isolates with probiotic potentials from indigenous food products were evaluated. Fresh palm wine, Ogi and Tiger nut drinks were bought from retailers in Obio-Akpor and Port Harcourt Local Government Area, Rivers State. These samples on getting to the lab in sterile containers were analysed using standard microbiological techniques for the enumeration and isolation of bacterial isolates. Identification of isolates relied on the biochemical and genomic techniques using standard methods. The probiotics were screened based on their ability to tolerate ethanol, bile salt, low pH, high salt concentration, lactose utilization and the production of biogenic amine. Antimicrobial susceptibility of the bacterial isolates (probiotics) was carried out using the Kirby-Bauer disc diffusion. Forty-two bacterial isolates which belonged to the genera: Lactobacillus sp, Pediococcus sp, Enterococcus sp and Streptococcus sp were identified. Genomic characterization of isolates showed that isolate NO2 has 83.4% pairwise identity with Bacillus firmus strain T1, Isolate NP2 has 86.5% pairwise identity with Bacillus cereus strain PKID1, NT8 has 80.3% pairwise identity with Bacillus cereus strain PV-G21. Results of screened probiotics showed that out of the forty-two bacterial isolates, only fifteen were non-spore producers and that they were tolerant to ethanol, low pH, NaCl and bile salt at all concentrations. Results of lactose utilization showed that only twelve out of the fifteen bacterial isolates utilized lactose. Results of biogenic amine production showed that only five out of fifteen bacterial isolates produced biogenic amine. The antibiotic susceptibility pattern of the screened bacterial isolates showed that they exhibited resistance to Pefloxacin, Gentamycin, Ampiclox, Amoxicillin, Rocephin, Ciprofloxacin; Streptomycin, Sceptrin and Erythromycin. They were highly resistant to Gentamycin and Zinnacef. Bacillus firmus strain T1, Bacillus cereus strain PKID1 and Bacillus cereus strain PV-G21 were identified as bacterial probiotics. Consumption of palm wine, Ogi and tiger nut drinks is highly recommended due to the availability of probiotics.

First report of halo blight of hop (Humulus lupulus) caused by Diaporthe humulicola in Quebec, Canada

Halo blight of hop caused by Diaporthe humulicola has recently been reported in Michigan and Connecticut (Higgins et al. 2021, Allan-Perkins et al 2020). In August 2020 growers in Quebec, Canada reported necrotic foliar lesions and desiccation of the hop strobile (cone) on Chinook and Nugget cultivars. The foliar lesions were dry concentric circles with a chlorotic halo surrounding the lesions; no pycnidia were observed on leaves or cones. Up to 100% of the infected bract tissue was dry and easily shattered, the grower estimated that more than 90% of the plants in the hopyard exhibited symptoms. Twenty-six isolates were obtained from surface-sterilized leaf and cone tissue by plating the leading edge of lesions on potato dextrose agar. Fungal isolates were hyphal tipped and were incubated at 22°C with a 12 h photoperiod. After 21-days, all cultures were white to beige with pycnidia. DNA was extracted from cultures using the MagMAX Plant DNA Isolation Kit (Applied Biosystems, Foster City, CA). DNA amplification of a representative isolate (CD6C) was performed with primers ITS1/ITS4 (White et al. 1990) for the internal transcribed spacer (ITS), CYLH3F/H3-1b (Glass and Donaldson 1995) for histone 3 (HIS), and Ef1728f/EF1-986R (Carbone and Kohn 1999) for translation elongation factor 1-α (TEF). Amplification primers were used for bidirectional Sanger sequencing, reads were assembled using Geneious Prime (Biomatters, New Zealand), and identified using NCBI BLAST. BLAST results showed that the sequences for TEF, ITS, and HIS all had 100% pairwise identity to Diaporthe sp. 1-MI (MT909101, MT909099, MT909093, OK001342, MZ934713, OK001341). Futhermore, BLAST results showed that ITS and HIS have 100% pairwise identity D. humulicola (MN152929, MN180214). The TEF sequence also had 99.7% pairwise identity to D. humulicola (MN180209). Koch’s postulates were conducted by inoculating six 3-mo-old ‘Chinook’ plants with conidia harvested from 28-day-old cultures and spraying 50 ml of inoculum (6 x 105 conidia/ml) or water to each plant. Plants were then stored in a greenhouse at 100% relative humidity at 22°C with a 14-h photo period. Lesions appeared on the adaxial side of the leaf after 21 days. D. humulicola was re-isolated from all infected leaf tissue, but not from any water inoculated plants and identified by conidial morphology using descriptions from Higgins et al. (2021). So far, Diaporthe sp. 1-MI appears to be synonymous with Diaporthe humulicola, but currently two names are being utilized (i.e. Diaporthe leaf spot and halo blight). In Higgins et al., (2021) it was proposed that the name halo blight might be more appropriate because disease symptoms are not confined to the leaves and cause significant blighting of cones. Halo blight caused by D. humulicola appears widespread in Michigan and Canada and may become an issue in other eastern North American growing regions with humid conditions.

Clinical performance characteristics of the Swift Normalase Amplicon Panel for sensitive recovery of SARS-CoV-2 genomes

Amplicon-based sequencing methods have been central in characterizing the diversity, transmission and evolution of SARS-CoV-2, but need to be rigorously assessed for clinical utility. Here, we validated the Swift Biosciences SARS-CoV-2 Swift Normalase Amplicon Panels using remnant clinical specimens. High quality genomes meeting our established library and sequence quality criteria were recovered from positive specimens with a 95% limit of detection of 40.08 SARS-CoV-2 copies/PCR reaction. Breadth of genome recovery was evaluated across a range of Ct values (11.3 - 36.7, median 21.6). Out of 428 positive samples, 406 (94.9%) generated genomes with < 10% Ns, with a mean genome coverage of 13,545X/SD 8,382X. No genomes were recovered from PCR-negative specimens (n = 30), or from specimens positive for non-SARS-CoV-2 respiratory viruses (n = 20). Compared to whole-genome shotgun metagenomic sequencing (n = 14) or Sanger sequencing for the spike gene (n = 11), pairwise identity between consensus sequences was 100% in all cases, with highly concordant allele frequencies (R2 = 0.99) between Swift and shotgun libraries. When samples from different clades were mixed at varying ratios, expected variants were detected even in 1:99 mixtures. When deployed as a clinical test, 268 tests were performed in the first 23 weeks with a median turnaround time of 11 days, ordered primarily for outbreak investigations and infection control.

Assessment of inter-laboratory differences in SARS-CoV-2 consensus genome assemblies between public health laboratories in Australia

Whole-genome sequencing of viral isolates is critical for informing transmission patterns and ongoing evolution of pathogens, especially during a pandemic. However, when genomes have low variability in the early stages of a pandemic, the impact of technical and/or sequencing errors increases. We quantitatively assessed inter-laboratory differences in consensus genome assemblies of 72 matched SARS-CoV-2-positive specimens sequenced at different laboratories in Sydney, Australia. Raw sequence data were assembled using two different bioinformatics pipelines in parallel, and resulting consensus genomes were compared to detect laboratory-specific differences. Matched genome sequences were predominantly concordant, with a median pairwise identity of 99.997%. Identified differences were predominantly driven by ambiguous site content. Ignoring these produced differences in only 2.3% (5/216) of pairwise comparisons, each differing by a single nucleotide. Matched samples were assigned the same Pango lineage in 98.2% (212/216) of pairwise comparisons, and were mostly assigned to the same phylogenetic clade. However, epidemiological inference based only on single nucleotide variant distances may lead to significant differences in the number of defined clusters if variant allele frequency thresholds for consensus genome generation differ between laboratories. These results underscore the need for a unified, best-practices approach to bioinformatics between laboratories working on a common outbreak problem.

A Pilot Study Investigating the Dynamics of Pigeon Circovirus Recombination in Domesticated Pigeons Housed in a Single Loft

Pigeon circovirus (PiCV) infects pigeon populations worldwide and has been associated with immunosuppression in younger pigeons. Recombination is a common mechanism of evolution that has previously been shown in various members of the Circoviridae family, including PiCV. In this study, three groups of pigeons acquired from separate lofts were screened for PiCV, and their genome sequence was determined. Following this, they were housed in a single loft for 22 days, during which blood and cloacal swab samples were taken. From these blood and cloacal swabs, PiCV genomes were determined with the aim to study the spread and recombination dynamics of PiCV in the birds. Genome sequences of PiCV were determined from seven pigeons (seven tested PiCV positive) before they were housed together in a loft (n = 58 sequences) and thereafter from the ten pigeons from blood and cloacal swabs (n = 120). These 178 PiCV genome sequences represent seven genotypes (98% pairwise identity genotype demarcation), and they share >88% genome-wide pairwise identity. Recombination analysis revealed 13 recombination events, and a recombination hotspot spanning the 3′ prime region, the replication-associated protein (rep) gene and the intergenic region. A cold spot in the capsid protein-coding region of the genome was also identified. The majority of the recombinant regions were identified in the rep coding region. This study provides insights into the evolutionary dynamics of PiCV in pigeons kept under closed rearing systems.