Short Communication. Virulence of barley leaf rust in the South of Russia in 2017-2019

Aim of study: To analyze the structure of Puccinia hordei populations by virulence in southern Russia during 2017-2019. Area of study: South of Russia, the leading Russian region for barley production where barley leaf rust is an important foliar disease. Material and methods: Uredinial samples of P. hordei were collected at the production sites of winter barley in the south of Russia. Single uredinial isolates (total 95) were tested for virulence with 17 differentials with Rph resistance genes. Main results: No isolates found virulent to the host line with the Rph13 gene. There was a decrease in the number of fungal isolates virulent to the host lines with Rph5 and Rph7 genes. In 2017 and 2019, isolates containing a large number of virulence alleles (from 11 to 15) prevailed. In 2018, isolates with low (1-5) and medium (6-10) frequency of virulent alleles prevailed, as well as avirulent isolates. The values of the Nei index via diversity showed high similarity of the pathogen populations in 2017-2018 (N = 0.05) and minor differences in 2017-2019 and 2018-2019 (N = 0.13 and 0.16, respectively). The greatest frequency of virulence alleles in accordance with the Nei (Hs) index was noted for the 2018 population (Hs = 0.36). For the 2017 and 2019 populations, this indicator was average (Hs = 0.29 and 0.20, respectively). Research highlights: Analysis of genetics of the P. hopdei population is important for the strategy of varietal distribution in the region and development of rust-resistant cultivars.

Multiple Cases of Bacterial Sequence Erroneously Incorporated Into Publicly Available Chloroplast Genomes

Public sequencing databases are invaluable resources to biological researchers, but assessing data veracity as well as the curation and maintenance of such large collections of data can be challenging. Genomes of eukaryotic organelles, such as chloroplasts and other plastids, are particularly susceptible to assembly errors and misrepresentations in these databases due to their close evolutionary relationships with bacteria, which may co-occur within the same environment, as can be the case when sequencing plants. Here, based on sequence similarities with bacterial genomes, we identified several suspicious chloroplast assemblies present in the National Institutes of Health (NIH) Reference Sequence (RefSeq) collection. Investigations into these chloroplast assemblies reveal examples of erroneous integration of bacterial sequences into chloroplast ribosomal RNA (rRNA) loci, often within the rRNA genes, presumably due to the high similarity between plastid and bacterial rRNAs. The bacterial lineages identified within the examined chloroplasts as the most likely source of contamination are either known associates of plants, or co-occur in the same environmental niches as the examined plants. Modifications to the methods used to process untargeted ‘raw’ shotgun sequencing data from whole genome sequencing efforts, such as the identification and removal of bacterial reads prior to plastome assembly, could eliminate similar errors in the future.

Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres

Nanopore long-read genome sequencing is emerging as a potential approach for the study of genomes including long repetitive elements like telomeres. Here, we report extensive basecalling induced errors at telomere repeats across nanopore datasets, sequencing platforms, basecallers, and basecalling models. We found that telomeres which are represented by (TTAGGG)n and (CCCTAA)n repeats in many organisms were frequently miscalled (~40-50% of reads) as (TTAAAA)n, or as (CTTCTT)n and (CCCTGG)n repeats respectively in a strand-specific manner during nanopore sequencing. We showed that this miscalling is likely caused by the high similarity of current profiles between telomeric repeats and these repeat artefacts, leading to mis-assignment of electrical current profiles during basecalling. We further demonstrated that tuning of nanopore basecalling models, and selective application of the tuned models to telomeric reads led to improved recovery and analysis of telomeric regions, with little detected negative impact on basecalling of other genomic regions. Our study thus highlights the importance of verifying nanopore basecalls in long, repetitive, and poorly defined regions of the genome, and showcases how such artefacts in regions like telomeres can potentially be resolved by improvements in nanopore basecalling models.

Studies on plant-parasitic nematodes associated with sweet potato (Ipomoea batatas L., Lam.) in Gombe State, Nigeria

Sweet potato (Ipomoea batatas L., Lam.) is one of the most frequently eaten food crops. Its production is affected by plant-parasitic nematodes as well as biotic factors. This study was conducted to document the different plant-parasitic nematodes (PPN) that limit the gainful production of sweet potato in Gombe State. Thirty soil core samples per hectare were collected at random from sweet potato farms in the three local government areas (Nafada, Kaltungo, and Yamaltu Deba) of Gombe state. The Whitehead and Hemming method and identification keys were used for the soil extraction and genera identification of the plant-parasitic nematodes respectively. A total of 15 plant-parasitic nematodes were recovered throughout the surveyed areas among which 7 are considered major nematode pests of global importance. Irrespective of the surveyed locations, Meloidogyne spp., was found to record the highest population density and prevalence value. The frequency of occurrence in Y/Deba and Nafada LGAs shows that Meloidogyne spp., wasthe most occurring (32 %) genera. In Kaltungo LGA however, Scutellonema spp., and Rotylenchusspp., were the most occurring (17 %) genera. There was a high similarity percentage (≥ 68 %) of PPN genera where 8 genera (Scutellonema spp., Nacobbus spp., Pratylenchus spp., Meloidogyne spp., Heterodera spp., Xiphinema spp., Trichodorus spp., and Rotylenchus spp.) were found to be common amongst the surveyed locations. This is the first report of plant-parasitic nematodes associated with sweet potato in Gombe state, Nigeria. Hence, it is critical to educate farmers in the regions about their effects on the crop and how to successfully manage them.

Oribatid mites (Acari, Oribatida) from “Parco Naturale delle Alpi Marittime” (Piedmont, Italy)

Oribatid mites were investigated in six sites in the Alpi Marittime Natural Park (Prov. Cuneo, Piedmont, northern Italy) which is part of the NATURA 2000 network. The selected locations cover 4 forested (fir, ash, 2 beech forests) and 2 grassland sites (mountain meadow, xeric grassland). Altogether 173 described oribatid species belonging to 51 families were encountered, complemented by one undetermined species (Scheloribates (Topobates) cf. carpathicus), added together 174 species. Among them 11 species are new records for Italy. A comparison with other Italian alpine provinces shows high similarity of the oribatid species composition from the investigated sites with the provinces of Bolzano, Trento, Sondrio. A total of 37 species from the Marittime Alps has also been recorded in the southern part of the nearby Swiss canton Ticino. The majority of the species in the investigated sites are known as silvicolous; xerophilous species were mainly found in the xeric grassland site at lower altitude. High species similarities are observed between the forested sites, which also show high species numbers (up to 96 spp. found in the fir forest), lowest similarities are found between the open grassland sites and the forested sites, as well as between the grassland sites themselves.

Exploration of the Species-specific Dna Markers Based on the Complete Chloroplast Genome for Discriminating Curcuma Comosa Roxb. From Curcuma Latifolia Roscoe and Other Related Species

Members of the Curcuma genus are among the most commonly used rhizomatous herbs worldwide. There are two species of Curcuma referred to as “Wan Chak Motluk” in Thai, C. comosa Roxb. and C. latifolia Roscoe, and their herbal materials are often confused. C. comosa is widely used as a traditional herbal remedy for its phytoestrogenic activity, but its morphology is highly similar to that of C. latifolia, which contains a compound that causes hepatotoxicity. In this study, the complete chloroplast (cp) genomes of these species were determined for the first time using Illumina sequencing. Our results showed that their cp genomes were 162,272 bp (C. comosa) and 162,289 bp (C. latifolia) in length. A total of 133 unique genes were identified, including 87 protein-coding genes, 38 tRNA genes and 8 rRNA genes. Comparative analyses with other species of Curcuma indicated high similarity in gene content and structural organization. The analyses also reveal variable hotspots in the genomes at ndhA, trnT-trnL, and ndhC-trnV that can serve as species-specific nucleotide barcodes. Indeed, mislabeling of these two species among samples sold at market was detected using these species-specific markers, indicating that cp genomes can provide more information for better elucidating and improving discriminatory power for species authentication.

Stable Luminescent Poly(Allylaminehydrochloride)-Templated Copper Nanoclusters for Selectively Turn-Off Sensing of Deferasirox in β-Thalassemia Plasma

Highly stable and facile one-pot copper nanoclusters (Cu NCs) coated with poly(allylamine hydrochloride) (PAH) have been synthesized for selectively sensing deferasirox (DFX) in β-thalassemia plasma. DFX is an important drug used for treating iron overloading in β-thalassemia, but needs to be monitored due to certain toxicity. In this study, the PAH-Cu NCs showed highly stable fluorescence with emission wavelengths at 450 nm. The DFX specifically interacted with the copper nanocluster to turn off the fluorescence of the PAH-Cu NCs, and could be selectively quantified through the fluorescence quenching effect. The linear range of DFX in plasma analyzed by PAH-Cu NCs was 1.0–100.0 µg/mL (r = 0.985). The relative standard deviation (RSD) and relative error (RE) were lower than 6.51% and 7.57%, respectively, showing excellent reproducibility of PAH-Cu NCs for sensing DFX in plasma. This method was also successfully applied for an analysis of three clinical plasma samples from β-thalassemia patients taking DFX. The data presented high similarity with that obtained through a capillary electrophoresis method. According to the results, the PAH-Cu NCs could be used as a tool for clinically sensing DFX in human plasma for clinical surveys.

New cyanobacterium Aliterella vladivostokensis sp. nov. (Aliterellaceae, Chroococcidiopsidales), isolated from temperate monsoon climate zone (Vladivostok, Russia)

A new coccoid cyanobacterium Aliterella vladivostokensis sp. nov. was described from an urban aerophytic habitat in a temperate monsoon climate (Vladivostok, Russia) using a polyphasic approach. Phylogenetic analyses based on the 16S rRNA gene sequences confirmed that our isolate was a member of the Aliterella genus clade. Aliterella species are hardly distinguishable from each other morphologically and were described from highly contrasting natural and artificial environments with only a few records from several continents. Despite high similarity of morphometric data for A. vladivostokensis and A. antarctica cells and a compensatory base change in the D1–D1′ helix shared by these species; high percent of dissimilarity (11.6±1.3) between their 16S–23S internal transcribed spacer sequences with at least 5 autapomorphic mutations in the D1–D1′ and Box-B helices, and distinct folding patterns of the Box-B helix allowed us to erect a new species.

Zooshikella harenae sp. nov., Isolated from Pacific Oyster Crassostrea gigas, and Establishment of Zooshikella ganghwensis subsp. marina subsp. nov. and Zooshikella ganghwensis subsp. ganghwensis subsp. nov.

Here, we describe the polyphasic taxonomy of a novel isolated strain WH53T from the genus Zooshikella isolated from the sand sediment located between the lumen of the Crassostrea gigas From Germany. Phylogenetic analysis determined that the strain WH53T had a high similarity to Zooshikella ganghwensis JC2044T (99.57%) and Zooshikella marina LMG 28823T (99.36%). Strain WH53T contained ubiquinone-9 (Q-9) as the predominant menaquinone, and the major fatty acids were C16:0, C16:1ω7c, and C18:1ω7c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, amino phospholipids, and unidentified phospholipids were identified as their polar lipid composition. The DNA G+C content and genome size of strain WH53T were 40.08 mol% and 5,914,969 bp, respectively. Digital DNA–DNA hybridisation (dDDH) for strain WH53T against Z. ganghwensis JC2044T and Z. marina LMG 28823T showed low relatedness values of 26.3% and 26.1%, respectively. The extract of strain WH53T exhibited antimicrobial property. Strain WH53T represents a novel species in the genus Zooshikella. We propose the name of Zooshikella harenae sp. nov., with the type strain WH53T (= DSM 111628T = NCCB 100808T). Furthermore, the dDDH, average nucleotide identity (ANI), percentage of conserved proteins (POCP), and amino acid identity (AAI) value between Z. marina LGM 28823T and Z. ganghwensis DSM 15267T were 79.9%, 97.84%, 76.08%, and 87.01%, respectively, suggesting that both of them should be reclassified as Z. ganghwensis subsp. marina subsp. nov. and Z. ganghwensis subsp. ganghwensis DSM 15267 subsp. nov.

Complete Genome Sequence of Bacteriophage EFC1 Infecting Enterococcus Faecalis From Chicken

In response to Enterococcus faecalis infection of chicken origin, a multi host lytic phage, EFC1 was isolated and characterized the double-stranded circular DNA genome with size of 56099 bp, containing 89 predicted protein coding genes as well as 2 tRNAs involved in intron, structure, transcription, packaging, DNA replication, modification, lysis. Observation of the structure by electron microscopy and comparative phylogenetic analysis of terminase large subunit showed that the phage EFC1 belongs to a new member of Siphoviridae, which is relatively distantly related to its high similarity phages. The phage EFC1 has no relevant virulence genes and antibiotic resistance genes.