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Dorylaim nematodes inhabit soil and are predatory, primarily feeding on other nematodes. This predatory behaviour positions them as a potential natural solution to combat plant-parasitic nematodes. By preying on their fellow nematodes, they contribute significantly to ecological diversity. Therefore, this molecular study was conducted in 2022 at the University of Limpopo to identify the soil nematodes from South Africa using a 28S rDNA marker. The recovered nematode was extracted using the tray method. The Chelex method was used to extract DNA, and the nematode was identified as Discolaimium. Afterward, 28S rDNA was amplified using specific primers to identify the nematode. The Nblast analysis based on the small subunit ribosomal DNA showed that South African Discolaimium has a 97% similarity (MG921263) with the Chinese population of Discolaimium. Phylogenetic analysis using maximum likelihood placed this species with those molecularly identified as Discolaimium in the same clade with highly supported (100) bootstrap values. In conclusion, this species was properly identified using 28S rDNA. However, other DNA markers are recommended to understand the Discolaimium phylogeny better. [ABSTRACT FROM AUTHOR]

Three new species of the monostiliferous hoplonemertean genus Oerstedia Quatrefages, 1864, are herein described using morphological and molecular data-Oerstedia pseudoculata sp. nov., from Akkeshi Bay and Oshoro Bay, Hokkaido, Japan, and from Aniwa Bay, Sakhalin, Russia; Oerstedia rugosa sp. nov. from Sagami Bay, Misaki, Kanagawa, Japan, and Van Phong Bay, Vietnam; and Oerstedia viridifusca sp. nov. from Manazuru, Kanagawa, Japan. As to the external morphology, O. pseudoculata sp. nov. can be differentiated from O. oculata only by its bright-orange ocelli visible on both sides of the head, and a proboscis pore opening at the ventral tip of the head. These two sister species repeat each other's color patterns, a phenomenon that can be explained by Vavilov's law of homologous series. Oerstedia rugosa sp. nov. can be identified by its carmine or deep-red to brownish-red body with several longitudinal, intertwined white lines or wrinkles running from the head to the posterior body, and by 17--23 vaguely bordered white bands composed of variedly sized dots encircling the body, arranged at irregular intervals. Oerstedia viridifusca sp. nov. can be distinguished from other Oerstedia by (i) the entire body flecked with minute greenish-brown dots, especially densely on the anterior portion of the dorsal surface, but sparsely on the posterior half of the ventral surface; (ii) a collar-like portion encircling the body along the posterior cephalic furrow where the greenish-brown dots are absent; (iii) the anterolateral edges of the head lacking the greenish-brown dots; and (iv) the ocelli being brownish-orange in color. Oerstedia phoresiae (Kulikova, 1987) is reported for the first time from Japan, in addition to its previous distribution record in Russia and in South Korea. Phylogenetic analyses based on the 16S, 18S, 28S ribosomal RNA, cytochrome c oxidase subunit I, and histone H3 genes show that the new species are true congeners of the genus Oerstedia with O. pseudoculata sp. nov. and O. viridifusca sp. nov. nested within the clade Paroerstediella whereas O. rugosa sp. nov. in the clade Oerstedia. This taxonomic work emphasizes the importance of DNA barcode sequence in the taxonomy and systematics of the polymorphic congeners of the genus Oerstedia. [ABSTRACT FROM AUTHOR]

Rust fungi (Pucciniales, Basidiomycota) are a species-rich (ca. 8000 species), globally distributed order of obligate plant pathogens. Rust species are host-specific, and as a group they cause disease on many of our most economically and/or ecologically significant plants. As such, the ability to accurately and rapidly identify these fungi is of particular interest to mycologists, botanists, agricultural scientists, farmers, quarantine officials, and associated stakeholders. However, the complexities of the rust life cycle, which may include production of up to five different spore types and alternation between two unrelated host species, have made standard identifications, especially of less-documented spore states or alternate hosts, extremely difficult. The Arthur Fungarium (PUR) at Purdue University is home to one of the most comprehensive collections of rust fungi in the world. Using material vouchered in PUR supplemented with fresh collections we generated DNA barcodes of the 28S ribosomal repeat from > 3700 rust fungal specimens. Barcoded material spans 120 genera and > 1100 species, most represented by several replicate sequences. Barcodes and associated metadata are hosted in a publicly accessible, BLAST searchable database called Rust HUBB (Herbarium-based Universal Barcode Blast) and will be continuously updated. [ABSTRACT FROM AUTHOR]

The HAP clade, mainly including Helichrysum Mill, Anaphalis DC., and Pseudognaphalium Kirp., is a major component of tribe Gnaphalieae (Asteraceae). In this clade, Anaphalis represents the largest genus of Asian Gnaphalieae. The intergeneric relationships among Anaphalis and its related genera and the infrageneric taxonomy of this genus are complex and remain controversial. However, there are few studies that have focused on these issues. Herein, based on the current most comprehensive sampling of the HAP clade, especially Anaphalis, we conducted phylogenetic analyses using chloroplast (cp) genome and nuclear ribosomal DNA (nrDNA) to evaluate the relationships within HAP clade, test the monophyly of Anaphalis, and examine the infrageneric taxonomy of this genus. Meanwhile, the morphological characters were verified to determine the circumscription and infrageneric taxonomy system of Anaphalis. Additionally, the biogeographical history, diversification processes, and evolution of crucial morphological characters were estimated and inferred. Our phylogenetic analyses suggested that Anaphalis is polyphyletic because it nested with Helichrysum and Pseudognaphalium. Two and four main clades of Anaphalis were identified in cp genome and nrDNA trees, respectively. Compared with nrDNA trees, the cp genome trees were more effective for phylogenetic resolution. After comprehensively analyzing morphological and phylogenetic evidence, it was concluded that the achene surface ornamentation and leaf base showed less homoplasy and supported the two Anaphalis lineages that were inferred from cp genome. Our biogeographical analyses based on cp genome indicated that HAP clade underwent rapid diversification from late Miocene to Pliocene. The two Anaphalis lineages appeared to have originated in Africa, then spread to Western and Southern Asia, and subsequently moved into Southwestern China forming a diversity center. The dispersal patterns of the two Anaphalis lineages were different. One dispersed around the world, except in Africa and South America. The other one dispersed to Eastern and Southeastern Asia from the ancestral origin region. [ABSTRACT FROM AUTHOR]

The present study sought to propose Ganoderma guixiense sp. nov. as a new species based on phenotypic and genotypic evidence. Phylogenetic analyses were carried out based on the internal transcribed spacer (ITS), the large subunit of nuclear ribosomal RNA gene (nLSU), and the second subunit of RNA polymerase II (RPB2) sequence data. G. guixiense has been characterized by pileate basidiomata, long stipe, in addition to reddish-black zonate pileal surface. Basidiospores are broadly ellipsoid with one end tapering at maturity, and measuring 9–12.8 × 6.5–9.3 μm. Basidia are oval to subglobose. This study marks the first exploration of the biological characteristics of G. guixiense. The result indicated that the optimal medium of mycelial growth was observed on malt extract agar (MEA) and yeast extract peptone dextrose agar (YPD) while the optimal temperature was found to be 25–30 °C with pH range of 6–7. [ABSTRACT FROM AUTHOR]

A new edible wild mushroom species, described herein as Panus sribuabanensis, was collected from local markets and natural forests located in northern Thailand. This species is characterized by its medium to large-sized basidiomata, broadly ellipsoid to ellipsoid-shaped basidiospores, dimitic hyphal system, and the absence of hyphal pegs. A molecular phylogenetic analysis of combined the internal transcribed spacer (ITS) and large subunit (nrLSU) of nuclear ribosomal DNA sequences supported the monophyly of P. sribuabanensis as a distinct lineage within the genus Panus. Full description, illustrations, color photographs, and a phylogenetic tree to show the placement of P. sribuabanensis are provided. The dried mushroom showed a nutritional composition within the range of 2.58%–2.67% for fat content, 27.10%–27.98% for protein, and 43.97%–44.10% for carbohydrates. The ethanolic extracts from this mushroom exhibited a total phenolic content ranging from 0.66 to 0.74 mg GAE/g dry weight (dw). Moreover, the antioxidant activities of ethanolic extracts evaluated by the 2,2-diphenyl-1-picrylhydrazyl (0.90–1.08 mg TE/g dw) and ferric reducing antioxidant power (0.93–1.08 mg TE/g dw) assays demonstrate higher activity compared to the 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) assay (0.44–0.51 mg TE/g dw). The outcomes of this study provide significant information on the nutritional value, phenolic content, and antioxidant activity potential of this new mushroom species discovered in northern Thailand. [ABSTRACT FROM AUTHOR]

In this study, 15 Lulworthiales strains isolated from the marine tunicate Halocynthia papillosa collected in the central Tyrrhenian Sea were characterized using a polyphasic approach (morpho-physiological, molecular, and phylogenetic analyses). Based on multi-locus phylogenetic inference and morphological characters, a new genus, Rambellisea, and two new species, R. halocynthiae and R. gigliensis (Lulworthiales), were proposed. Multi-locus phylogenetic analyses using the nuclear ribosomal regions of DNA (nrITS1-nr5.8S-nrITS2, nrLSU, and nrSSU) sequence data strongly supported the new taxa. Phylogenetic inference, estimated using Maximum Likelihood and Bayesian Inference, clearly indicates that Rambellisea gen. nov. forms a distinct clade within the order Lulworthiales. Moreover, the two new species were separated into distinct subclades, solidly supported by the analyses. This is the first report of Lulworthiales species isolated from animals. [ABSTRACT FROM AUTHOR]

Simple Summary: The application of molecular methods in the studies of biological diversity revealed that there are many more species than we can recognise by their appearance. Species pairs or groups, which are difficult to recognise and are known as cryptic species, may differ in their ecological traits, place in trophic networks, and their functional role in ecosystems. It is important to separate cryptic species, particularly if we apply species composition or other diversity metrics for an assessment or monitoring of the ecosystem state or human pressures and impacts. In our study, we revealed a new cryptic species of aphid-hunting wasp that is virtually indistinguishable from a well-known one by morphology. These two species can be easily segregated using molecular characters, and presumably they differ also by nesting habitat. Upon exploring the mitotype diversity of the aphid-hunting wasp, Diodontus tristis, we revealed specimens with highly divergent mitotypes from two localities in Lithuania and nesting in clayey substrate, while the specimens with typical mitotypes were found nesting in sandy sites. The comparison of inter- and intra-specific distances and application of delimitation algorithms supported the species status of the clay-nesting populations. Using a set of DNA markers that included complete or partial sequences of six mitochondrial genes, three markers of ribosomal operon, two homeobox genes, and four other nuclear genes, we clarified the phylogenetic relationships of the new cryptic species. The endosymbiotic bacteria infestation was checked, considering the option that the divergent populations may represent clades isolated by Wolbachia infection; however, it did not demonstrate any specificity. We found only subtle morphological differences in the new clay-nesting species, D. argillicola sp. nov.; the discriminant analysis of morphometric measurements did not reliably segregate it as well. Thus, we provide the molecular characters of the cryptic species, which allow confident identification, its phylogenetic position within the genus, and an updated identification key for the D. tristis species group. [ABSTRACT FROM AUTHOR]

Solanaceae is one of the prominent plant families that provide medicine and food. For the diagnosis of its species (Physalis peruviana and Physalis angulata), the use of molecular markers with reliable and precise nuclear ribosomal DNA (nrDNA) ITS sequences has helped in the presumption of molecular evolution and phylogenetic studies of the plants. It precisely measured the variance between two samples of Physalis L. Purified fragments' sequencing using BLAST to align each sequence, evaluate its relationship with other sequences, and confirm the species of different sequences. The genetic analysis program, MEGA V.11, aided in performing multiple sequence alignment and phylogenetic analysis. The first sample showed a relation to the species Physalis peruviana voucher Smith 217 (WIS) placed in the GenBank with the serial number DQ314161.1 by 96.91%, which belonged to a strain located in the USA. The researcher registered the species as Physalis peruviana isolate AH-ZE1, with serial number OQ616506.1. However, the second sample, after contrasting it with the global species sequences, indicated a connection to the species Physalis angulata isolate LHR28I deposited in the Genome Bank with the serial number MK412130.1 at a rate of 98.02%, which belonged to a Spanish strain. The species' registration by the researcher continued as Physalis angulata isolate AHZE1, sequence number OQ616509.1. The current study results revealed the diagnosis of two species of Physalis identified for the first time in Iraq, as they incur registration in the National Center for Biotechnology Information. The recording depended on the molecular characteristics' differences in the ribosomal DNA (rDNA) region, knowing the evolutionary relationship between the Physalis species and comparing them to the sequences found in the GenBank for previously defined types. The results also showed that the ITS2 region provided success ability. Therefore, using other DNA barcodes as auxiliary factors to distinguish between Physalis species would be beneficial. [ABSTRACT FROM AUTHOR]

Helictotrichon sempervirens (blue oatgrass) is a perennial grass widely grown for ornamental use in Canada. Rusted blue oatgrass plants with diseased leaves covered with uredinia were collected from two locations at metropolitan Vancouver, British Columbia (BC), in summer 2022. The rust fungus was identified as Puccinia gibberosa (= P. coronata var. gibberosa) based on combined results of morphological characteristics and molecular analyses. The internal transcribed spacer two (ITS2) and partial large subunit ribosomal DNA were amplified and sequenced. The sequence obtained for the rust fungus showed 99.9% identity with the previously reported P. coronata var. gibberosa from USA. This is the first report of rust caused by P. gibberosa on blue oatgrass in Canada. Evidence from phylogenetic analyses supports the recognition of this rust at the species level. A revised description for P. gibberosa is provided, including synonyms, host range and distribution across the globe, and incorporating comprehensive molecular and morphological results for several North American and European specimens. In addition, a lectotype and an epitype are designated here for the rust species. [ABSTRACT FROM AUTHOR]

In the present study, the mycobiomes of two soils with different ecological conditions located in Benin (West Africa) were investigated by environmental sequencing (Illumina MiSeq) of the ITS2-region of ribosomal DNA to gain information about the influence of pedological stratification on fungal diversity. For each soil depth and horizon, fungal diversity and community composition were analyzed as well as the potential impact of site characteristics, like vegetation, on these traits. The retrieved sequences revealed in all their replicates high similarities between fungal communities of samples from the same site and soil horizon, but differed within one site in their horizons. It was possible to assign a saprotrophic, symbiotrophic, or parasitic lifestyle to 24% of the recorded fungal mOTUs. Plant parasites were found in all samples in similar proportions. The presence of ectomycorrhizal fungi in one site could be linked to the presence of ectomycorrhizal trees. Overall, it was observed that fungal diversity decreased with increasing depth if only one horizon was present, whereas a deeper horizon present at one site contained communities with a distinct composition regarding the taxonomical affiliations and lifestyles of the fungi found compared to the upper layer. Hence, soil horizonation seems to drive differences in the composition of fungal communities, and should be regarded with more attention when analyzing soil mycobiomes. [ABSTRACT FROM AUTHOR]

Circadian-paced biological processes are key to physiology and required for metabolic, immunologic, and cardiovascular homeostasis. Core circadian clock components are transcription factors whose half-life is precisely regulated, thereby controlling the intrinsic cellular circadian clock. Genetic disruption of molecular clock components generally leads to marked pathological events phenotypically affecting behavior and multiple aspects of physiology. Using a transcriptional signature similarity approach, we identified anti-cancer protein synthesis inhibitors as potent modulators of the cardiomyocyte molecular clock. Eukaryotic protein translation inhibitors, ranging from translation initiation (rocaglates, 4-EGI1, etc.) to ribosomal elongation inhibitors (homoharringtonine, puromycin, etc.), were found to potently ablate protein abundance of REV-ERBα, a repressive nuclear receptor and component of the molecular clock. These inhibitory effects were observed both in vitro and in vivo and could be extended to PER2, another component of the molecular clock. Taken together, our observations suggest that the activity spectrum of protein synthesis inhibitors, whose clinical use is contemplated not only in cancers but also in viral infections, must be extended to circadian rhythm disruption, with potential beneficial or iatrogenic effects upon acute or prolonged administration. [ABSTRACT FROM AUTHOR]

Marine macroalgae produce abundant and diverse polysaccharides, which contribute substantially to the organic matter exported to the deep ocean. Microbial degradation of these polysaccharides plays an important role in the turnover of macroalgal biomass. Various members of the Planctomycetes-Verrucomicrobia-Chlamydia (PVC) superphylum are degraders of polysaccharides in widespread anoxic environments. In this study, we isolated a novel anaerobic bacterial strain NLcol2T from microbial mats on the surface of marine sediments offshore Santa Barbara, CA, USA. Based on 16S ribosomal RNA (rRNA) gene and phylogenomic analyses, strain NLcol2T represents a novel species within the Pontiella genus in the Kiritimatiellota phylum (within the PVC superphylum). Strain NLcol2T is able to utilize various monosaccharides, disaccharides, and macroalgal polysaccharides such as agar and ɩ-carrageenan. A near-complete genome also revealed an extensive metabolic capacity for anaerobic degradation of sulfated polysaccharides, as evidenced by 202 carbohydrate-active enzymes (CAZymes) and 165 sulfatases. Additionally, its ability of nitrogen fixation was confirmed by nitrogenase activity detected during growth on nitrogen-free medium, and the presence of nitrogenases (nifDKH) encoded in the genome. Based on the physiological and genomic analyses, this strain represents a new species of bacteria that may play an important role in the degradation of macroalgal polysaccharides and with relevance to the biogeochemical cycling of carbon, sulfur, and nitrogen in marine environments. Strain NLcol2T (= DSM 113125T = MCCC 1K08672T) is proposed to be the type strain of a novel species in the Pontiella genus, and the name Pontiella agarivorans sp. nov. is proposed. [ABSTRACT FROM AUTHOR]

Auricularia cornea is an important edible mushroom crop in China but the occurrence of cobweb disease has cause significance economic loss in its production. The rate of disease occurrence is 16.65% all over the country. In the present study, a new pathogen Hypomyces cornea sp. nov. was found to cause the cobweb disease. In July 2021, three strains of fungal pathogen were isolated from infected fruiting bodies and identified as H. cornea based on morphological studies and molecular phylogenetic analysis of internal transcribed spacer (ITS) of nuclear ribosomal DNA, mitochondrial large subunit (LSU) of rRNA and the partial translation elongation factor 1-alpha genes. The representative isolates of the pathogenic Hypomyces species used to perform pathogenicity test with spore suspension that caused similar symptoms as those observed in the cultivated field, and same pathogens could be re-isolated, which fulfill Koch's postulates. The typical biological characterization was examined of the serious pathogen to determine its favorable growth conditions, including suitable temperature, pH, carbon, nitrogen sources and light conditions. The findings revealed an optimum temperature of 25 °C, pH of 6, and soluble starch and peptone as the preferred carbon and nitrogen sources, respectively. The hyphal growth inhibition method was used for primary in vitro screening test of seven common fungicides, and the most suitable fungicide is Prochloraz manganese chloride complex, the EC 50 values of cobweb pathogen and mushrooms were 0.085 μg/mL and 2.452 μg/mL, respectively. The results of our research provide an evidence-based basis for the effective prevention and treatment of A. cornea cobweb disease. [ABSTRACT FROM AUTHOR]

Cystic fibrosis-related diabetes (CFRD) affects 40%–50% of adults with CF and is associated with a decline in respiratory health. The microbial flora of the lung is known to change with the development of CF disease, but how CFRD affects the microbiome has not been described. We analyzed the microbiome in sputa from 14 people with CF, 14 with CFRD, and two who were classed as pre-CFRD by extracting DNA and amplifying the variable V3-V4 region of the microbial 16S ribosomal RNA gene by PCR. Sequences were analyzed and sources were identified to genus level. We found that the α-diversity of the microbiome using Shannon’s diversity index was increased in CFRD compared with CF. Bray Curtis dissimilarity analysis showed that there was separation of the microbiomes in CF and CFRD sputa. The most abundant phyla identified in the sputum samples were Firmicutes and Proteobacteria, Actinobacteriota and Bacteroidota, and the ratio of Firmicutes/Bacteroidota was reduced in CFRD compared with CF. Pseudomonas, Azhorizophilus, Porphyromonas, and Actinobacillus were more abundant in CFRD compared with CF, whereas Staphylococcus was less abundant. The relative abundance of these genera did not correlate with age; some correlated with a decline in FEV1/FVC but all correlated with hemoglobin A1C (HbA1c) indicating that development of CFRD mediates further changes to the respiratory microbiome in CF. NEW & NOTEWORTHY Cystic fibrosis-related diabetes (CFRD) is associated with a decline in respiratory health. We show for the first time that there was a change in the sputum microbiome of people with CFRD compared with CF that correlated with markers of raised blood glucose. [ABSTRACT FROM AUTHOR]

Chamaecrista is a Pantropical legume genus of the tribe Cassieae, which includes six other genera. In contrast to most of the other Cassieae genera, Chamaecrista shows significant variability in chromosome number (from 2n = 14 to 2n = 56), with small and morphologically similar chromosomes. Here, we performed a new cytomolecular analysis on chromosome number, genome size, and rDNA site distribution in a molecular phylogenetic perspective to interpret the karyotype trends of Chamaecrista and other two genera of Cassieae, seeking to understand their systematics and evolution. Our phylogenetic analysis revealed that Chamaecrista is monophyletic and can be divided into four major clades corresponding to the four sections of the genus. Chromosome numbers ranged from 2n = 14, 16 (section Chamaecrista) to 2n = 28 (sections Absus, Apoucouita, and Baseophyllum). The number of 5S and 35S rDNA sites varied between one and three pairs per karyotype, distributed on different chromosomes or in synteny, with no obvious phylogenetic significance. Our data allowed us to propose x = 7 as the basic chromosome number of Cassieae, which was changed by polyploidy generating x = 14 (sections Absus, Apoucouita, and Baseophyllum) and by ascending dysploidy to x = 8 (section Chamaecrista). The DNA content values supported this hypothesis, with the genomes of the putative tetraploids being larger than those of the putative diploids. We hypothesized that ascending dysploidy, polyploidy, and rDNA amplification/deamplification are the major events in the karyotypic diversification of Chamaecrista. The chromosomal marks characterized here may have cytotaxonomic potential in future studies. [ABSTRACT FROM AUTHOR]

Background: The role of the intestinal microbiota in the pathogenesis of inflammatory bowel disease combined with axial spondyloarthritis (axSpA) is gaining widespread interest. Aims: This study was conducted to investigate the clinical and fecal microbiota characteristics of patients with both ulcerative colitis (UC) and axSpA. Methods: Clinical data were collected from patients with UC. Patients were divided into the axSpA and non-axSpA groups according to human leukocyte antigen-B27 serology and sacroiliac joint imaging results. We obtained fecal specimens from 14 axSpA and 26 non-axSpA patients. All samples underwent 16S ribosomal DNA sequencing. Results: Seventy-three patients with UC were included in this study, and the axSpA incidence was 19.2%. This incidence was significantly higher in patients with C-reactive protein > 10 mg/L. Firmicutes and Faecalibacterium abundances were decreased, and Proteobacteria and Escherichia_Shigella abundances were increased in the axSpA group compared with those of the non-axSpA group. Indicator analysis showed that Escherichia_Shigella was more likely to be an indicator species of axSpA. Additionally, many biosynthetic and metabolic pathways, including glutathione metabolism, fatty acid degradation, geraniol degradation, and biosynthesis of siderophore group nonribosomal peptides, were upregulated in the axSpA group. Conclusion: Patients with UC have a high axSpA incidence, which may be related to the relative abundances of Escherichia_Shigella in these patients. The abundances of various biosynthetic and metabolic pathways of the fecal flora were upregulated in patients with axSpA. [ABSTRACT FROM AUTHOR]

Background: Despite the many cheap and fast ways to generate genomic data, good and exact genome assembly is still a problem, with especially the repeats being vastly underrepresented and often misassembled. As short reads in low coverage are already sufficient to represent the repeat landscape of any given genome, many read cluster algorithms were brought forward that provide repeat identification and classification. But how can trustworthy, reliable and representative repeat consensuses be derived from unassembled genomes? Results: Here, we combine methods from repeat identification and genome assembly to derive these robust consensuses. We test several use cases, such as (1) consensus building from clustered short reads of non-model genomes, (2) from genome-wide amplification setups, and (3) specific repeat-centred questions, such as the linked vs. unlinked arrangement of ribosomal genes. In all our use cases, the derived consensuses are robust and representative. To evaluate overall performance, we compare our high-fidelity repeat consensuses to RepeatExplorer2-derived contigs and check, if they represent real transposable elements as found in long reads. Our results demonstrate that it is possible to generate useful, reliable and trustworthy consensuses from short reads by a combination from read cluster and genome assembly methods in an automatable way. Conclusion: We anticipate that our workflow opens the way towards more efficient and less manual repeat characterization and annotation, benefitting all genome studies, but especially those of non-model organisms. [ABSTRACT FROM AUTHOR]

Entomopathogenic fungi comprise an ecologically important group of specialized pathogens infecting other fungi, invertebrates, and plants. These fungi are species-rich with high diversity and broad distribution worldwide. The majority of entomopathogenic fungi belong to clavicipitoids, which consist of the hypocrealean families, Clavicipitaceae, Cordycipitaceae, Ophiocordycipitaceae, and Polycephalomycetaceae. The latter is a newly established entomopathogenic family that recently separated from the family Ophiocordycipitaceae to accommodate the genera, Perennicordyceps, Pleurocordyceps, and Polycephalomyces. In recent years, Polycephalomycetaceae has been enriched with parasitic and hyperparasitic fungi. With 16 species spread across China, Ecuador, Japan, and Thailand, Pleurocordyceps is the most speciose genus in the family. In this study, we expand the number of taxa in the genus by introducing four new Pleurocordyceps species from China, namely, P. clavisynnema, P. multisynnema, P. neoagarica, and P. sanduensis. We provide detailed descriptions and illustrations and infer genus-level phylogenies based on a combined 6-loci gene sequence dataset comprising the internal transcribed spacer gene region (ITS), small subunit ribosomal RNA gene region (SSU), large subunit rRNA gene region (LSU), translation elongation factor 1-alpha gene region (TEF-1a), RNA polymerase II largest subunit gene region (RPB1), and RNA polymerase II second largest subunit (RPB2). This study contributes to knowledge with regard to the diversity of Pleurocordyceps specifically and entomopathogenic Hypocreales more broadly. [ABSTRACT FROM AUTHOR]

Guigarra cailaoensis is a member of family Cyprinidae, subfamily Labeoninae (Cypriniformes) which was recently discovered in southwestern China. Following its initial description, additional information on this species has remained notably scarce. In the current study, we assemble the complete mitochondrial genome (mitogenome) of G. cailaoensis using the Illumina sequencing platform. The mitogenome is identified as a circular, double-stranded DNA sequence of 16,593 base pairs, encompassing 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Maximum-likelihood and Bayesian-inference approaches were used to construct phylogenetic trees for three datasets: (i) PCG sequences of the complete mitogenome (dataset 1); (ii) PCG sequences of the complete mitogenome combined with nuclear DNA (ncDNA) (Rag1) sequence (dataset 2); and (iii) ncDNA (Rag1) sequences (dataset 3). Phylogenetic analyses position G. cailaoensis as a sister taxon to the lineage consisting of Paraqianlabeo lineatus Zhao, Sullivan, Zhang & Peng, 2014 and Pseudogyrinocheilus prochilus Fang, 1933 in dataset 1, and to Pseudogyrinocheilus prochilus in dataset 2, species lacking an oral disc on the lower lip. However, G. cailaoensis showed a close relationship to the lineage consisting of Discogobio and Discocheilus in dataset 3, species possessing an oral disc on the lower lip. Nonetheless, a variety of species with an oral disc on the lower lip are clustered into different lineages across the three datasets that may indicate that the development of the oral disc is homoplastic within the subfamily Labeoninae. The outcomes of this study have the potential to support conservation efforts for this species and to enrich our understanding of genetic resources in the area. [ABSTRACT FROM AUTHOR]

Asynchronously cycling cells pose a challenge to the accurate characterization of phase-specific gene expression. Current strategies, including RNAseq, survey the steady state gene expression across the cell cycle and are inherently limited by their inability to resolve dynamic gene regulatory networks. Single cell RNAseq (scRNAseq) can identify different cell cycle transcriptomes if enough cycling cells are present, however some cells are not amenable to scRNAseq. Therefore, we merged two powerful strategies, the CDT1 and GMNN degrons used in Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) cell cycle sensors and the ribosomal protein epitope tagging used in RiboTrap/Tag technologies to isolate cell cycle phase-specific mRNA for sequencing. The resulting cell cycle dependent, tagged ribosomal proteins (ccTaggedRP) were differentially expressed during the cell cycle, had similar subcellular locations as endogenous ribosomal proteins, incorporated into ribosomes and polysomes, and facilitated the recovery of cell cycle phase-specific RNA for sequencing. ccTaggedRP has broad applications to investigate phase-specific gene expression in complex cell populations. [ABSTRACT FROM AUTHOR]

Background: Different anopheline species (even within a species group/complex) can differ in their feeding and resting behaviours, which impact both malaria transmission patterns as well as the efficacy of vector control interventions. While morphological identification of sampled specimens is an important first step towards understanding species diversity and abundance, misidentification can result in the implementation of less effective vector control measures, and consequently smaller reductions in the number of local malaria cases. Focusing on southern Mozambique, a malaria pre-elimination area where malaria remains persistent, the aims of this preliminary study were to use molecular identification (CO1 and ITS2 barcoding) to (1) validate the results from the morphological identification (with a particular focus on Anopheles pharoensis and Anopheles squamosus), and (2) have a closer look at the Anopheles coustani group (which includes Anopheles tenebrosus and Anopheles ziemanni). Methods: Female anopheline mosquitoes (n = 81) were identified morphologically and subsequently sequenced at the ribosomal DNA internal transcribed spacer region 2 (ITS2) and/or cytochrome oxidase subunit 1 (CO1) loci towards species determination. Results: Out of the 62 specimens that were identified morphologically to species, 4 (6.5%) were misidentified. Regarding the An. coustani group, morphological identification showed that several members are present in southern Mozambique, including An. coustani sensu lato (s.l.), An. ziemanni and An. tenebrosus. However, based on both ITS2 and CO1 sequences, the exact species remains unknown for the latter two members until voucher sequences are available for comparison. Conclusion: The reason(s) for morphological misidentification of anopheline mosquitoes need to be mitigated. This is usually related to both the capacity (i.e. training) of the microscopist to identify anopheline species, and the information provided in the dichotomous identification key. As the An. coustani complex contributes to (residual) malaria transmission in sub-Saharan Africa, it may play a role in the observed persistent malaria in southern Mozambique. A better baseline characterizing of the local anophelines species diversity and behaviours will allow us to improve entomological surveillance strategies, better understand the impact of vector control on each local vector species, and identify new approaches to target those vector species. [ABSTRACT FROM AUTHOR]

The harmful algal bloom (HAB) species Pseudo-nitzschia multiseries is widely distributed worldwide and is known to produce the neurotoxin domoic acid, which harms marine wildlife and humans. Early detection and preventative measures are more critical than late management. However, the major challenge related to early detection is the accurate and sensitive detection of microalgae present in low abundance. Therefore, developing a sensitive and specific method that can rapidly detect P. multiseries is critical for expediting the monitoring and prediction of HABs. In this study, a novel assay method, recombinase polymerase amplification combined with lateral flow dipstick (RPA-LFD), is first developed for the detection of P. multiseries. To obtain the best test results, several important factors that affected the amplification effect were optimized. The internal transcribed spacer sequence of the nuclear ribosomal DNA from P. multiseries was selected as the target region. The results showed that the optimal amplification temperature and time for the recombinase polymerase amplification (RPA) of P. multiseries were 37 °C and 15 min. The RPA products could be visualized directly using the lateral flow dipstick after only 3 min. The RPA-LFD assay sensitivity for detection of recombinant plasmid DNA (1.9 × 100 pg/μL) was 100 times more sensitive than that of RPA, and the RPA-LFD assay sensitivity for detection of genomic DNA (2.0 × 102 pg/μL) was 10 times more sensitive than that of RPA. Its feasibility in the detection of environmental samples was also verified. In conclusion, these results indicated that the RPA-LFD detection of P. multiseries that was established in this study has high efficiency, sensitivity, specificity, and practicability. Management measures made based on information gained from early detection methods may be able to prevent certain blooms. The use of a highly sensitive approach for early warning detection of P. multiseries is essential to alleviate the harmful impacts of HABs on the environment, aquaculture, and human health. [ABSTRACT FROM AUTHOR]

Entamoeba histolytica (E. histolytica) exhibits a remarkable capacity to respond to thermal shock stress through a sophisticated genetic regulation mechanism. This process is carried out via Heat Shock Response Elements (HSEs), which are recognized by Heat Shock Transcription Factors (EhHSTFs), enabling fine and precise control of gene expression. Our study focused on screening for HSEs in the promoters of the E. histolytica genome, specifically analyzing six HSEs, including Ehpgp5, EhrabB1, EhrabB4, EhrabB5, Ehmlbp, and Ehhsp100. We discovered 2578 HSEs, with 1412 in promoters of hypothetical genes and 1166 in coding genes. We observed that a single promoter could contain anywhere from one to five HSEs. Gene ontology analysis revealed the presence of HSEs in essential genes for the amoeba, including cysteine proteinases, ribosomal genes, Myb family DNA-binding proteins, and Rab GTPases, among others. Complementarily, our molecular docking analyses indicate that these HSEs are potentially recognized by EhHSTF5, EhHSTF6, and EhHSTF7 factors in their trimeric conformation. These findings suggest that E. histolytica has the capability to regulate a wide range of critical genes via HSE-EhHSTFs, not only for thermal stress response but also for vital functions of the parasite. This is the first comprehensive study of HSEs in the genome of E. histolytica, significantly contributing to the understanding of its genetic regulation and highlighting the complexity and precision of this mechanism in the parasite's survival. [ABSTRACT FROM AUTHOR]

Background: Strongyloidiasis is a neglected tropical disease (NTD) that is caused mainly by Strongyloides stercoralis, with an estimated 600 million people infected worldwide, and in fewer cases by Strongyloides fuelleborni fuelleborni and Strongyloides fuelleborni kellyi. A number of studies have been conducted on the genetic diversity of S. stercoralis in East and Southeast Asia; however, there is very limited corresponding information from West Asian countries, including Iran. Methods: For Strongyloides worms collected from patients in southwestern Iran, the hypervariable regions I (HVR-I) and IV (HVR-IV) of the nuclear 18S ribosomal DNA (rDNA) locus (SSU) and a fragment of the subunit 1 mitochondrial cytochrome c oxidase gene (cox-1) were sequenced. For a subset of the worms, whole-genome sequencing data were generated. Results: The cox-1 sequences of 136 worms isolated from 23 patients indicated that all isolates were S. stercoralis. Among the cox-1 sequences, 33 polymorphic sites and 13 haplotypes were found. The phylogenetic analysis demonstrated that some sequences clustered fairly closely with sequences from humans and dogs from other parts of the world, while others formed a separate, Iran-specific group. Among 64 S. stercoralis analyzed, we found three of the previously described SSU HVR-I haplotypes, with haplotype II being the most frequent haplotype. In contrast to Southeast Asia, where S. stercoralis heterozygous for different haplotypes at the HVR-I locus are rare, we found 20 worms to be heterozygous for two different HVR-I haplotypes, 18 of which fell into the Iran-specific cox-1 cluster. SSU-heterozygous worms also showed elevated heterozygosity at the whole-genome level. Conclusions: We conclude that the S. stercoralis population from the Khuzestan province shares much of the genetic diversity with the population in Southeast Asia, but there is an indication of additional genetic input. There appears to be some population structure with different subpopulations, which however do interbreed at least occasionally. [ABSTRACT FROM AUTHOR]

Background: Hybridization is a useful strategy to produce offspring with more desirable phenotypic characteristics than those of parents. The hybrid grouper derived from the cross of Cromileptes altivelis (♀, 2n = 48) with Epinephelus lanceolatus (♂, 2n = 48) exhibits improved growth compared with its female parent, which makes it valuable to aquaculture. However, the genetic traits of the hybrid grouper are poorly understood. Results: The observations showed that the hybrid grouper was diploid (2n = 48) and displayed intermediate morphology with the parent's measurable characteristics. The ribosomal DNA (rDNA) and mitochondria DNA (mtDNA) were characterized at molecular and phylogenetic level. High similarity and low genetic distance of 5S rDNA and mtDNA sequences between the hybrid grouper and C. altivelis showed that the hybrid grouper had a closer genetic relationship with female parents. The reconstructed phylogenetic tree based on COI gene and D-loop region of mtDNA recovered that mtDNA was maternally inherited in the hybrid grouper. Additionally, the DNA methylation level of 5S rDNA intergenic spacers (IGS) sequence was tested in here. The results showed that the DNA methylation status of the hybrid grouper was significantly lower than that of C. altivelis. Conclusion: Results of this study provide important data on the genetic characteristics of the hybrid derived from the cross of C. altivelis and E. lanceolatus, and contribute the knowledge of both evolution and marine fish breeding. [ABSTRACT FROM AUTHOR]

Cactaceae are American members of arid and semi-arid regions and are also present in tropical forests and temperate climates. The taxonomy is complex owing to large morphological variability, and polyploidy is a significant mechanism in cactus speciation associated with geographical and environmental range expansions. In South America, Cactaceae have a wide distributional range and provide an informative model in which to examine the correlation between ploidy levels and genome sizes with geographical and bioclimatic variables. We tested whether ploidy levels and DNA contents are related to elevation and the 19 WorldClim variables, and we mapped chromosome numbers and amounts of DNA on a molecular phylogeny to interpret their evolution. We performed Pearson correlation tests between the response variables and each climatic variable and used a multivariate analysis to assess the pattern of variation among variables and chromosome numbers. Our data suggest that polyploidy had independent origins within each subfamily. Chromosome numbers were related to variables associated with temperature, whereas DNA contents were related mostly to precipitation. A negative correlation was observed between the amount of DNA in one chromosome set and the increase in the ploidy level. Based on the results, the small genome can be considered ecologically important as an adaptation to higher temperatures and droughts. [ABSTRACT FROM AUTHOR]

SUMMARY: Minorisa is a group of tiny uniflagellates belonging to the Cercozoa. These flagellates are the closest heterotrophic relatives of photosynthetic chlorarachniophytes and are one of the most abundant bacterivorous eukaryotes in coastal marine environments. Despite their evolutionary and ecological importance, taxonomic studies on Minorisa have not been conducted since the original description. In the present study, we isolated five Minorisa strains and performed molecular phylogenetic and microscopic analyses. Molecular phylogenetic analysis using small subunit ribosomal RNA gene sequences indicated that the strains form four different subclades in Minorisa. Microscopic observations revealed that these Minorisa strains possess an amoeboid stage that lacks a flagellum. In the amoeboid stage, cells possess lobose and/or extrusive pseudopodia. Based on the phylogenetic analysis and morphological observations, we revised the description of Minorisa and described the following three novel Minorisa species: Minorisa fusiformis sp. nov., Minorisa magna sp. nov. and Minorisa megafusiformis sp. nov. [ABSTRACT FROM AUTHOR]

Lilium growth is severely impeded by continuous cropping, and crop rotation is essential to reducing the detrimental effects of monocultures. Soil (0–20 cm) was collected in three Lilium cropping patterns in Longshan County, Hunan Province, including continuous Lilium cropping (Lilium), corn upland rotation with Lilium (Corn), and paddy rotation with Lilium (Rice). Using Illumina high-throughput sequencing technology, the fungal ribosomal DNA internal-transcribed spacer 1 (ITS1) was examined to evaluate the features of soil fungi communities among three cropping patterns. Crop rotation has an impact on soil properties and the microbial community. Rice soil has a significantly higher pH than Lilium and corn soil, while corn and rice soil have a greater total nitrogen and total phosphorus content than Lilium soil. Rotation cropping clearly shifted the fungi community diversity based on the results of principal coordinate analysis (PCoA) and nonmetric multidimensional scaling (NMDS). Ascomycota was the most prevalent phylum, with the highest levels in Lilium soil. Genetic analysis revealed that paddy rotation led to a clear reduction in or non-detection of eight potentially pathogenic fungal genera and a noticeable accumulation of eight beneficial fungal genera compared to Lilium continuous cropping. Fungi communities and their abundant taxa were correlated with soil pH and nutrients. Altogether, we propose that rice rotation, with its ability to mitigate soil acidification, reducing pathogenic and accumulating beneficial communities, may be an effective strategy for alleviating the continuous cropping barrier. [ABSTRACT FROM AUTHOR]

The characterization of natural fungal diversity impacts our understanding of ecological and evolutionary processes and can lead to novel bioproduct discovery. Russula and Lactarius, both in the order Russulales, represent two large genera of ectomycorrhizal fungi that include edible as well as toxic varieties. Based on morphological and phylogenetic analyses, including nucleotide sequences of the internal transcribed spacer (ITS), the 28S large subunit of ribosomal RNA (LSU), the second largest subunit of RNA polymerase II (RPB2), the ribosomal mitochondrial small subunit (mtSSU), and the translation elongation factor 1-α (TEF1-α) gene sequences, we here describe and illustrate two new species of Russula and one new species of Lactarius from southern China. These three new species are: R. junzifengensis (R. subsect. Virescentinae), R. zonatus (R. subsect. Crassotunicatae), and L. jianyangensis (L. subsect. Zonarii). [ABSTRACT FROM AUTHOR]

Ganoderma is a genus of biomedical fungus that is used in the development of numerous health products throughout the world. The Lower Volta River Basin of Ghana is an undulating land surface covered by extensive vegetation and water bodies and is rich in polypore mushrooms resembling various members of the Ganoderma genus. Despite the extensive biopharmaceutical benefits of Ganoderma spp., the isolates from the Lower Volta River Basin have not been properly characterized, thus limiting their use in the development of biotechnological products. In this study, Ganoderma spp. collected from the Lower Volta River Basin were genetically analyzed using the nuclear ribosomal sequences, the internal transcribed spacer 2 (ITS 2), the complete internal transcribed spacer (ITS), and the nuclear large subunit (nLSU). Blastn search and sequence analysis revealed that the sample we coded as Ganoderma LVRB-2 belongs to G. mbrekobenum, whereas Ganoderma LVRB-1, Ganoderma LVRB-14, and Ganoderma LVRB-16 belong to the species G. enigmaticum. Our analysis further demonstrates that Ganoderma LVRB-17 belongs to the species G. resinaceum. Thus, the five samples collected in the present study were positioned in three different distinct groups, namely G. mbrekobenum, G. enigmaticum, and G. resinaceum. The current data may serve as reference points for future studies. [ABSTRACT FROM AUTHOR]

A novel species of earthstar from China, Geastrum sanglinense is described. Phylogenetic analyses based on sequences of the nuclear ribosomal DNA internal transcribed spacer (ITS), large subunit nuclear ribosomal RNA (nrLSU), and subunit 6 of ATP synthase (atp6) regions showed that the species belongs to subsect. Epigaea in sect. Myceliostroma. The sequences of the new taxon formed a sister group to G. yanshanense and G. rubellum. This species was mainly characterized by scattered or clustered basidiomata (1.9-2.2 cm in width × 2.3-2.5 cm in height), small to medium-sized saccate exoperidium (1.9-4.3 cm diam. when expanded), smooth endoperidial bodies (1.2-2.7 cm diam.), and globose to subglobose basidiospores (3.7-4.1 µm diam.), surface with short columnar warts. The species can also be distinguished by ITS, nrLSU, and atp6 sequences. The new species was described in detail and can provide a reference for the investigation of macrofungi resources in Shanxi Province, China. [ABSTRACT FROM AUTHOR]

With 74 genera and subgenera and approximately 740 species, Saprininae represent one of the largest subfamilies of Histeridae (Coleoptera: Histeroidea). Here, we present a phylogenetic hypothesis for Saprininae based on comprehensive taxonomic sampling. This is the first phylogenetic study combining molecular and morphological approaches (cytochrome c oxidase subunit 1, 18S ribosomal RNA and 93 morphological characters). As a result, we propose a new classification; five new tribes are erected: Myrmetini Portevin stat. and sens. nov.; Euspilotini Lackner, trib. nov.; Eremosaprinini Lackner, trib. nov.; Saprinini Blanchard, sens. nov.; and Hypocaccini Lackner, trib. nov. Additional nomenclatural acts are as follows: Chelyoxenus Hubbard is downgraded to a subgenus of Geomysaprinus Ross, thus Geomysaprinus (Chelyoxenus) stat. nov., Nessus Reichardt is transferred from a subgenus of Hypocaccus C. Thomson to a subgenus of Hypocacculus Bickhardt, thus Hypocacculus (Nessus) stat. rest. The following taxa Paraphilothis Vienna, Styphrus Motschulsky, Xerosaprinus Wenzel, Lophobregmus Wenzel, Vastosaprinus Wenzel, Auchmosaprinus Wenzel, Hemisaprinus Kryzhanovskij & Reichardt, Reichardtia Wenzel and Australopachylopus Lackner & Leschen are all downgraded into subgenera of Saprinus Erichson. Thus, Saprinus (Paraphilothis) stat. nov., Saprinus (Styphrus) stat. nov., Saprinus (Xerosaprinus) stat. nov., Saprinus (Vastosaprinus) stat. nov., Saprinus (Auchmosaprinus) stat. nov., Saprinus (Lophobregmus) stat. nov., Saprinus (Hemisaprinus) stat. rest., Saprinus (Reichardtia) stat. nov., Saprinus (Australopachylopus) stat. nov. A new genus, Paraxenus Lackner gen. nov., is proposed for the former South African and Namibian members of the genus Pholioxenus Reichardt, with the following new combinations: Paraxenus diasi (Vienna) comb. nov.; Paraxenus eremicola (Thérond) comb. nov.; Paraxenus namibiensis (Vienna) comb. nov.; Paraxenus oleolus (Thérond) comb. nov.; Paraxenus therondi (Olexa) comb. nov.; and Paraxenus uhligi (Mazur) comb. nov. Additionally, based on the analysis of the dispersal patterns, Myrmetini appear to be a bipolar (amphitropical) clade, while Eremosaprinini appear to be exclusive to the Western Hemisphere. Euspilotini are strongly represented in the Western Hemisphere, with only a handful of species known from the Palaearctic/Oriental regions. Saprinini and Hypocaccini are spread worldwide but are poorly represented in South America. The Holarctic (in particular the Nearctic) Region is proposed as the centre of origin of the subfamily around 80 million years ago (Ma). Inquilinism is hypothesised to be the ancestral state for the group, with several subsequent independent shifts in life histories. Saprininae cladogenesis occurred mainly during the Palaeogene (66–23.03 Ma) and could be linked to the diversification of mammals. [ABSTRACT FROM AUTHOR]

Available DNA barcodes of freshwater zooplankton are scarce in regions like the Iberian Peninsula, which harbours many rare and endemic species and is considered a hotspot of crustacean biodiversity. Recently, a new species of Ceriodaphnia (Cladocera: Daphniidae) was described using morphological analysis of specimens in the Mediterranean region and molecular data on a single locality in southern Spain. In our study, we detected the presence of the newly discovered taxa and here, we provide new DNA sequences on the barcoding region mitochondrial cytochrome c oxidase I together with ecological information of the recently described Ceriodaphnia smirnovi. Additionally, we built a molecular phylogenetic tree and genetically compared these specimens with previously available mitochondrial DNA sequences and with new sequences of the genus recovered in Iberia. Our data suggest that this morphospecies might contain some cryptic taxa and might be more common than previously thought, occupying temporary to semi‐permanent ecosystems, with vegetation and highly variable pH and turbidity conditions. Moreover, the existence of a non‐identified clade within our phylogenetic tree requires additional morphological research. Our study highlights the need for further research on microcrustacean biota to better constrain its spatial boundaries, phylogenetic relationship and determine species hiding cryptic diversity. [ABSTRACT FROM AUTHOR]

Razor clams, belonging to the Pharidae and Solenidae families, are ecologically and economically important; however, very little research has been conducted on the Pharidae family. The genus Novaculina is a marine-derived freshwater lineage, and Novaculina chinensis is a rare freshwater species of the Pharidae family. In order to understand the phylogenetic relationships of N. chinensis, we sequenced the mitochondrial genome of the genus Novaculina, which is 16,262 bp in length and consists of 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The phylogenetic relationships of 69 Imparidentian mitochondrial genomes (mitogenomes) indicated that N. chineisis is closely related to Sinonovacula constricta of the order Adapedonta. Our study also found that the Ka/Ks ratios of 12 protein-coding genes in the Pharidae family are lower than one, indicating the occurrence of negative purification selection. Morphological observations of the siphons of N. chinensis, Novaculina myanmarensis, and Novaculina gangetica indicate that N. chinensis may be the ancestral clade of the genus Novaculina, which has not been proposed in previous studies. Our study provides useful molecular information on the phylogenetic and evolutionary relationships of Pharidae and also contributes to the conservation and management of the germplasm resources of N. chinensis. [ABSTRACT FROM AUTHOR]

In recent years, the role of liquid–liquid phase separation (LLPS) and intrinsically disordered proteins (IDPs) in cellular molecular processes has received increasing attention from researchers. One such intrinsically disordered protein is TSPYL5, considered both as a marker and a potential therapeutic target for various oncological diseases. However, the role of TSPYL5 in intracellular processes remains unknown, and there is no clarity even in its intracellular localization. In this study, we characterized the intracellular localization and exchange dynamics with intracellular contents of TSPYL5 and its parts, utilizing TSPYL5 fusion proteins with EGFP. Our findings reveal that TSPYL5 can be localized in both the cytoplasm and nucleoplasm, including the nucleolus. The nuclear (nucleolar) localization of TSPYL5 is mediated by the nuclear/nucleolar localization sequences (NLS/NoLS) identified in the N-terminal intrinsically disordered region (4–27 aa), while its cytoplasmic localization is regulated by the ordered NAP-like domain (198–382 aa). Furthermore, our results underscore the significant role of the TSPYL5 N-terminal disordered region (1–198 aa) in the exchange dynamics with the nucleoplasm and its potential ability for phase separation. Bioinformatics analysis of the TSPYL5 interactome indicates its potential function as a histone and ribosomal protein chaperone. Taken together, these findings suggest a significant contribution of liquid–liquid phase separation to the processes involving TSPYL5, providing new insights into the role of this protein in the cell's molecular life. [ABSTRACT FROM AUTHOR]

Nowadays, fungal contamination of medical Cannabis inflorescences during postharvest has become an increasingly frequent and worrisome problem for consumers and the industry in general. This is because some of these microorganisms can produce secondary metabolites, such as mycotoxins, which can be toxic to humans. To assess the risk posed by fungal contamination and evaluate the potential for fungal isolates to produce mycotoxins, samples of medicinal Cannabis were tested for the presence of mycotoxin-forming fungi. Inflorescences were isolated on PDA agar at 23 ± 2 °C for ten days, and the microorganisms were identified. The strain with morphological characteristics compatible with the genus Aspergillus spp. was selected as the fungus with the highest risk of forming hazardous mycotoxins. This isolate was characterized conventionally and by molecular identification using primers for the internal transcribed spacer region (ITS) of ribosomal DNA and different coding genes and was identified as Aspergillus westerdijkiae. To determine mycotoxin formation, the genome of A. westerdijkiae was sequenced using the Illumina Novaseq platform in South Korea. The antiSMASH tool was used to search for gene clusters associated with producing secondary metabolites, and genes related to toxins were manually curated. Regions where the cluster of genes directly involved in OTA biosynthesis (otaA, otaB, otaC, otaR and otaD) were found, suggesting a potential risk of synthesis of this toxin. [ABSTRACT FROM AUTHOR]

Summary: The pine wood nematode, Bursaphelenchus xylophilus (Steiner et Buhrer), is the causative agent of pine wilt disease. It is native to North America and has been devastating pine forests in East Asia and West Europe since its introduction. The pathogenic nematode is transmitted by cerambycid beetle adults of Monochamus alternatus Hope in East Asia and M. galloprovincialis (Olivier) in West Europe. Bursaphelenchus mucronatus Mamiya et Enda is widely distributed in Eurasia and has no or little pathogenicity to pine species. If hybrids between the two species are backcrossed with B. xylophilus nematodes repeatedly, a small proportion of B. mucronatus genes will be infused into B. xylophilus genome (introgression) and may lead to adaptation to locally harsh environments. Inoculation tests in this study revealed that two of eight hybrid-derived populations from crossing B. xylophilus and B. mucronatus caused pine seedling mortalities of 36-70%. The pathogenic hybrid-derived populations carried nuclear ribosomal DNA (rDNA) of two species and B. xylophilus extra-nuclear genes, whereas non-pathogenic populations carried B. mucronatus rDNA and extranuclear genes of B. xylophilus or B. mucronatus. Thus, it is inferred that a gene or genes associated with pathogenicity are present in the nuclear genome of B. xylophilus. A laboratory experiment revealed that the pathogenic hybrid-derived population had as great an ability to board M. alternatus adults as the parental-lineage B. xylophilus isolate. Thus, the introgressive hybridisation is considered to occur in pine forests if two species cohabit in host trees. [ABSTRACT FROM AUTHOR]

Neuwiedia singapureana is a rare and endangered plant of the Apostasioideae subfamily. The Apostasioideae subfamily has a unique evolutionary status, as it is considered to be the most primitive group forming the base of the Orchidaceae evolutionary tree. Therefore, N. singapureana has high scientific research and conservation value. The endophytic fungal communities associated with orchids are rich and diverse, but few studies have investigated the endophytic fungi of Neuwiedia orchid plants. In the present study, the aim was to examine the endophytic fungal community structures associated with wild N. singapureana rhizomes and normal roots in the ground and with bare prop roots in the air at two sampling sites in China. High-throughput sequencing of nuclear ribosomal DNA fragments of the internal transcribed spacer regions was conducted, and cultivable methods were adopted. A total of 2161 endophytic fungal operational taxonomic units (OTUs) were obtained at a 97% sequence similarity threshold. The endophytic fungal diversity differed among the samples but not significantly. There were many more non-mycorrhizal endophytic fungal than orchid mycorrhizal (OM) fungal species detected in the N. singapureana orchid, about 98.33% OTUs of non-mycorrhizal fungi contrasting with 1.67% OTUs of potential orchid mycorrhizal fungi, among which Ceratobasidiaceae, Russulaceae, and Thelephoraceae were the dominant orchid mycorrhizal fungi. One culturable OM fungal Epulorhiza sp. isolated from the rhizome was capable of significantly promoting the seed germination and seedling growth of Dendrobium officinale and Epidendrum secundum orchids, respectively, with different efficiencies. These endophytic fungal strains with growth-promoting functions will provide materials for orchid conservation and for the study of the mechanisms underlying orchid symbiotic associations. [ABSTRACT FROM AUTHOR]

Eukaryotrophic protists are ecologically significant and possess characteristics key to understanding the evolution of eukaryotes; however, they remain poorly studied, due partly to the complexities of maintaining predator–prey cultures. Kaonashia insperata, gen. nov., et sp. nov., is a free‐swimming biflagellated eukaryotroph with a conspicuous ventral groove, a trait observed in distantly related lineages across eukaryote diversity. Di‐eukaryotic (predator–prey) cultures of K. insperata with three marine algae (Isochrysis galbana, Guillardia theta, and Phaeodactylum tricornutum) were established by single‐cell isolation. Growth trials showed that the studied K. insperata clone grew particularly well on G. theta, reaching a peak abundance of 1.0 × 105 ± 4.0 × 104 cells ml−1. Small‐subunit ribosomal DNA phylogenies infer that K. insperata is a stramenopile with moderate support; however, it does not fall within any well‐defined phylogenetic group, including environmental sequence clades (e.g. MASTs), and its specific placement remains unresolved. Electron microscopy shows traits consistent with stramenopile affinity, including mastigonemes on the anterior flagellum and tubular mitochondrial cristae. Kaonashia insperata may represent a novel major lineage within stramenopiles, and be important for understanding the evolutionary history of the group. While heterotrophic stramenopile flagellates are considered to be predominantly bacterivorous, eukaryotrophy may be relatively widespread amongst this assemblage. [ABSTRACT FROM AUTHOR]

Background: Various genotypes of Echinococcus granulosus have been studied in high-disease-risk areas and identified as causative agents of cystic echinococcosis (CE). This study was performed to examine and identify the molecular hydatid cyst in the dissected human specimens in paraffin tissue, and the dissected animal cyst was characterized using the DNA polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of internal transcribed spacer 1 (ITS1). Materials and Methods: To determine the molecular properties of E. granulosus, 20 hydatid cyst samples (including 6 sheep samples, 9 camel samples, and 10 human paraffin samples) were collected from Zahedan and Zabol cities. After DNA extraction, molecular PCR was performed, and RFLP was evaluated. In this study, the Taq1 endonuclease cleavage enzyme was used. Results: The patterns of DNA bands found in the isolates from human CE and animal bladder cysts were the same, as indicated by the results of ribosomal DNA-ITS1 amplification from E. granulosus. Two nested primer pairs were used. The rough size of the enhanced ITS1 piece was 444 and 391 base pairs (bp), individually. After cutting the PCR product with the Taq1 enzyme, the patterns of the fragments revealed that the samples had two identical RFLP patterns. The aftereffects of this study showed that the parasite genotypes confined to sheep, camels, and people had hereditary changes. Conclusion: The transcendent type of E. granulosus sensu lato in the area is E. granulosus sensu stricto, which featured the meaning of the sheep/canine cycle in human transmission. Albeit the band profile in the camel is now and again like the sheep strain, RLFP can be recognized utilizing the PCR strategy, and two differentiating band profiles using the chemical were found in this review. [ABSTRACT FROM AUTHOR]

Fimbrora Monniot & Monniot, 1991, a macrophagous ascidian genus within the family Ascidiidae Adams & Adams, 1858, is currently monotypic, represented by F. calsubia Monniot & Monniot, 1991, a species previously recorded from the bottom of the South Pacific at depths of 1000–1860 m. The taxonomic status of Fimbrora has remained ambiguous because characteristics in its branchial papillae and neural-gland opening are incompletely known in previous studies, while these traits are essential for distinguishing other ascidiid genera. So far, no nucleotide sequence representing F. calsubia is available. In this study, we collected a single specimen of F. calsubia at a depth of 2027 m, about 400 km off the Pacific coast of Honshu, Japan. This is the deepest record, as well as the first report from the North Pacific, for the species. Our examination indicates that Fimbrora is morphologically similar to another ascidiid genus, Psammascidia Monniot, 1962, by having only secondary branchial papillae in the pharynx. Our phylogenetic analysis, based on the 18S ribosomal RNA and cytochrome c oxidase subunit I genes, along with those of 27 ascidian species available in public databases, showed that F. calsubia was more closely related to Ascidia zara Oka, 1935, Phallusia fumigata (Grube, 1864) and Phallusia mammilata (Cuvier, 1815) than to Ascidia ceratodes (Huntsman, 1912), Ascidiella aspersa (Müller, 1776) and Ascidiella scabra (Müller, 1776). Our results also indicated that acquisitions of macrophagous feeding by deep-sea members happened independently at least three times in the evolutionary history of the entire Ascidiacea. [ABSTRACT FROM AUTHOR]

The giant deep-sea oyster Neopycnodonte zibrowii Gofas, C. Salas & Taviani, 2009 is a keystone deep-sea habitat builder species. Discovered about fifteen years ago in the Azores, it has been described and assigned to the genus Neopycnodonte Fischer von Waldheim, 1835 based on morphological features. In this study, we generated DNA sequence data for both mitochondrial (COI and 16S) and nuclear (ITS2 and 28S) markers based on the holotype specimen of N. zibrowii to establish a molecular phylogenetic framework for the systematic assessment of this species and to provide a reliable (i.e., holotype-based) reference sequence set for multilocus DNA barcoding approaches. Molecular data provide compelling evidence that the giant deep-sea oyster is a distinct species, rather than a deep-water ecophenotype of Neopycnodonte cochlear (Poli, 1795), with extremely high genetic divergence from any other gryphaeid. Multilocus phylogenetic analyses place the giant deep-sea oyster within the clade "Neopycnodonte/Pycnodonte" with closer affinity to N. cochlear rather than to P. taniguchii Hayami & Kase, 1992, thus supporting its assignment to the genus Neopycnodonte. Relationships within this clade are not well supported because mitochondrial variation is inflated by saturation that eroded phylogenetic signal, implying an old split between taxa within this clade. Finally, the set of reference barcode sequences of N. zibrowii generated in this study will be useful for a wide plethora of barcoding applications in deep-sea biodiversity surveys. Molecular validation of recent records of deep-sea oysters from the Atlantic Ocean and the Mediterranean Sea will be crucial to clarify the distribution of N. zibrowii and assess the phenotypic variation and ecology of this enigmatic species. [ABSTRACT FROM AUTHOR]

Infectious bovine keratoconjunctivitis (IBK) is associated with 2 species of Moraxella: M. bovis and M. bovoculi. A third novel Moraxella spp., designated tentatively as M. oculi, has been identified from the eyes of cattle with and without pinkeye. These 3 Moraxella spp. can be found in various combinations within the same clinical sample, making speciation of this genus directly from a sample impossible with Sanger sequencing. Assessing Moraxella diversity found in IBK- and non-IBK–affected cattle eyes, independent of culture, may provide additional information about IBK by avoiding the selectivity bias of culturing. We developed a targeted NGS panel to detect and speciate these 3 Moraxella spp. directly from bovine ocular swabs. Our targeted panel amplifies bacterial essential genes and the 16S-23S ribosomal RNA intergenic spacer region (ITS) of the 3 Moraxella spp. and speciates based on these sequences. Our panel was able to differentiate the 3 species directly from DNA extracted from 13 swabs (6 from healthy animals, 7 from animals with IBK), and every swab except one (clinically healthy eye) had the 3 Moraxella spp. Targeted NGS with sequencing of Moraxella spp. housekeeping genes appears to be a suitable method for speciation of Moraxella directly from ocular swabs. [ABSTRACT FROM AUTHOR]

Phenolic compounds have gained international interest due to their carcinogenic, toxic, and bioaccumulative properties, causing adverse effects in both animals and humans. As a result, there is a growing interest in finding alternative and eco-friendly treatment routes for phenol by exploring new microbial cultures with potential adaptation and biodegradation capabilities. In this study, the phenol removal efficiency of Yarrowia lipolytica YQ22 under laboratory conditions was determined. The YQ22 strain was obtained from diesel samples from a fuel station in Trujillo, Peru, isolated through serial dilutions on Sabouraud agar, and identified through its morphological characteristics using microscopy and molecular analysis by polymerase chain reaction of the ribosomal DNA internal transcribed spacer (ITS) and 5.8S regions. In the treatment, the effect of pH (5, 6 and 7) and temperature (25°C, 30°C and 35°C) on phenol removal with 2% (v/v) inoculum of Yarrowia lipolytica from 48-hour growth was evaluated. Phenol concentration was measured by high-performance liquid chromatography. A maximum phenol removal percentage of 61.18 was obtained for YQ22 at 30°C, pH 5 and 120 rpm during 48 hours. These findings demonstrate the ability of Yarrowia lipolytica to remove phenol and suggest its potential use in the field of bioremediation of phenolic compounds and their derivatives. [ABSTRACT FROM AUTHOR]

Branch canker diseases are important in forest ecosystems, causing economic and ecological losses. Members of Cytospora are common on cankered branches and associated with the diseases. Investigations on Cytospora cankers were conducted in Tibet, China, during 2022 and 2023. Samples were collected from Euonymus japonicus, Larix gmelinii, Malus pumila, M. spectabilis and Rosa omeiensis f. pteracantha, and cultures were obtained and identified by morphological features and molecular phylogeny of a combination of internal transcribed spacer region rDNA (ITS), the partial actin (act) region, RNA polymerase II second largest subunit (rpb2) gene, the translation elongation factor 1-alpha (tef1) gene and the partial beta-tubulin (tub2) gene. As a result, a new species is proposed herein named Cytospora lhasaensis and four known species are described for the first time from Tibet, viz. C. euonymina, C. gigaspora, C. mali and C. schulzeri. The current research enhances our understanding of the Cytospora species associated with woody host diseases in Tibet, China. [ABSTRACT FROM AUTHOR]

BACKGROUND AND OBJECTIVES: Soil is an essential abiotic component serving as a habitat for numerous organisms, including cellulolytic bacteria commonly found in mangrove ecosystems. This bacteria could produce active enzymes needed to improve environmental quality by accelerating the organic matter decomposition. The unique mangrove environment may contain new types of cellulolytic bacteria with new characteristics. Despite several mangrove areas being explored as sources of cellulolytic bacteria, there is currently unexplored data on its diversity in Aceh Province, Indonesia. Accordingly, it is necessary to analyze the molecular biological approach, namely the 16 svedberg ribosomal ribonucleic acid gene, to identify the diversity of cellulolytic bacteria and analyze the phylogenetic relationships between them. METHODS: Bacteria isolates were collected from mangrove soil at six research locations with three replications. A purposive sampling method was applied to determine the research location. Isolates from soil samples were streaked and purified in carboxymethyl cellulose as selective media for cellulolytic bacteria. Molecular identification adopted 16 svedberg ribosomal ribonucleic acid gene sequencing, and the sequencing data were matched with GenBank data. Phylogenetic analysis and genetic distance between species were evaluated using molecular evolutionary genetics analysis. FINDINGS: Thirteen isolates were sequenced, and nine species of cellulolytic bacteria dominated by the Bacillus genus were identified. These species exhibited an identity value of 97.77-100 percent when compared to data from GenBank, and B. velezensis was found to have a close relationship with B. amyloliquefaciens at a value of 0.002 percent. Interestingly, the non-rehabilitated mangrove areas had more bacterial species than the rehabilitated ones. Two Bacillus genus had different nucleotide bases, proving they were distinct species. CONCLUSION: Nine cellulolytic bacteria species were identified; the two closely interspecies genetic distance related were B. velezensis and B. amyloliquefaciens, whereas the farthest were Bacillus sp1. and Bacillus sp2. Small genetic distances of interspecies indicate a close relationship between species. In comparing the two sampling sites, the non-rehabilitated mangrove contains higher bacterial cellulolytic species than the rehabilitated and Bacillus-dominated site. The findings provide valuable insights into the diversity of cellulolytic bacteria in mangrove ecosystems. The abundance of bacterial species could serve as sources of cellulase enzymes with different characteristics, essential in an environmental aquatic management. [ABSTRACT FROM AUTHOR]

Beauveria bassiana (B. bassiana) is a significant entomopathogenic fungus (EPF) in agriculture as a sprayable biocontrol agent. It has the potential to be established as an endophyte (ENP) in various crops, resulting in beneficial effects for the host plants, including resistance to pest insects and increased growth and yield. However, it is not known whether a B. bassiana strain has such a favorable impact on the plant, since it is a common soil microorganism. Therefore, techniques that allow strain monitoring will be advantageous. To date, methods for detecting or monitoring a specific EPF strain after external application are scarce. In the present study, an in planta nested PCR technique was standardized to differentiate between three B. bassiana strains (GHA, PTG4, and BB37) established as endophytes in bean plants under laboratory conditions by detecting the insertion profile of four group I introns located in the 28S gene of B. bassiana ribosomal DNA. This technique recognized a distinct pattern of bands of different sizes for each strain, with a sensitivity of 1 pg per 10 ng of plant DNA. This molecular approach may be more effective monitoring B. bassiana strains after application to evaluate their significance on crops. [ABSTRACT FROM AUTHOR]

Around 300 different plant species are infected by the plant-parasitic reniform nematode (Rotylenchulus reniformis), including cotton. This is a devasting nematode with a preference for cotton; it is commonly found in Alabama farms and causes severe reduction in yields. Its first internal transcribed spacer (ITS1) region can be sequenced, and potential mutations can be found in order to study the population dynamics of the reniform nematode. The goal of our study was to sequence the ITS1 rDNA region in male and female RNs that were collected from BelleMina, Hamilton, and Lamons locations in Alabama. After separating the single male and female RNs from the samples collected from the three selected listed sites above, the ITS1 region was amplified selectively using specific primers, and the resulting products were cloned and sequenced. Two distinct bands were observed after DNA amplification of male and female nematodes at 550 bp and 730 bp, respectively. The analysis of sequenced fragments among the three populations showed variation in average nucleotide frequencies of female and male RNs. Singletons within the female and male Hamilton populations ranged from 7.8% to 10%, and the variable sites ranged from 13.4% to 26%. However, female and male BelleMina populations had singletons ranging from 7.1% to 19.7% and variable regions in the range of 13.9% to 49.3%. The female and male Lamons populations had singletons ranging from 2.5% to 8.7% and variable regions in the range of 2.9% to 14.2%. Phylogenetic (neighbor-joining) analysis for the two ITS1 fragments (ITS-550 and ITS-730) showed relatively high intra-nematode variability. Different clone sequences from an individual nematode often had greater similarity with other nematodes than with their own sequences. RNA fold analysis of the ITS1 sequences revealed varied stem and loop structures, suggesting both conserved and variable regions in the variants identified from female and male RNs, thus underscoring the presence of significant intra- and inter-nematodal variation among RN populations in Alabama. [ABSTRACT FROM AUTHOR]

Food-borne zoonoses are of serious public health concern, with a high risk on human health in both developed and developing countries. Thus, this study aimed to determine the prevalence of zoonotic Anisakis larvae in smoked imported herring fish (Clupea harengus) and frozen mackerel (Scomber scomberus) from Assiut and Menoufia governorates, respectively in Egypt. All herring specimens were heavily infected with Anisakis larvae, while 9 out of 15 mackerel fish were infected. A total of 434 Anisakis larvae were collected from stomach, abdominal cavity, liver, between skin, muscles and gonads of 45 herring fish. In frozen mackerel, number of detected larvae was 78. Sequencing and phylogenetic analysis of internal transcribed spacer rDNA (ITS-rDNA) ribosomal DNA confirmed that the Anisakis larvae belonged to Anisakis simplex species. Furthermore, by employing light and scanning electron microscope, the morphological characters of Anisakis larvae were also determined. These findings highlight the importance of detecting health hazards in seafood products for helping in the management and prevention of anisakiasis. [ABSTRACT FROM AUTHOR]