Several members of the genus Peziza sensu stricto occur at the edge of melting snow. These nivicolous species have been widely reported in the Northern Hemisphere and are also known from Australia and New Zealand. We have used 16 specimens from North America and Australia to study morphology and to perform DNA sequencing. In sequence analyses, we have used ITS1 and ITS2 (internal transcribed spacers), 28S, RPB2 (RNA polymerase II gene), and two genes new to these studies, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and HSP90 (heat shock protein 90). Although not all regions are available for all samples, we have recognized the following species: Peziza heimii, P. nivalis, and P. nivis. Phylogenetic analyses were done using ITS alone; combined ITS1-5.8S-ITS2, 28S, and RPB2; ITS, and 28S, RPB2, GAPDH, and HSP90. Even with this augmented set of genes and despite their widespread occurrence in North America, Europe, Australia, and New Zealand, we have not definitively distinguished species within this group. To assess these results, pairwise homoplasy index (PHI) analysis was employed. This showed evidence of recombination among the samples of P. nivalis and further supports the view of P. nivalis as a monophyletic cosmopolitan species. As part of this study, we also examined the variation in ITS copies in P. echinospora, for which a genome is available.

The present study aims at clarifying the poorly known phylogenetic relationships and systematics of cestodes of the family Davaineidae Braun, 1900 (Cyclophyllidea), primarily the genus Raillietina Fuhrmann, 1920 and of the subfamily Inermicapsiferinae (Anoplocephalidae) from mammals (mostly rodents, 31 new isolates) and birds (eight new isolates). Phylogenetic analyses are based on sequences of the large subunit ribosomal RNA gene (28S) and mitochondrial NADH dehydrogenase subunit 1 gene (nad1). The main phylogenetic pattern emerging from the present analysis is the presence of three independent lineages within the main clade of the subfamily Davaineinae, one of which is almost entirely confined to species from rodents and the other two show a mixture of species from birds and mammals. It is suggested that the major diversification of the main clade took place in birds, possibly in galliforms. The subsequent diversification included repeated host shifts from birds to mammals and to other birds, and from rodents to other mammals, showing that colonisation of new host lineages has been the main driver in the diversification of davaineine cestodes. It is also shown that all isolates of Inermicapsifer Janicki, 1910, mainly from rodents, form a monophyletic group positioned among Raillietina spp. in the \"rodent lineage\", indicating that the genus Inermicapsifer is a member of the family Davaineidae. This means that the subfamily Inermicapsiferinae and the family Inermicapsiferidae should be treated as synonyms of the Davaineidae, specifically the subfamily Davaineinae. Three additional genera generally included in the Inermicapsiferinae, i.e. Metacapsifer Spasskii, 1951, Pericapsifer Spasskii, 1951 and Thysanotaenia Beddard, 1911, are also assigned here to the Davaineidae (subfamily Davaineinae). Raillietina spp. were present in all three main lineages and appeared as multiple independent sublineages from bird and mammalian hosts, verifying the non-monophyly of the genus Raillietina and suggesting a presence of multiple new species and genera.

Lady Tankerville, a rare orchid species (Phaius tankervilleae (Banks ex L\'Hér.) Blume) in Vietnam, not only enhances the aesthetic value of the surroundings with its enchanting blooms but also holds high economic value (Aver\'janov & Averyanova, 2003). Investigating the necrosis symptom on the root system and declined Lady Tankerville in the market in Hai Duong province in Vietnam from 11/2020 to 12/2021, we discovered a substantial infestation (24/24 plants were infected) of a spiral nematode, Helicotylenchus sp. The nematode population was extracted from the rhizosphere soil, roots, and stems of a single orchid using the modified Baermann tray technique (Whitehead & Hemming, 1965), for thorough characterization. The average nematode density was measured at 525±85 (350-670) nematodes/250 cm3 of soil, 202±56 (198-264) nematodes/15 g of roots, and 80±15 (72-95) nematodes/15 g of stem. Two hundred nematodes from the same population were inoculated into another healthy orchid for preservation and further infection tests. This species was morphologically identified as Helicotylenchus dihystera according to the key of Fotedar and Kaul (1985) and the description of Sher (1966). Morphometric measurements of the females (n = 12) are as follows: body length = 632-725 (681 ± 32) µm; a = 24-34 (28 ± 3); b = 5.1-7.2 (6.0 ± 0.6); b\' = 4.3-6.4 (5.3 ± 0.6); c = 33-46 (39 ± 5); c\' = 1.1-1.4 (1.2 ± 0.1); V = 62-78 (65 ± 4)%; O = 30 -49 (39 ± 6); stylet length = 21-26 (24 ± 2) µm; DGO = 9.2-12.4 (10.8 ± 1.1) µm. To validate morphological observations, molecular analyses of the ITS (Vrain et al., 1992) and the D2-D3 of 28S rRNA (Subbotin et al., 2006) were conducted. The ITS and D2-D3 sequences from this study (accession number: PP060444 and PP033748) exhibited the highest similarity of 99.8% and 100% to the sequence of H. dihystera in GenBank (KM506885 and MW023215), respectively. The infection test took place in a greenhouse at 28 ± 2℃. Three-month-old Phaius tankervilleae (n=8) were individually grown in 15 x 15 cm deep pots filled with sterilized sand and inoculated with 500 gravid females of H. dihystera (Rashid & Azad, 2013). Two noninoculated plants served as controls. After 60 days of inoculation, symptoms such as sunspots and root necrosis, observed in the market, appeared in the tested plants (Fig. S1). The presence and diagnosis of H. dihystera infestation in soil, roots, and stems across growth stages of orchids indicates the nematode to be an obligate parasite. The nematodes penetrate the roots, causing characteristic necrotic lesions initially yellow, then turn reddish-brown to black, along with brown root flecks in discolored tissues. Heavy infestations post-flowering led to extensive necrosis, distortion, and decay of the roots. The average reproduction factor (final population/initial population) of H. dihystera in this study was 22.2. Control plants remained symptom-free. Notably, 100% of tested plants were infected, highlighting the severe impact of H. dihystera. The nematodes were successfully reisolated and identified as H. dihystera through molecular analyses (accession number: PP060615 (ITS) and PP033748 (D2-D3)), reaffirming its identity. In addition to 32 host plants in Vietnam (Nguyen et al., 2023), our study reveals a strain of H. dihystera parasitizing Lady Tankerville orchids with a relatively high reproduction factor and infection rate. This marks the first reported instance of H. dihystera parasitizing Lady Tankerville orchids in Vietnam, emphasizing the need for proactive measures to protect this plant.

Food fraud is a problematic yet common phenomenon in the food industry. It impacts numerous sectors, including the market of edible mushrooms. Morel mushrooms are prized worldwide for their culinary and medicinal use. They represent a taxonomically complex group in which food fraud has already been reported. Among the methods to evaluate food fraud, some rely on comparisons of genetic sequences obtained from a sample to existing databases. However, the quality and usefulness of the results are limited by the type of comparison tool and the quality of the database used. The Centroid-based approach is applied by SmartGene in a proprietary artificial intelligence-based method for the generation of automatically curated reference databases that can be further expert curated. In this study, using sequences of the ribosomal internal transcribed spacer (ITS) of the genus Morchella (true morels), we compared this approach to the traditional pairwise alignment tool using two other databases: UNITE and Mycobank (MLST). The Centroid-based approach using an expert-curated database was more performant for the identification of 53 representative ITS sequences corresponding to validated species (83% accuracy, compared to 36% and 47% accuracy for UNITE and MLST, respectively). The Centroid method also revealed an inaccurate taxonomic annotation for sequences of commercial cultivars submitted to public databases. Combined with the web-based commercial software IDNS® available at Smartgene, the Centroid-based approach constitutes a valuable tool to ensure the quality of morel products on the market for actors of the food industry. PRACTICAL APPLICATION: The Centroid-based approach can be used by agri-food actors who need to identify true morels down to the species level without any prior taxonomical knowledge. These include routine laboratories of the food industry, food distributors, and public surveillance agencies. This is a reliable method that requires minimal skills and resources, therefore being particularly adapted for nonspecialists.

Trematodes of the genus Leucochloridium exhibit an unusual transmission strategy among mollusks (intermediate host). The fully developed sporocyst, housing encysted metacercariae, displays vivid coloration and rhythmic activity in the snail\'s tentacle, mimicking insect larvae. These strategies attract insectivorous birds, their final hosts, thereby increasing the chances of completing their life cycle. In South America, the reports of adults and larval stages of Leucochloridium are scarce. Brown-banded broodsac of Leucochloridium sp. were obtained from Omalonyx unguis collected in a shallow lake from Corrientes Province, Argentina. Here, we morphologically characterized the larval stages (broodsac and metacercaria), identified the parasite through DNA sequences from nuclear 28S-rRNA (28S) and the mitochondrial cytochrome c oxidase I (COI) genes, and explored its evolutionary affinities with the Leucochloridium species available in GenBank. The present broodsac displays brown bands, with a yellowish background in the first two-thirds and yellowish-white in the last third. Based on morphological comparisons, the broodsac and metacercaria described in this study could not be conclusively categorized under any known South American species of Leucochloridium. In relation to the phylogenetic reconstructions, Leucochloridium sp. consistently clustered with L. perturbatum, and species delimitation analyses resulted in recognized Leucochloridium sp. from Argentina as a distinct species. The DNA sequences obtained in this study constitute the first genetic data generated for sporocyst broodsacs in South America. Future studies, incorporating morphology, genetic, and biological data, will be essential for both species identification and the elucidation of leucochloridiid diversity in the region.

Here we describe a new species of the genus Saccocoelioides found parasitizing Astyanax dissimilis Garavello & Sampaio, Psalidodon bifasciatus (Garavello and Sampaio) and Bryconamericus ikaa Casciotta, Almirón & Azpelicueta from the Iguazu National Park, Misiones province, Argentina. Saccocoelioides miguelmontesi n. sp. was studied based on morphological and molecular (28S rDNA and COI mtDNA sequences) data. The COI mtDNA tree indicated that the specimens collected from the three fish hosts are conspecific, with an intragroup p-distance of 0%. The new species shows an intermediate morphological configuration between the diminutive and robust forms described for Saccocoelioides by Curran (2018). Although, in the 28S rDNA tree, it is placed in a well-supported clade with the two robust species analysed (S. elongatus and S. magnus; p-distance of 1 and 2%, respectively), it differs from the robust group by the range of body size, mature egg size, oral and ventral sucker size, sucker ratio, oral sucker to pharynx ratio, and post-cecal or post-testis/body length percentage. Our results led us to redefine the robust group as having eggs shorter or equal in length to the pharynx. Saccocoelioides miguelmontesi n. sp. the 10th species reported from Argentina and the 7th species within the robust group.

Xerampelinae is a subsection composed of species of ectomycorrhizal fungi belonging to the hyperdiverse and cosmopolitan genus Russula (Russulales). Species of Xerampelinae are recognized by their fishy or shrimp odor, browning context, and a green reaction to iron sulfate. However, species delimitation has traditionally relied on morphology and analysis of limited molecular data. Prior taxonomic work in Xerampelinae has led to the description of as many as 59 taxa in Europe and 19 in North America. Here we provide the first multilocus phylogeny of European and North American members based on two nrDNA loci and two protein-coding genes. The resulting phylogeny supports the recognition of 17 species-rank Xerampelinae clades; however, higher species richness (~23) is suggested by a more inclusive nuclear rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) analysis. Phylogenetic and morphological analyses support three new species with restricted geographic distributions: R. lapponica, R. neopascua, and R. olympiana. We confirm that the European species R. subrubens is present in North America and the North American species R. serissima (previously known as R. favrei) is present in Europe. Most other Xerampelinae appear restricted to either North America or Eurasia, which indicates a high degree of regional endemism; this includes R. xerampelina, a name widely applied to North American taxa, but a species restricted to Eurasia.

Abundant host and bacterial sequences can obscure the detection of less prevalent viruses in untargeted next-generation sequencing (NGS). Efficient removal of these non-targeted sequences is vital for accurate viral detection. This study presents a novel 28S ribosomal RNA (rRNA) RT-qPCR assay designed to assess the efficiency of avian rRNA depletion before conducting costly NGS for the detection of avian RNA viruses. The comprehensive evaluation of this 28S-test focuses on substituting DNase I with alternative DNases in our established depletion protocols and finetuning essential parameters for reliable host rRNA depletion. To validate the effectiveness of the 28S-test, we compared its performance with NGS results obtained from both Illumina and Nanopore sequencing platforms. This evaluation utilized swab samples from chickens infected with highly pathogenic avian influenza virus, subjected to established and modified depletion protocols. Both methods significantly reduced host rRNA levels, but using the alternative DNase had superior performance. Additionally, utilizing the 28S-test, we explored cost- and time-effective strategies, such as reduced probe concentrations and other alternative DNase usage, assessed the impact of filtration pre-treatment, and evaluated various experimental parameters to further optimize the depletion protocol. Our findings underscore the value of the 28S-test in optimizing depletion methods for advancing improvements in avian disease research through NGS.

Pratylenchus penetrans is one of the world\'s most common and destructive root-lesion nematodes and can parasitize more than 400 plant species. P. penetrans has been reported to cause serious damage to artichokes in several countries, such as Greece, Brazil, and France. Until now, there have been no reports of P. penetrans associated with artichokes in Vietnam. In this study, we recorded this species in artichoke fields in Lam Dong province, Vietnam with an average density of 50 nematodes/100g of soil (frequency of appearance at 64.7%). This nematode was associated with symptoms such as yellowing leaves, stunt, and root necrosis of artichokes in Vietnam, indicating its high damaging potential and a need for suitable control strategies. The identification of this species in our study was confirmed by morphology, morphometric data, and molecular characterization of 18S and 28S rRNA regions. Our study also provides the first molecular data of P. penetrans in Vietnam. The inclusion of molecular data for P. penetrans in Vietnam represents a significant contribution to the scientific community and a pivotal advancement in addressing nematode-related challenges in agriculture. This dataset serves as an invaluable reference for various molecular-focused endeavors, including but not limited to molecular identification, pathogenicity studies, and the development of effective management strategies.

The discoveries of new taxonomic features of digenean species through the application of contemporary techniques, such as scanning electron microscopy (SEM) and molecular analysis are still growing. Two species of trematodes Glossidium pedatum and Tylodelphys mashonensis from the intestine and vitreous humour of Clarias gariepinus were recovered from Lake Ol\'Bolossat, Kenya. The two endo-helminths were prepared for morphological examination using SEM and molecular characterisation. Additional morphological features were observed for G. pedatum such as domed papillae in the anterior extremity and a protruding cirrus which was unarmed, laterally folded and with a blunt tip as the first such observation for the genus and led to additional characteristics of the diagnosis of the genus. Tylodelphys mashonensis was characterised by a round oral sucker and tribocytic organ rounded with rows of papillae symmetrically arranged. The molecular analyses using ribosomal marker 28S large subunit (LSU) rDNA and mitochondrial (mtDNA) cytochrome c oxidase subunit 1 (cox1) for both G. pedatum and T. mashonensis confirmed the identity of the species and their phylogenetic relationship within the subclass Digenea. This study provides the first mitochondrial (mt)DNA sequence for G. pedatum and also extends the geographical record of two parasites to Kenya.