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The genus Phellodon (Thelephorales, Basidiomycota) in Europe: Four new species, one new combination, four new typifications and a first European record

Phellodon is a globally distributed genus of stipitate hydnoid fungi recognised by a white spore print and an ectomycorrhizal life strategy. In Europe, many Phellodon species have declining populations and are used as indicators of forests with high conservation values. However, their use in this context and the correct assessment of their extinction risk, according to IUCN guidelines, are currently hampered by inconsistent name usage and unclear species delimitations, primarily within the species complexes of P. melaleucus, P. niger and P. tomentosus. We analysed 286 ITS sequences of Phellodon, of which 51 were also analysed in conjunction with the corresponding LSU regions. This work included 102 newly sequenced collections, primarily sourced from Sweden and the UK. Our phylogenetic results show that four species are new to science and hence we formally describe P. castaneoleucus within the P. melaleucus morphological complex, P. aquiloniniger and P. frondosoniger within the P. niger complex and P. dititomentosus as a sister species to P. tomentosus. The combination P. melilotinus is made to accommodate an additional, previously described, species that belongs in the P. niger complex. We designate lectotypes and epitypes for P. melaleucus, P. niger and P. tomentosus as well as an epitype for P. melilotinus. Phellodon ellisianus is recorded as new to Europe and the ecological amplitude of P. secretus and P. violaceus is revealed to be wider than previously believed. We provide a key to all 13 species currently known in Europe and assign them to three habitat-based assemblages based on data from the Nordic countries and the UK. We hope this will facilitate the assessment of such habitats for legal protection and other conservation-related actions. Citation: Svantesson S, Larsson E, Larsson K-H, Parfitt D, Suz LM, Ainsworth AM (2025). The genus Phellodon (Thelephorales, Basidiomycota) in Europe: Four new species, one new combination, four new typifications and a first European record. Fungal Systematics and Evolution 15: 1-45. doi: 10.3114/fuse.2025.15.01.

Avian metapneumovirus subtype B in a Northern shoveler (Spatula clypeata) wintering in Italy: implications for the domestic-wild bird interface?

Avian metapneumovirus (aMPV) is an important pathogen in poultry, primarily affecting chickens and turkeys, and it causes acute respiratory disease or reproductive disorders. Considering previous molecular or serological evidence of aMPV in different wild bird species, the role of non-domestic hosts in the virus epidemiology has been called into question. A molecular survey was therefore performed on wild aquatic bird species sampled during the Italian Avian Influenza Surveillance plan from 2021-2023 in the Bologna province. A total of 250 oropharyngeal swabs were collected and screened for all circulating aMPV subtypes through multiplex real-time RT-PCR. An aMPV-B strain, named aMPV/B/Italy/Northern_shoveler/80/21, was detected in an adult Northern shoveler (Spatula clypeata) wintering in Italy in 2021, and it was characterized by partial amplification and sequencing of the attachment glycoprotein gene. Phylogenetic analysis showed close relationships between this strain and those circulating in Italian poultry from 2014-2019. Given the high aMPV-B burden on the Italian poultry sector and the similarity of aMPV/B/Italy/Northern_shoveler/80/21 strain to those circulating in chickens and turkeys, potential virus spillover from domestic to wild birds could have occurred at the livestock-wildlife interface. Considering that aMPV-B is well adapted to gallinaceans, this represents one of the rare molecular detections of this subtype in waterfowl species. Expanding aMPV monitoring and conducting further biological studies on wild hosts are essential for a better understanding of their role in maintaining aMPV circulation.RESEARCH HIGHLIGHTSWild birds sampled in Italy tested for aMPV detection and characterization.aMPV-B found for the first time in a wintering Northern shoveler.Close phylogenetic relationship with aMPV-B strains circulating in Italian poultry.

Freshwater fish community assessment using eDNA metabarcoding vs. capture-based methods: Differences in efficiency and resolution coupled to habitat and ecology

Environmental DNA (eDNA) metabarcoding has revolutionized ecological and environmental research by describing communities without relying on direct observations, making it a powerful, non-invasive, and cost-effective tool in biodiversity monitoring. However, the adoption of eDNA as a standard protocol in long-term monitoring programs, which have traditionally relied on capture-based methods, presents challenges in terms of data comparability. Here, we compared freshwater fish communities assessed through eDNA metabarcoding and electrofishing, across 35 sampling sites in the lower Tagus River basin, Portugal. For the majority of species or species-groups analysed individually (13 out of 17), a significant correspondence was observed between electrofishing and eDNA metabarcoding detections. A weaker correspondence was found between the number of specimens captured by electrofishing with the number of eDNA metabarcoding reads, with seven out of 13 taxa showing significant relationships. Species richness estimates based on the two methods were very similar at the basin level. The methods yielded significantly different species compositions, although these differences were driven by samples collected in the Tagus main channel, which is wider and has higher flow rates than tributaries. Benthic and shoreline fish communities showed similar species composition in the two methods, but this was not the case for pelagic communities, probably due to the higher water turnover of the pelagic zone and electrofishing inefficiency. Our results highlight the high potential of eDNA metabarcoding as a complementary method to electrofishing for freshwater fish monitoring, though further validation is needed to assess biases related to site-specific hydrological conditions and the ecology of the target species.

Revisiting the emergence of the Chikungunya virus in Alagoas, Northeast of Brazil

Chikungunya virus (CHIKV), an Alphavirus, emerged in the Americas in 2013 and was first documented in Brazil in September 2014, in the states of Pará and Bahia. Although Alagoas state officially reported its first case in late 2015, this study investigated potential earlier unreported cases by analyzing samples from a 2013-2014 Orthoflavivirus serological survey. We screened sera from patients with acute febrile illness, initially suspected of dengue but negative in molecular tests for the genus Orthoflavivirus, using ELISA (IgM/IgG), viral isolation, PCR, and next-generation sequencing. Two samples collected in June and August 2014 tested positive for anti-CHIKV IgM, and four additional samples collected between June and September 2014 tested positive for anti-CHIKV IgG antibodies. From one sample IgM-positive (630H) collected in August 2014, we isolated and sequenced a nearly complete genome (95.53% coverage, 2714× depth) classified as the East-Central-South-African (ECSA) genotype. Phylogenetic analyses revealed that the Alagoas-2014 genome formed a distinct, well-supported clade separate from the Bahia 2014 lineage. Temporal inference dated this lineage's origin to October 2013 (90% CI: April 2013-March 2014), suggesting a new introduction of ECSA into Alagoas. This genomic evidence, along with serological data, confirms the undetected early circulation of CHIKV in Alagoas and suggests a possible introduction of ECSA in Brazil in 2014, distinct from the well-documented introduction in Bahia.

Horizontal transmission of functionally diverse transposons is a major source of new introns

Since the discovery of spliceosomal introns in eukaryotic genomes, the proximate molecular and evolutionary processes that generate new introns have remained a critical mystery. Specialized transposable elements (TEs), introners, are thought to be one of the major drivers of intron gain in diverse eukaryotes. However, the molecular mechanism(s) and evolutionary processes driving introner propagation within and between lineages remain elusive. Here, we analyze 8,716 genomes, revealing 1,093 introner families in 201 species spanning 1.7 billion years of evolution. Introners are derived from functionally diverse TEs including families of terminal-inverted-repeat DNA TEs, retrotransposons, cryptons, and helitrons as well as mobile elements with unknown molecular mechanisms. We identify eight cases where introners recently transferred between divergent host species and show that giant viruses that integrate into genomes may facilitate introner transfer across lineages. We propose that ongoing intron gain is primarily a consequence of TE activity in eukaryotes, thereby resolving a key mystery of genome structure evolution.

Phylogenetic relationships and the identification of allopolyploidy in circumpolar Silene sect. Physolychnis

PREMISE

Species complexes are groups of closely related species with ambiguous delimitation, often composed of recently diverged lineages. Polyploidization and uniparental reproduction (i.e., selfing and apomixis) can play important roles in the origin of species complexes. These complexes pose challenges for species-based scientific questions, such as the estimation of species richness or conservation prioritization.

METHODS

We determined the potential of resolving taxonomically complex groups using target enrichment in the circumpolar Silene uralensis complex (Caryophyllaceae). We proposed a metric using genetic distances between phased alleles to distinguish diploids from allopolyploids.

RESULTS

Our results identified geographic structure of populations, with the northern American and Greenlandic samples having a common ancestor. We found little phylogenetic support for the most recent taxonomic treatment of the Silene uralensis complex.

CONCLUSIONS

The study highlights the use of target enrichment in testing taxonomic hypotheses in diploids and the challenges of studying recently diverged lineages.

Comparative proteomics of biofilm development in Pseudoalteromonas tunicata discovers a distinct family of Ca2+-dependent adhesins

The marine bacterium, Pseudoalteromonas tunicata, is a useful model for studying biofilm development due to its ability to colonize and form biofilms on a variety of marine and eukaryotic host-associated surfaces. However, the pathways responsible for P. tunicata biofilm formation are not fully understood, in part due to a lack of functional information for a large proportion of its proteome. We used comparative shotgun proteomics to explore P. tunicata biofilm development from the planktonic phase throughout early, middle, and late biofilm stages. A total of 248 biofilm-associated proteins were identified, including many hypothetical proteins, as well as previously known P. tunicata biofilm-related proteins, such as the autocidal enzyme AlpP, violacein proteins, S-layer protein SLR4, and various pili proteins. We further investigated the top identified biofilm-associated protein, a previously uncharacterized 1,600-amino acid protein (EAR30327), which we designate as "BapP." Based on AlphaFold modeling and genomic context analysis, we predicted BapP as a distinct Ca2+-dependent biofilm adhesin. Consistent with this prediction, a ΔbapP knockout mutant was defective in forming both pellicle- and surface-associated biofilms and rescued by re-insertion of bapP into the genome. Similar to the mechanisms of RTX Bap-like adhesins, BapP-mediated biofilm formation was influenced by Ca2+ levels, and BapP is potentially exported by a Type 1 secretion system. Ultimately, our work not only provides a useful proteomic data set for studying biofilm development in an ecologically relevant organism but also adds to our knowledge of bacterial adhesin diversity, emphasizing Bap-like proteins as widespread determinants of biofilm formation in bacteria.

IMPORTANCE

Understanding how bacteria form biofilms is essential because biofilms play a crucial role in bacterial survival and interaction with their environments. The marine bacterium Pseudoalteromonas tunicata is a valuable model for studying biofilm formation, as it colonizes diverse marine surfaces and host organisms. By identifying proteins involved in biofilm development, our study sheds light on the specific proteins that help P. tunicata transition from a free-swimming state to a stable biofilm. This work highlights the role of a large, calcium-dependent protein, BapP, which we found to be essential for biofilm stability and structure. This protein and hundreds of others identified provide new insights into bacterial adhesion mechanisms, expanding our understanding of biofilm formation in marine environments and potentially informing broader studies on biofilm-related processes in other bacteria.

Caspase Domain Duplication During the Evolution of Caspase-16

Caspases are cysteine-dependent aspartate-directed proteases which have critical functions in programmed cell death and inflammation. Their catalytic activity depends on a catalytic dyad of cysteine and histidine within a characteristic protein fold, the so-called caspase domain. Here, we investigated the evolution of caspase-16 (CASP16), an enigmatic member of the caspase family, for which only a partial human gene had been reported previously. The presence of CASP16 orthologs in placental mammals, marsupials and monotremes suggests that caspase-16 originated prior to the divergence of the main phylogenetic clades of mammals. Caspase-16 proteins of various species contain a carboxy-terminal caspase domain and an amino-terminal prodomain predicted to fold into a caspase domain-like structure, which is a unique feature among caspases known so far. Comparative sequence analysis indicates that the prodomain of caspase-16 has evolved by the duplication of exons encoding the caspase domain, whereby the catalytic site was lost in the amino-terminal domain and conserved in the carboxy-terminal domain of caspase-16. The murine and human orthologs of CASP16 contain frameshift mutations and therefore represent pseudogenes (CASP16P). CASP16 of the chimpanzee displays more than 98% nucleotide sequence identity with the human CASP16P gene but, like CASP16 genes of other primates, has an intact protein coding sequence. We conclude that caspase-16 structurally differs from other mammalian caspases, and the pseudogenization of CASP16 distinguishes humans from their phylogenetically closest relatives.

Two new species of Neohelicosporium (Tubeufiaceae, Tubeufiales) from freshwater and terrestrial habitats in China

Neohelicosporium species are a group of helicosporous hyphomycetes with the potential to produce novel bioactive natural compounds. During our investigation on helicosporous hyphomycetes, six isolates were collected from freshwater and terrestrial habitats in the tropical and subtropical regions of southern China. Based on multi-gene phylogenetic analyses (LSU-ITS-tef1-α-rpb2) and morphological comparisons of Neohelicosporium taxa, two new species (N.guizhouense and N.wuzhishanense) are introduced. Detailed micro-morphological descriptions, illustrations, and DNA molecular data are provided for the newly introduced species to confirm their taxonomic placements.

Cytauxzoon paradoxurus n. sp., a novel Cytauxzoon species identified in common palm civets in Singapore

BACKGROUND

The common palm civet (Paradoxurus musangus) is a species native to Southeast Asia. Highly adapted to urbanised environments, these civets can often be found in proximity to humans and companion animals, raising the concern of pathogen transmission at the human-wildlife and wildlife-domestic animal interface. Whilst there have been reports of various bacteria and viruses detected in civets, little is known about the protozoa that they may harbour. In this study, we screened the common palm civets in Singapore for tick-borne protozoan parasites known as piroplasms.

METHODS

Over a 2-year period, blood samples were opportunistically collected from 135 wild common palm civets following a physical examination. The sex and weight of each civet were recorded, and any ectoparasites detected were identified through DNA barcoding. DNA extracts of blood samples were screened using a PCR assay targeting the 18S rRNA gene of piroplasmids.

RESULTS

A novel Cytauxzoon species was detected in 29 civets (21.5%), and a statistically significant association was found between infection and the civet's weight. Two cat flea (Ctenocephalides felis) specimens were discovered on two sampled civets; however, Cytauxzoon DNA was not detected in either the flea or the sampled civet. Phylogenetic analysis of the Cytauxzoon 18S rRNA gene sequences from 29 civets revealed that this piroplasmid is most closely related to a Cytauxzoon sp. detected in meerkats in South Africa but molecularly distinct from the six currently described Cytauxzoon species.

CONCLUSIONS

This detection documents the first molecular confirmation of Cytauxzoon sp. infection in Southeast Asia and the first report of Cytauxzoon sp. in a viverrid host. Further studies are required to determine the vector involved in the transmission of this novel Cytauxzoon species, as no ticks were found on the sampled civets. The discovery of Cytauxzoon paradoxurus n. sp. highlights the importance of expanded biosurveillance to better understand the diversity of piroplasms harboured by wildlife in the region and its potential for cross-species transmission.

Revealing the Taxonomic Profile of a Wild Edible Mushroom From Tribal Cuisine and Its Pharmacological Significance

The historical use of wild mushrooms as food and medicine has been documented in several countries, including India. The Indian macrofungal flora consists of a diverse range of distinct species that have long been valued by various tribal groups for their medicinal and culinary qualities. During the process of documenting indigenous mushroom species, one unique edible Russula sp. was collected from the Pinus-dominated forest of the East Khasi Hills district of Meghalaya. Following a thorough assessment of the morphological traits and molecular phylogenetic analysis, this distinct species has been identified as Russula pseudojaponica, a new record from India. In order to investigate its therapeutic potential, a methanolic fraction was prepared and characterized for myco-chemicals. A substantial quantity of different secondary metabolites like carotenoids, ascorbic acid, and phenolics has been detected. The methanolic fraction also had notable antioxidant activity, displaying strong capabilities in scavenging DPPH and ABTS radicals, possessing high reducing power, and chelating capacity. In addition, the extract demonstrated the capacity to hinder the growth of Listeria monocytogenes, Bacillus subtilis, Pseudomonas aeruginosa, Escherichia coli, Salmonella typhi, and Staphylococcus aureus, as seen in the broth microdilution experiment. Furthermore, it induced morphological changes in bacterial cells, which were seen by scanning electron microscopy. Moreover, the extract demonstrated the ability to inhibit the proliferation, clonogenicity, and migratory potential of lung carcinoma cells, suggesting its potential as an anticancer agent. The extract successfully arrested the cell cycle progression in the S phase of cell division. Involvement of the intrinsic mitochondrial pathway of apoptosis was also observed after extract treatment. Hence, based on the findings of this study, this exceptional fungus has the capacity to function as an organic reservoir for the creation of novel medications to counteract illnesses associated with oxidative stress, bacterial ailments, and cancer.

Distinct Molecular Epidemiology, Transmission Patterns, and Resistance Mutations of HIV-1 Subtypes A1, A6, and A7 in Bulgaria

By 2022, Bulgaria's National Reference Laboratory had confirmed 4024 HIV cases. We analyzed 132 pol gene sequences to characterize the molecular epidemiology of HIV-1 subtypes A1, A6, and A7 (2001-2022). A1 accounted for 50.0% (66/132) of cases, increasing after 2014, with peaks in 2019 and 2022. A6 comprised 48.5% (64/132), dominating from 2005 to 2014 before stabilizing. A7 was rare (1.5%, 2/132), detected in 2003 and 2011. Transmission patterns varied: A1 was linked to men who have sex with men (MSM) (62.1%), while A6 was primarily heterosexual (HET) (82.8%) with a balanced gender distribution (56.3% male, 43.8% female). Resistance mutations were identified in 29.6% of cases, with A6 showing higher rates of nucleoside reverse transcriptase inhibitor (NRTI) (20.3%) and non-nucleoside reverse transcriptase inhibitor (NNRTI) (7.8%) resistance than A1. Phylogenetic analysis revealed that 13 Bulgarian sequences (9.8%) were involved in transmission clusters, including 10 (7.6%) from sub-subtype A1 and 3 (2.3%) from sub-subtype A6, highlighting distinct genetic diversity and transmission patterns. Despite significant migration from Ukraine in 2022, A6 prevalence remained unchanged, suggesting localized transmission dynamics. These findings highlight a shifting HIV-1 sub-subtype distribution in Bulgaria and emphasize the need for targeted prevention, diagnosis, and treatment strategies tailored to the evolving molecular landscape.

Morphology and phylogeny of the centrohelid heliozoans Raphidocystidae and their ability to consume cyanobacteria

The centrohelid family Raphidocystidae is a large group of heliozoans whose morphology and biology are poorly understood and whose taxonomy and phylogenetic relationships are currently confusing. Here, we report the results of a study of clonal cultures of raphidocystids belonging to the species Raphidocystis tubifera, R. ambigua, R. marginata and R. symmetrica. The cells were examined using light microscopy as well as scanning and transmission electron microscopy. New data on the morphology of the studied species were obtained and compared with other representatives of Raphidocystidae. For the first time, R. ambigua and R. symmetrica are reported for Kazakhstan and China, respectively. Cases of taxonomic confusion within Raphidocystidae have been detected and discussed. Molecular phylogenetic analyses based on 18S rRNA sequences clarified the relationships within raphidocystids and confirmed that scales with smooth surfaces are apparently characteristic of the common ancestor of all Raphidocystidae, and scales with a reticular structure were acquired evolutionarily later. Cysts within the Raphidocystidae species were apparently a later evolutionary acquisition. The ability of centrohelid heliozoans to consume cells of toxic and nontoxic cyanobacteria, which cause the most dangerous harmful algal blooms, has been demonstrated for the first time.

Free-living clinging flatworms (Rhabditophora, Polycladida) associated with Sargassum from the Caribbean Coast of Colombia

Background

Polyclads are a diverse group of marine free-living flatworms, with some species adapted to life in floating Sargassum mats. Recent studies suggest that, rather than being inherently pelagic, these flatworms should be classified as "clinging fauna", as they rely on floating substrates for habitat.

New information

This study documents, for the first time, the occurrence of Gnesiocerossargassicola and Chatziplanagrubei in Sargassum along the Caribbean coast of Colombia. High-definition photographs of whole mounts and histological sections are provided for both species, along with detailed observations of their reproductive structures and 28S rDNA barcodes. These findings underscore the importance of exploring the fauna associated with Sargassum, contributing to a better understanding of polyclad distribution and raising the number of recorded species for Colombia to 26.

Ortholinea paraensis n. sp. (Myxosporea: Ortholineidae) infecting the urinary bladder of Ageneiosus ucayalensis Castelnau, 1855 (Siluriformes: Auchenipteridae) in the Amazon region of Brazil

The present study describes a new parasite species of the myxozoan genus Ortholinea, based on the interpretation of morphological and molecular parameters. This species was found infecting the urinary bladder of the driftwood catfish Ageneiosus ucayalensis, captured in the region of Santo Antônio and Guajará bays, in the Amazonian state of Pará, Brazil. Plasmodia and myxospores were observed in pairs in the urinary bladder, either floating freely or adhered to the mucosa. The myxospores are spherical in the frontal view and valvular, with two equal, sub-spherical polar capsules, oriented divergently, containing 6-7 coils of the polar tubule. Scanning electron microscopy revealed ridges on the surface of the spore, which confer it with the appearance of a ball of wool, covering the entire surface of the valve, a slightly undulating suture line, and the presence of discharge pores for the polar tubule on opposite sides of the suture, that permit the extrusion of the polar tubule. The new species presents morphological characteristics typical of the genus Ortholinea. In the phylogenetic analysis, Ortholinea paraensis n. sp. occupied a basal position within a clade of species from the Amazon region. The sum of the morphological and molecular evidence clearly supports the description of a new species, denominated Ortholinea paraensis n. sp., which is the first Ortholinea species reported from Brazil.

Genetic diversity, virulence genes, antimicrobial resistance genes, and antimicrobial susceptibility of group B Streptococcus (GBS) associated with mass mortalities of cultured Nile tilapia in Brazil

Streptococcus agalactiae, group B Streptococcus (GBS), stands as the primary bacterial pathogen affecting cultured Nile tilapia (Oreochromis niloticus) globally, leading to significant mortalities throughout the farming cycle. This study investigated the genetic diversity, virulence and antibiotic resistance (AMR) genes presence, and antimicrobial susceptibility of 72 GBS strains associated with mass mortalities of Nile tilapia in Brazil. Isolate identity was confirmed by morphological, biochemical and molecular analyses. Capsular serotype, multi-locus sequence typing (MLST) allelic profiles and putative pathogenic factors were determined through polymerase chain reaction (PCR), gel electrophoresis, DNA sequencing and molecular analyses. The presence of AMR genes and antimicrobial susceptibility to florfenicol (FFC), oxytetracycline (OTC), thiamphenicol (TAP) and their combination were evaluated by PCR, followed by gel electrophoresis, and broth microdilution antimicrobial susceptibility testing, respectively. All clinical isolates studied were confirmed to be GBS, one from serotype III (IA2201) and 71 from serotype Ib, suggesting that serotype Ib was the most prevalent strain between 2011 and 2016 in the southern region of Brazil. Eight different allelic profiles were identified for the first time, with adhP-52, pheS-2, atr-31, glnA-4, sdhA-2, tkt-19 being the most predominant. Between one (glcK) and three (adhP and glnA) alleles were present at each locus. All strains, except IA2201, were negative for the glcK gene. Hyaluronate lyase (hlyB) and the GBS immunogenic bacterial adhesin A (bibA) were detected in all strains, except for 18P, which was negative for hlyB. On the other hand, α and β antigens of the C protein were only detected in IA2201. All antimicrobials showed high minimum inhibitory concentration (MIC ≥ 16 μg/mL) values against several strains with negative results for resistance genes. The combination involving OTC and TAP or FFC is a likely candidate for improving the treatment of streptococcosis caused by GBS using combination therapy, even for strains showing phenotypic and genotypic resistance to OTC. This study provides important data on pathogenic GBS genetic diversity, the presence of virulence and antimicrobial resistance genes and antimicrobial susceptibility, which may be useful in the development of effective vaccines and therapeutic strategies for the prevention and control of streptococcosis in aquaculture farms.

Ixodes inopinatus infesting cattle in high plateaus areas from North-Eastern Algeria: Sympatric occurrence with Ixodes ricinus, comments on its geographic distribution, and detection of Rickettsia spp

Ixodes ricinus and Ixodes inopinatus are closely related sister taxa which show high morphological similarity resulting in challenges to proper species determination. It is unclear how these two species are geographically distributed in areas where both species could occur (i.e., North Africa) and what this could mean towards potential pathogenic microorganisms. Here we report on Ixodes ticks (n = 31) collected from cattle in high plateau areas (Guelma province) of north-eastern Algeria. Three Ixodes species (I. ricinus, n = 10; I. inopinatus, n = 19; I. ventalloi, n = 2) were identified morphological and confirmed molecularly through analysis of the trospa gene sequence. Clear morphological markers between the three species were found in line with the original descriptions, although molecular analysis did not support morphological identification for all I. ricinus and I. inopinatus ticks (n = 7). With this we found no significant association between the molecular and morphological identification of I. inopinatus (phi coefficient of rϕ = 0.088, p = 0.71). Taking molecular identification as a standard, a literature search was performed to determine the geographic extent of I. inopinatus and associate this with Köppen and Geiger climate classifications. Geographically, I. inopinatus is likely restricted to the western Mediterranean Basin of North Africa and Europe and most likely adapted to the Mediterranean climate (Csa). The three investigated tick species were tested to be positive for DNA of Rickettsia helvetica and Rickettsia monacensis. This study confirmed the sympatric presence of I. inopinatus and I. ricinus as well as reported, for the first time, the occurrence of I. ventalloi in the high plateaus from north-eastern Algeria. In addition, the present study highlights the detection of R. helvetica and R. monacensis in I. inopinatus infesting cattle, which represent valuable findings of significant epidemiological interest, opening potential questions on the influence I. inopinatus could play in relation to rickettsioses in cattle.

A New Paramoeba Isolate From Florida Exhibits a Microtubule-Bound Endosymbiont Closely Associated With the Host Nucleus

The genera Paramoeba and Neoparamoeba, within the family Paramoebidae (order Dactylopodida), are distinguished by their dactylopodial pseudopodia and the presence of an intracellular eukaryotic symbiont, the Perkinsela-like organism (PLO). Taxonomic classification within these genera has been challenging due to overlapping morphological traits and close phylogenetic relationships. They are marine, with some playing significant roles as parasites. Notably, they have been implicated in sea urchin mass mortality events and are known causative agents of Amoebic Gill Disease (AGD) in fish. Despite their ecological and economic importance, many aspects of their diversity, biology, evolution, and host interactions remain poorly understood. In this study, we describe a novel amoeba species, Paramoeba daytoni n. sp., isolated from Daytona Beach, Florida. Morphological and molecular analyses confirm its placement within the Paramoeba clade, closely related to P. eilhardi, P. karteshi, and P. aparasomata. Phylogenetic assessments using 18S rDNA (18S) and Cytochrome c Oxidase I (COI) markers demonstrate the limitations of the 18S gene for species delineation, highlighting COI as a more reliable genetic marker for this group. Additionally, observations on PLO morphology, movement, and microtubule association provide insights into the endosymbiotic relationship, reinforcing the need for further research into this unique eukaryote-eukaryote symbiosis.

Mango Microcosm: Unveiling the species diversity and pathogenic potential of fungi isolated from mango (Mangifera indica) in northern Thailand

This study aimed to identify fungal pathogens responsible for diseases affecting mango orchards and fruits in the primary mango-growing regions of northern Thailand, and to evaluate their pathogenicity against mango. Mango leaves, branches, and fruits showing fruit and leaf anthracnose, leaf spots, fruit rot, stem-end rot, fruit decline, leaf and stem blight, and shoot dieback were collected and examined from Chiang Rai, Kalasin, Nan, and Sakon Nakhon provinces located in northern Thailand. The isolated fungi were identified based on morphological characteristics and multi-locus phylogenetic analysis based on the most reliable markers and loci combinations suggested for each genus. This study illustrates and describes nine pathogenic genera, including eight known genera and one new genus, Pseudopallidocercospora. Botryosphaeria fabicerciana, Botryosphaeria scharifii, Colletotrichum asianum, Colletotrichum gigasporum, Colletotrichum guajavae, Colletotrichum musae, Colletotrichum plurivorum, Colletotrichum siamense, Diaporthe rosae, Diaporthe siamensis, Diaporthe subellipicola, Neofusicoccum sinoeucalypti, Neopestalotiopsis chrysea, Neopestalotiopsis cubana, Neopestalotiopsis dendrobii, Neopestalotiopsis psidii, Neopestalotiopsis rhododendri, Neoscytalidium dimidiatum, Pestalotiopsis humicola and Pestalotiopsis menhaiensis were identified as known species. Five new species, including Neopestalotiopsis mangiferae, Neopestalotiopsis mangifericola, Neopestalotiopsis mangiferigena, Pseudopallidocercospora mangiferae, and Zasmidium mangiferae were fully illustrated and justified. Moreover, this study reports twelve globally new host-fungus occurrences and six new geographical records. Furthermore, pathogenicity assessment revealed that the majority of the isolates (91.6 %) were pathogenic against mango, while their virulence was significantly different. C. asianum was found to be the predominant pathogenic species with a frequency of 31.6 %. Haplotype networks generated using ITS sequence data for 220 C. asianum strains isolated from mango across 14 countries revealed eight haplotypes, indicating high genetic diversity (Hd = 0.5936) within the species. However, the analysis did not reveal a clear grouping of isolates based on their country of origin.

Diversity of tremellalean Pertusaria-associated fungi in Norway and the role of secondary metabolites in host specificity

The diversity and host relationships of lichen-inhabiting tremellalean fungi remain understudied, partly due to their asymptomatic yeast phase. This study employs ITS2 metabarcoding to investigate the diversity and colonization patterns of these fungi within 13 Pertusaria lichen species collected in Norway. We discovered a high prevalence, with tremellalean fungi present in 57 % of the examined specimens, representing 12 of the 13 species included, 10 of which were not previously recognized as hosts. Our findings suggest a broad host range for the presumed yeast phase of these fungi, though occurrences of the five most frequent OTUs appeared non-random across different host species. Additionally, negative-binomial general linear models indicated a negative correlation between the presence of tremellalean fungi and the occurrence of specific secondary metabolites, such as thiophaninic acid, fumarprotocetraric acid, and gyrophoric acid, in Pertusaria hosts. These results highlight previously undocumented genetic diversity within tremellalean fungi and suggest that host chemotype significantly influences colonization patterns. Our findings demonstrate a higher frequency of asymptomatic colonization than previously reported, emphasizing the need for further research into their ecological roles and interactions.

Investigation of the epidemiology of calicivirus infection of cats using molecular and virus isolation techniques

Feline calicivirus (FCV) an important and widely detected upper respiratory system agent in cats. Being genetically diverse, FCV can cause different symptoms, such as pneumonia, oral lesions, conjunctivitis, arthritis, and, recently, virulent systemic disease. The present study first determined the presence/prevalence of FCV infection in sampled vaccinated/unvaccinated cats with suspected FCV and/or clinically healthy. Second, it compared PCR and virus isolation (VI) in detecting FCV in these cats. It also aimed to diagnose FCV, and evaluate the advantages/disadvantages of the region and primers used for PCR. Third, it genetically characterized the FCV strains, targeting the VP1 (A-B and E) gene region. A total of 331 diagnostic materials (conjunctival, nasal, oropharyngeal swab samples, and EDTA-containing blood samples) were obtained from 107 cats and checked using PCR and VI. Including both tests, the overall FCV positivity rate was 43.93 % (47/107). The FCV positivity rate was 35.99 % (21/59)/53.33 % (24/45) in vaccinated/unvaccinated and 58.06 % (18/31)/38.16 % (29/76) in clinically infected/clinically healthy cats, respectively. As a result of direct nested RT-PCR, FCV positivity was detected in 23.08 % of oropharyngeal swabs, 15.24 % of nasal swabs and 14.02 % of conjunctival swabs based on diagnostic material. FCV was also detected in 19.63 % (21/107) of the cats after virus isolation. Those samples that were FCV positive for VP1 A-B and VP1 E were subjected to sequence and phylogenetic analysis. Regarding many of the detected viruses were similar to the viruses in Genogroup I, while two viruses (ANK111OSW and ANK113OSW) were phylogenetically similar to both Genogroup I and Genogroup II at the same rate (74.30 %). The findings indicate a, higher overall FCV detection rate than in previous studies in Türkiye. Molecular diagnostic methods are not always sufficient for diagnosing infection due to FCV's genetic diversity from mutation and, recombination. Hence, including VI techniques in FCV evaluation will help prevent false negative results. Furthermore, testing oropharyngeal, nasal and conjunctival swabs together for FCV is believed to provide more accurate results.

Sequencing and description of mitochondrial genome of Coquillettidia venezuelensis, Trichoprosopon digitatum and Uranotaenia calosomata (Diptera: Culicidae)

Mosquitoes constitute a monophyletic taxon with approximately 3,700 species, widely distributed across continents and recognized as primary vectors of various infectious agents. Despite their medical importance, limited information is available on the evolutionary biology and molecular taxonomy of many mosquito species. In this study, we report the complete mitochondrial genome sequences of Coquillettidia venezuelensis Theobald, 1912, Trichoprosopon digitatum Rondani, 1848, and Uranotaenia calosomata Dyar & Knab, 1907, collected from the Brazilian Amazon. Sequencing was performed using the NextSeq 500 platform, resulting in genomes averaging 15,329 bp in length, comprising 37 functional subunits (13 PCGs, 22 tRNA, and 2 rRNA) and an A+T-rich control region. Comparative analyses revealed conserved genome organization, codon usage bias favoring AT-rich codons, and evidence of purifying selection acting on PCGs. Notably, a unique tRNA gene rearrangement was identified in Tr. digitatum, supporting its association with the Sabethini tribe. Phylogenetic reconstruction using concatenated PCGs confirmed the monophyly of major mosquito lineages, corroborating current taxonomic classifications and previous molecular and morphological studies. Our findings enrich the genetic resources available for Culicidae, contributing to improved molecular taxonomy and evolutionary understanding of these taxa. Additionally, this study highlights the potential of using transcriptomic data to recover mitochondrial genomes, offering a valuable tool for future systematic and eco-epidemiological research. Integration of mitochondrial data with nuclear markers and expanded taxonomic sampling is recommended to enhance resolution of deeper phylogenetic relationships within Culicidae.

Neanderthal and Denisovan Glutamate Dehydrogenase 2 Evolution and Clinical Significance

Mammalian glutamate dehydrogenase (GDH) is an indispensable metabolic enzyme. GDH duplication has led to the presence of two paralogs, GDH1 and GDH2, in apes. Multiple GDH pseudogenes are also present in the human genome. The novel GDH2, supposed to be a target of positive selection, differs from GDH1 in regulation and is believed to be tightly linked to brain development. Although the differences of modern human GDH2 from GDH2 of other apes have been studied, the evolution of ancient human GDH2 remains a blank space. The goal of this work was to elucidate GDH2 evolution in the genus Homo using the accumulated data on the ancient genomes with high coverage-three Neanderthal and one Denisovan genome. Such analysis clarifies the difference between GDH2 of the last common ancestor of humans and chimpanzees and all Homo to be in M468L substitution, localized in the regulatory "antenna" region of the protein. A few novel missense mutations have been found in Denisovan and Altai Neanderthal GDH2, namely R76H, present in both genomes, and Denisovan-specific T154P, I358L, and S498A substitutions. Another mutation, R352K, has likely occurred independently in modern humans and later Neanderthals. The potential impact of these mutations was estimated using GDH2 structural data and evidence from contemporary medical data. All substitutions are supposed to be benign, with only the S498A GDH2 substitution connected to Parkinson's disease with late onset. Additionally, the ancient genomes were revealed to have all GDH pseudogenes present in modern humans, including the RNA-coding ones. The GLUD1P3 RNA expression was found to correlate negatively with GDH1 in human tissues. A possible regulatory role has been proposed, and the GLUD1P3 RNA sequence identity in all the studied human genomes suggests its conservation in the genus Homo.

Possible Involvement of Ghost Introgressions in the Striking Diversity of Vomeronasal Type 1 Receptor Genes in East African Cichlids

Cichlids that have undergone adaptive radiation are genetically close but exhibit extreme ecological and morphological diversity, making them useful for understanding speciation mechanisms. Vomeronasal type 1 receptors (V1R) are highly conserved among teleost fish at the amino acid sequence level and are believed to play a fundamental role in reproduction. We previously reported the surprisingly high sequence diversity of V1Rs among certain cichlid species, suggesting a possible role for V1Rs in their speciation. In this study, we investigated the process of evolutionary diversification of all 6 V1Rs (V1R1-6) by using the genome data of 528 cichlid species, encompassing nearly all lineages. In the case of V1R2, two highly divergent alleles (1.17%: variant sites/coding sequence [CDS] length) without recombination were preserved and shared among cichlids found in all of the East African Great Lakes. In the case of V1R6, numerous highly variable alleles that could be derived from multiple recombination events between two highly divergent alleles (1.39%: variant sites/CDS length) were found among the Lake Victoria cichlids. Additionally, we identified highly divergent alleles of V1R1 within the tribe Tropheini, and of both V1R3 and V1R6 within Trematocarini and Ectodini. However, despite extensive investigations, we could not identify the source lineages for these introgressions, implying that they may have become extinct. This study revealed the potential role of introgression in explaining the remarkable diversity of V1Rs in East African cichlids.

Strong bat predation and weak environmental constraints predict longer moth tails

Elaborate traits evolve via intense selective pressure, overpowering ecological constraints. Hindwing tails that thwart bat attack have repeatedly originated in moon moths (Saturniidae), with longer tails having greater anti-predator effect. Here, we take a macroevolutionary approach to evaluate the evolutionary balance between predation pressure and possible limiting environmental factors on tail elongation. To trace the evolution of tail length across time and space, we inferred a time-calibrated phylogeny of the entirely tailed moth group (Actias + Argema) and performed ancestral state reconstruction and biogeographical analyses. We generated metrics of predation via estimates of bat abundance from nearly 200 custom-built species distribution models and environmental metrics via estimates of bioclimatic variables associated with individual moth observations. To access community science data, we developed a novel method for measuring wing lengths from un-scaled photos. Integrating these data into phylogenetically informed mixed models, we find a positive association between bat predation pressure and moth tail length and body size, and a negative association between environmental factors and these morphological traits. Regions with more insectivorous bats and more consistent temperatures tend to host longer-tailed moths. Our study provides insight into tradeoffs between biotic selective pressures and abiotic constraints that shape elaborate traits across the tree of life.

The Pluteus leoninus clade in the Holarctic region: existing names evaluated and seven new species described

Pluteus leoninus is a commonly reported species, characterized by a yellow pileus, yellow colors on the stipe, pleurocystidia provided with digitiform excrescences, and a pileipellis composed of long, fusiform elements. Several species related to P. leoninus have been described from the temperate and boreal areas of the Northern Hemisphere, and previous phylogenetic studies have shown that more than one species can be recognized around P. leoninus, but it was unclear how many, or which names, would be correct for them. We studied 141 holarctic collections in the /leoninus clade and available type collections of species in this group. Taking into account the morphological, molecular (ITS, tef1), ecological, and geographic variation in our data set, we recognize 12 holarctic species, six in Eurasia (P. favrei, P. leoninus, P. roseipes, P. ochraceoleoninus, sp. nov. P. ussuriensis, sp. nov. P. variabilicolor) and six in North America (P. aureus, sp. nov. P. croceus, sp. nov. P. flavofuligineus, P. hesperius, sp. nov. P. insularis, sp. nov. P. pumae, sp. nov.). Tropical species included by Singer in stirps Leoninus are briefly discussed: P. chrysaegis, originally described from Srik Lanka, is confirmed to occur in North America (Florida, Puerto Rico); we provide the first modern description and molecular data for P. conizatus, originally described from Sri Lanka, which is confirmed to be part of Pluteus sect. Hispidoderma but does not belong in the /leoninus clade.

Congenital Aphakia Associated With a GJA8 Pathogenic Variant: A Case Report

Congenital aphakia is a rare eye condition in which the lens fails to form properly. It is typically caused by pathogenic variants within the FOXE3 or HCCS genes; however, it can also be associated with GJA8 pathogenic variants. GJA8 should be included in the genetic testing of patients with this condition.

Chronic Dengue Virus Encephalitis: A Case Study and Metagenomic Analysis

BACKGROUND AND OBJECTIVES

Dengue virus (DENV) infection can cause acute encephalitis. Chronic encephalitis with progressive dementia is rarely reported.

METHODS

We present a case of chronic encephalitis with rapidly progressive dementia, in which a potential DENV brain infection was identified with brain tissue metagenomic next-generation sequencing. Brain pathology and molecular diagnosis are also presented.

RESULTS

A 20-year-old man from SP, Brazil, presented with rapidly progressive dementia, speech apraxia, and apathy in June 2022. By January 2023, cognitive testing showed severe global impairment (MMSE score of 18/30). MRI revealed white matter abnormalities and atrophy; CSF analysis disclosed a mild lymphocytic pleocytosis, mildly elevated protein levels, and positive CSF oligoclonal bands. Despite extensive testing ruling out common infectious and inflammatory causes, the patient's condition worsened with executive dysfunction, language impairment, tremors, and myoclonus. In August 2023, a brain biopsy and next-generation sequencing identified DENV-1 genotype V, linked to Brazilian sequences from 2000 to 2022.

DISCUSSION

This case highlights a challenging instance of encephalitis with unknown etiology, where metagenomic analysis detected DENV-1 RNA in brain tissue, suggesting a possible cause.

Is the Gelatinous Matrix of Nassellaria (Radiolaria) a Strategy for Coping With Oligotrophy?

Radiolaria are heterotrophic protists abundant in the world's oceans, playing important roles in biogeochemical cycles. Some host photosynthetic algae, contributing to primary production. Such mixotrophic behaviour is believed to explain their success in oligotrophic waters, notably Collodaria, exclusively mixotrophic radiolarians within a gelatinous matrix. Yet, understanding of Radiolaria ecology is limited to direct observations, as they have so far withstood reproduction in culture and lack genome data. Sampling oligotrophic California Current revealed abundant, rarely observed Nassellaria of the genus Phlebarachnium, characterised to live within a gelatinous matrix. Phylogenetic reconstruction of ribosomal DNA suggests that distantly related Nassellaria lineages independently developed the ability to produce a gelatinous matrix ~150 million years ago. By matching physical samples with genetic data, we identified these rarely observed organisms in global datasets, revealing their affinity for oligotrophic conditions. Co-occurrence networks showed distinct biogeography patterns for gelatinous matrix-forming Radiolaria compared to those without. Results suggest the matrix might be an adaptation to oligotrophic waters, increasing the effective volume, favouring prey capture, and creating a larger microenvironment for symbionts, thus promoting ecological success in nutrient-depleted waters. This study advances our understanding of the adaptation of poorly known eukaryotic groups, specifically when evolution occurs independently across lineages.

Outbreak of Enterovirus D68 in Young Children, Brescia, Italy, August to November 2024

Enterovirus D68 (EV-D68) is responsible for a plethora of clinical manifestations ranging from asymptomatic infections to severe respiratory symptoms and neurological disorders. EV-D68 was first detected in children with pneumonia in 1962 and, from then, only sporadic cases were reported until 2014, when outbreaks were notified across the world. After the withdrawal of preventive measures against SARS-CoV-2, a significant increase in EV-D68 infections has been reported in 2021-2022. A surveillance program to evaluate the incidence of enterovirus/rhinovirus (EV/RV) infections was implemented at the Brescia Civic Hospital, Italy. Fifty-five EV/RV-positive respiratory samples, belonging to pediatric patients, were subjected to NGS. We observed that 61.8% of samples were positive for EV, with EV-D68 as the most prevalent genotype predominantly detected between August and November 2024. Phylogenetic analysis revealed that EV-D68 sequences formed two monophyletic clades corresponding to the A2 and B3 lineages, highlighting their recent introduction in Italy. Interestingly, 40% of pediatric EV-D68 infections were detected with at least one other EV/RV. Our study highlights the crucial role played by genomic surveillance of respiratory infections to monitor the circulation of emerging and re-emerging viruses, as well as their evolution. This will be fundamental to enable prompt intervention strategies.

Morpho-molecular analyses reveal two novel species and two new records of Dictyosporiaceae (Pleosporales) from Dulongjiang River in northwestern Yunnan Province, China

Yunnan Province is rich in freshwater resources, providing a favorable environment for freshwater fungi. As a result, numerous new species have been described in recent years, further supporting the extensive diversity of freshwater fungi in this region. During an investigation of lignicolous freshwater fungi from the Dulongjiang River, six fresh isolates of Dictyosporiaceae were obtained. The new collection includes two new species (Dictyocheirosporasplendida and Jalapriyaguttulata), two new records (D.nabanheensis and Dictyosporiumhughesii), and one known species (Dictyosporiumduliujiangense). They are introduced based on morphological evidence and molecular phylogenetic analysis of combined ITS, LSU, and tef1-α sequence data. Detailed descriptions and illustrations of these species are provided, and morphological comparison with similar taxa is discussed.

Comparative Phylogenetics Reveal Clade-specific Drivers of Recombination Rate Evolution Across Vertebrates

Meiotic recombination is an integral cellular process, required for the production of viable gametes. Recombination rate is a fundamental genomic parameter, modulating genomic responses to selection. Our increasingly detailed understanding of its molecular underpinnings raises the prospect that we can gain insight into trait divergence by examining the molecular evolution of recombination genes from a pathway perspective, as in mammals, where protein-coding changes in later stages of the recombination pathway are connected to divergence in intra-clade recombination rate. Here, we leverage increased availability of avian and teleost genomes to reconstruct the evolution of the recombination pathway across two additional vertebrate clades: birds, which have higher and more variable rates of recombination and similar divergence times to mammals, and teleost fish, which have much deeper divergence times. Rates of molecular evolution of recombination genes are highly correlated between vertebrate clades and significantly elevated compared to control panels, suggesting that they experience similar selective pressures. Avian recombination genes are significantly more likely to exhibit signatures of positive selection than other clades, unrestricted to later stages of the pathway. Signatures of positive selection in genes linked to recombination rate variation in mammalian populations and those with signatures of positive selection across the avian phylogeny are highly correlated. In contrast, teleost fish recombination genes have significantly less evidence of positive selection despite high intra-clade recombination rate variability. Gaining clade-specific understanding of patterns of variation in recombination genes can elucidate drivers of recombination rate and thus, factors influencing genetic diversity, selection efficacy, and species divergence.

A phylogenetic analysis of the CDKL protein family unravels its evolutionary history and supports the Drosophila model of CDKL5 deficiency disorder

The human CDK-like (CDKL) family of serine‒threonine kinases has five members (CDKL1-5), with a conserved N-terminal kinase domain and variable C-termini. Among these, CDKL5 is of particular interest because of its involvement in CDKL5 deficiency disorder (CDD), a rare epileptic encephalopathy with several comorbidities for which there are no specific treatments. Current CDD vertebrate models are seizure resistant, which could be explained by the genetic background, including leaky expression of other CDKLs. Thus, phylogenetic analysis of the protein family would be valuable for understanding current models and developing new ones. Our phylogenetic studies revealed that ancestral CDKLs were present in all major eukaryotic clades and had ciliary/flagellar functions, which may have diversified throughout evolution. The original CDKL, which was likely similar to human CDKL5, gave rise to the remaining family members through successive duplications. In addition, particular clades have undergone further gene duplication and loss, a pattern that suggests some functional redundancy among them. A separate study focusing on the C-terminal tail of CDKL5 suggested that this domain is only functionally relevant in jawed vertebrates. We have developed a model of CDD in Drosophila based on downregulation of the single Cdkl gene by RNAi, which results in phenotypes similar to those of CDD patients, that are rescued by re-expression of fly Cdkl and human CDKL5. CDKL proteins contain a conserved kinase domain, originally involved in ciliary maintenance; therefore, invertebrate model organisms can be used to investigate CDKL functions that involve the aforementioned domain.

Morphological and molecular analyses revealed four new wood-inhabiting fungal species (Hymenochaetales, Basidiomycota) from Yunnan

Hymenochaetales is one of the fungal orders mainly composed of wood-inhabiting macrofungi within the class Agaricomycetes, Basidiomycota. Four new Hymenochaetales wood-inhabiting fungi, Hymenochaetebannaensis, Lyomycesasiaticus, Peniophorellaalbohymenia, and P.punctata collected from China are proposed based on morphological characteristics and molecular evidence. H.bannaensis is distinguished by flocculent basidiomata with cinnamon to yellowish brown to rust-brown hymenial surface, generative hyphae with simple septa and broadly ellipsoid to globose basidiospores. L.asiaticus is characterized by the membranaceous basidiomata with white to cream hymenial surface with tuberculate, a monomitic hyphal system with clamped generative hyphae and ellipsoid basidiospores. In addition, P.albohymenia is delimited by membranaceous basidiomata with white hymenial surface, four types of cystidia as stephanocyst, fusiform, cylindrical and capitate, and ellipsoid basidiospores. P.punctata is unique in the membranaceous, punctate basidiomata with white to pale yellow hymenial surface, fusiform cystidia, and allantoid basidiospores. Sequences of ITS and nLSU rRNA markers based on phylogenetic analyses were performed using the Maximum Likelihood, Maximum Parsimony and Bayesian Inference methods.

Molecular Profile and Dynamics of Commensal Viruses in Brazilian Patients Who Underwent Allogeneic Hematopoietic Stem Cell Transplantation

BACKGROUND

Commensal viruses are typically well-tolerated by healthy individuals, but their behavior in immunocompromised patients is not fully understood.

METHODS

This study investigated the prevalence, molecular dynamics, and circulating genotypes of human pegivirus-1 (HPgV-1) and three types of torque teno viruses (TTV-3, -16, and -22) in Brazilian patients undergoing allogeneic hematopoietic stem cell transplantation (HSCT). Plasma samples from 20 patients were collected at three time points: pretransplantation (D+0), 30 days post-transplantation (D+30), and 100 days post-transplantation (D+100). We conducted longitudinal screening for HPgV-1 and three TTV variants using real-time PCR, comparing cycle threshold values across these intervals.

RESULTS

The overall HPgV-1 RNA prevalence at all collection points was 45% (n = 9/20), with all infected individuals carrying genotype 2. HPgV-1 infections exhibited stable, closely related strains over time, though virus evolution was highly individualized. The overall prevalence of TTV types was 5% for TTV-3, 30% for TTV-16, and 60% for TTV-22. Notably, all commensal viruses showed a decrease in cycle threshold at D+100, indicating a possible increase in viral load.

CONCLUSION

These findings underscore the importance of commensal viruses in the context of HSCT and suggest their potential role as biomarkers for immune suppression and transplantation outcomes. Further research is warranted to elucidate their implications.

Non-radiative origin for alpine endemics of Draba (Brassicaceae) in the central mountains of the Japanese Archipelago

Diversity of endemic species may result from two evolutionary processes: in-situ diversification (radiation) or phylogenetically independent divergences (non-radiation). To explore the evolutionary history of endemic-rich alpine flora in the Japanese Archipelago, we investigated the phylogenetic relationships of four endemic taxa of Draba (Brassicaceae) from the high mountains of central Honshu: D. kitadakensis, D. sachalinensis var. shinanomontana, D. sakuraii var. nipponica, and D. shiroumana. Using molecular phylogenetic analyses on plastid trnL-F and nuclear ITS sequence of 157 taxa, we found that the four taxa endemic to central Honshu did not form a monophyletic group and diverged from at least two evolutionary independent lineages. Moreover, ancestral area reconstruction further revealed that some of their ancestral species may have originated from different geographical regions. These findings indicate that the endemic Draba in central Honshu diverged through non-radiative evolutionary origin. Our study suggests that the richness of endemic species in the alpine zone of the Japanese Archipelago is associated with multiple sources with high species diversity located in nearby geographical regions.

Ancient Host-Virus Gene Transfer Hints at a Diverse Pre-LECA Virosphere

The details surrounding the early evolution of eukaryotes and their viruses are largely unknown. Several key enzymes involved in DNA synthesis and transcription are shared between eukaryotes and large DNA viruses in the phylum Nucleocytoviricota, but the evolutionary relationships between these genes remain unclear. In particular, previous studies of eukaryotic DNA and RNA polymerases often show deep-branching clades of eukaryotes and viruses indicative of ancient gene exchange. Here, we performed updated phylogenetic analysis of eukaryotic and viral family B DNA polymerases, multimeric RNA polymerases, and mRNA-capping enzymes to explore their evolutionary relationships. Our results show that viral enzymes form clades that are typically adjacent to eukaryotes, suggesting that they originate prior to the emergence of the Last Eukaryotic Common Ancestor (LECA). The machinery for viral DNA replication, transcription, and mRNA capping are all key processes needed for the maintenance of virus factories, which are complex structures formed by many nucleocytoviruses during infection, indicating that viruses capable of making these structures are ancient. These findings hint at a diverse and complex pre-LECA virosphere and indicate that large DNA viruses may encode proteins that are relics of extinct proto-eukaryotic lineages.

Characterization of the Giant Foxtail's (Setaria faberi) ALS Gene and Its Enhanced Metabolism-Based Cross-Resistance to Nicosulfuron and Rimsulfuron

BACKGROUND

Weed herbicide resistance is a serious problem in crop protection globally. Giant foxtail (Setaria faberi R.A.N. Herrm.) populations cannot be controlled by acetolactate synthase (ALS)-inhibiting herbicides in a few corn (Zea mays L.) monoculture fields.

METHODS

Five putative resistant giant foxtail populations, originating from corn monoculture fields in northeastern Greece, were evaluated for possible evolution of ALS-inhibitor resistance (nicosulfuron, rimsulfuron). The resistance ratio, the underlying resistance mechanism, and its impact on competitive ability against corn were studied.

RESULTS

The whole-plant rate-response assays showed that these populations were resistant (R) to the sulfonylureas nicosulfuron and rimsulfuron, but susceptible (S) to imidazolinone imazamox, triketone 4-hydroxyphenylpyruvate dioxygenase inhibitor tembotrione, and acetyl-CoA carboxylase inhibitor cycloxydim. The sequencing of the ALS gene did not reveal the presence of resistance-associated point mutations, indicating that the resistance was probably not target-site mediated. This was confirmed by the application of piperonyl butoxide two hours before nicosulfuron application, which reversed the resistance in all R giant foxtail populations, supporting the evidence of enhanced metabolism-mediated resistance. The competition study between corn and R or S giant foxtail populations indicated no stable trend reduction in corn traits, suggesting that the resistance mechanism was not associated with the competitive ability of the R populations. The novel ALS genotype in S. faberi, characterized for the first time and submitted to the GenBank database with accession number PV016837, indicated a closer genetic relationship with the S. viridis ALS gene than with S. italica.

CONCLUSIONS

Five giant foxtail populations have evolved metabolism-based resistance to the ALS-inhibiting herbicides nicosulfuron and rimsulfuron.

Theobroma cacao Virome: Exploring Public RNA-Seq Data for Viral Discovery and Surveillance

Cocoa (Theobroma cacao L.) is a major agricultural commodity, essential for the global chocolate industry and the livelihoods of millions of farmers. However, viral diseases pose a significant threat to cocoa production, with Badnavirus species causing severe losses in Africa. Despite its economic importance, the overall virome of T. cacao remains poorly characterized, limiting our understanding of viral diversity and potential disease interactions. This study aims to assess the cocoa-associated virome by analyzing 109 publicly available RNA-seq libraries from nine BioProjects, covering diverse conditions and geographic regions. We implemented a comprehensive bioinformatics pipeline integrating multiple viral sequence enrichment steps, a hybrid assembly strategy using different assemblers, and sequence similarity searches against NCBI non-redundant databases. Our approach identified ten putative novel viruses associated with the cocoa microbiome and a novel Badnavirus species. These findings provide new insights into the viral landscape of T. cacao, characterizing the diversity of cacao-associated viruses and their potential ecological roles. Expanding the catalog of viruses associated with cocoa plants not only enhances our understanding of plant-virus-microbiome interactions but also contributes to the development of more effective disease surveillance and management strategies, ultimately supporting sustainable cocoa production.

Collaborative metabolic curation of an emerging model marine bacterium, Alteromonas macleodii ATCC 27126

Inferring the metabolic capabilities of an organism from its genome is a challenging process, relying on computationally-derived or manually curated metabolic networks. Manual curation can correct mistakes in the draft network and add missing reactions based on the literature, but requires significant expertise and is often the bottleneck for high-quality metabolic reconstructions. Here, we present a synopsis of a community curation workshop for the model marine bacterium Alteromonas macleodii ATCC 27126 and its genome database in BioCyc, focusing on pathways for utilizing organic carbon and nitrogen sources. Due to the scarcity of biochemical information or gene knock-outs, the curation process relied primarily on published growth phenotypes and bioinformatic analyses, including comparisons with related Alteromonas strains. We report full pathways for the utilization of the algal polysaccharides alginate and pectin in contrast to inconclusive evidence for one-carbon metabolism and mixed acid fermentation, in accordance with the lack of growth on methanol and formate. Pathways for amino acid degradation are ubiquitous across Alteromonas macleodii strains, yet enzymes in the pathways for the degradation of threonine, tryptophan and tyrosine were not identified. Nucleotide degradation pathways are also partial in ATCC 27126. We postulate that demonstrated growth on nitrate as sole nitrogen source proceeds via a nitrate reductase pathway that is a hybrid of known pathways. Our evidence highlights the value of joint and interactive curation efforts, but also shows major knowledge gaps regarding Alteromonas metabolism. The manually-curated metabolic reconstruction is available as a "Tier-2" database on BioCyc.

Detectable episodic positive selection in the virion strand a-strain Maize streak virus genes may have a role in its host adaptation

Maize streak virus (MSV) has four genes: cp, encoding the coat protein; mp, the movement protein; and repA and rep, encoding two distinct replication-associated proteins from an alternatively spliced transcript. These genes play roles in encapsidation, movement, replication, and interactions with the external environment, making them prone to stimuli-driven molecular adaptation. We accomplished selection studies on publicly available curated, recombination-free, complete coding sequences for representative A-strain maize streak virus (MSV-A) cp and mp genes. We found evidence of gene-wide selection in these two MSV genes at specific sites within the genes (cp 1.23% and mp 0.99%). Positively selected sites have amino acids that are 60% hydrophilic and 40% hydrophobic in nature. We found significant evidence of positive selection at branches (cp: 0.76 and mp:1.66%) representing the diversity of MSV-A-strain in South Africa, which is related to the MSV-A-matA isolate (GenBank accession number: AF329881), well disseminated and adapted to the maize plant in sub-Saharan Africa. In the mp gene, selection significantly intensified for the overall diversities of the MSV-A sequences and those more related to the MSV-Mat-A isolate. These findings reveal that despite predominantly undergoing non-diversifying selection, the detectable diversifying positive selection observed in these genes may play a major role in MSV-A host adaptive evolution, ensuring sufficient pathogenicity for onward transmission without killing the host.

Higher Genotyping Performance of the Applied Biosystems TaqPath Seq HIV-1 Genotyping Kit Against ViroSeq HIV-1 Genotyping Kit in HIV Protease, Reverse Transcriptase, and Integrase Regions

Purpose

We assessed the performance of Applied Biosystems TaqPath Seq HIV-1 Genotyping Kit (CE-IVD) (TaqPath Kit) against the ViroSeq HIV-1 Genotyping Assays in genotyping HIV protease (PR), reverse transcriptase (RT), and integrase (INI) regions.

Methods

The study included 43 HIV-1 plasma specimens: 20 from people living with HIV-1C and 23 well-characterized HIV-positive Virology Quality Assurance (VQA) samples with PR-, RT-, and INI mutations. VQA samples included HIV-1 subtypes A, B, C, D, F, G, CRFO2_AG and URF. HIV-1 RNA extracted from all specimens was tested with both genotyping assays. Known HIV drug resistance mutations (DRMs) were identified using the Stanford HIV drug resistance database. Sequencing success rates, nucleotide identity, and DRMs from the two commercial assays were compared.

Results

Of 43 samples, TaqPath Kit amplified 93.0% (40) for HIV PR/RT and 97.7% (42) for HIV INI regions, compared to ViroSeq Assays, which amplified 69.8% (30) and 72.1% (31) for PR/RT and INI, respectively. The TaqPath Kit successfully sequenced 90.0% (36/40) PR/RT and 97.6% (41/42) INI amplicons, while ViroSeq Assays sequenced 53.3% (16/30) PR/RT and 87.1% (27/31) INI amplicons. The mean nucleotide similarity was 98.8% (SD ± 1.30), 99.6% (SD ± 1.32) and 99.2% (SD ± 0.72) for paired RT, PR and INI sequences, respectively. The TaqPath Kit detected 97.2% (35/36) of DRMs identified by the ViroSeq Assays and an additional 83 mutations and polymorphisms in samples that failed genotyping with the ViroSeq Assays. Among these, 85.5% (71/83) were confirmed by the reference sequence, including 39 major DRMs.

Conclusion

The TaqPath Kit demonstrated higher genotyping performance compared to the ViroSeq assays. The TaqPath Kit was able to detect DRMs in the PR, RT and INI regions of various HIV-1 subtypes, offering a critical tool to identify and monitor HIV drug resistance to new and existing antiretroviral drugs targeting these regions.

Population genetic structure and demographic history of Dermacentor marginatus Sulzer, 1776 in Anatolia

Dermacentor marginatus is a medically important tick species due to its preference humans and domestic animals as hosts and its vectorial competence, yet it remains understudied in many regions. This study aimed to examine the population structure and demographic history of D. marginatus using the cox1 and ITS2 genes, focusing on populations from Central and Northeast Anatolia-two regions on either side of the Anatolian Diagonal, a natural biogeographical barrier. A total of 361 host-seeking adult D. marginatus ticks from 31 sampling sites were analyzed, revealing 131 haplotypes for cox1 and 104 genotypes for ITS2. Neutrality tests and mismatch distribution patterns rejected the null hypothesis of the neutral theory, indicating that the population of D. marginatus in Anatolia has undergone a recent demographic expansion. Significant genetic differentiation and population structuring were observed between the Central and Northeastern Anatolian populations of D. marginatus, correlating with geographic distance and suggesting that the Anatolian Diagonal acts as a potential barrier to gene flow. Intrapopulation gene flow was higher in Central Anatolian populations compared to Northeastern Anatolian populations. Bayesian phylogeny revealed a highly divergent D. marginatus haplotype within the Northeastern Anatolian population, clustering into a Central Asian clade. Additionally, phylogenetic trees of the subgenus Serdjukovia revealed taxonomic ambiguities, including the absence of a distinct clade for D. niveus and potential misidentifications of D. marginatus and D. raskemensis specimens. Furthermore, the monophyletic relationship between D. marginatus and D. raskemensis supports the likelihood of sympatric speciation. These findings enhance our understanding of the genetic structure, phylogeography, and evolutionary dynamics of D. marginatus while providing a framework for future research on tick populations.

Ephemeral Speciation in a New Guinean Honeyeater Complex (Aves: Melidectes)

Speciation is a fundamental concept in evolutionary biology, and understanding the mechanisms driving speciation remains the foremost research topic within this field. Hybridisation is often involved in speciation and can influence its rates, potentially accelerating, decelerating or even reversing the process. This study investigates the evolutionary history of the New Guinean bird genus Melidectes, consisting of six species that inhabit various montane regions at different elevations. While most Melidectes species have allopatric distributions, two species overlap in the central mountain range and hybridise. However, plumage differences and elevational adaptations are assumed to maintain the species' boundaries. Utilising specimens from natural history collections and comprehensive genomic analyses, including a de novo genome assembly, we characterise allopatric speciation patterns within the genus and highlight how future speciation could potentially be driven by climate change. Contrary to previous hypotheses, our findings suggest that in the two distributionally overlapping species, phenotypic differences do not prevent gene flow. We find limited acoustic differentiation and extensive admixture across most of their distributions. Divergence and admixture levels conform poorly to the current taxonomy and follow a geographical pattern in which the most isolated populations at the ends of the distributions are most divergent and show least admixture. However, in contrast, their mitochondrial genomes do group in accordance with species identity, namely, into two deeply divergent lineages. We propose that this system demonstrates the ephemeral nature of speciation, in which two incipient species have started mixing extensively as they came into secondary contact, resulting in nearly complete fusion into a single lineage.

Molecular phylogeny and morphology reveal four novel species in Cordycipitaceae in China

Cordycipitaceae is a well-known family in Hypocreales, comprising numerous arthropod-pathogenic species. Many taxa in this family have been identified and described through integrated morphological and molecular analyses. In this study, phylogenetic analyses using nrLSU, ITS, nrSSU, 3P_TEF, rpb1, and rpb2 revealed a new species, Pleurodesmosporasanduensis, and a new collection of Akanthomycesbaishanensis. Additionally, a concatenated 5P_TEF+3P_TEF+rpb1+MCM7 dataset was employed to clarify interspecific relationships within Samsoniella, identifying three new species: Samsoniellalurida, S.subasiatica, and S.torquatistipitata. Detailed morphological descriptions and illustrations are provided for each studied species.

Validating a Target-Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals

In the last three decades, DNA sequencing of ancient animal osteological assemblages has become an important tool complementing standard archaeozoological approaches to reconstruct the history of animal domestication. However, osteological assemblages of key archaeological contexts are not always available or do not necessarily preserve enough ancient DNA for a cost-effective genetic analysis. Here, we develop an in-solution target-enrichment approach, based on 80-mer species-specific RNA probes (ranging from 306 to 1686 per species) to characterise (in single experiments) the mitochondrial genetic variation from eight domesticated animal species of major economic interest: cattle, chickens, dogs, donkeys, goats, horses, pigs and sheep. We also illustrate how our design can be adapted to enrich DNA library content and map the Y-chromosomal diversity within Equus caballus. By applying our target-enrichment assay to an extensive panel of ancient osteological remains, farm soil, and cave sediments spanning the last 43 kyrs, we demonstrate that minimal sequencing efforts are necessary to exhaust the DNA library complexity and to characterise mitogenomes to an average depth-of-coverage of 19.4 to 2003.7-fold. Our assay further retrieved horse mitogenome and Y-chromosome data from Late Pleistocene coprolites, as well as bona fide mitochondrial sequences from species that were not part of the probe design, such as bison and cave hyena. Our methodology will prove especially useful to minimise costs related to the genetic analyses of maternal and paternal lineages of a wide range of domesticated and wild animal species, and for mapping their diversity changes over space and time, including from environmental samples.

General features and evolution of mitochondrial genomes in Dictyostelia (Amoebozoa)

Dictyostelia exhibits high diversity; however, mitochondrial genome data remain scarce for many genera. Although key features of some dictyostelid mitogenomes have been identified, several aspects remain unclear, including core gene content, segmental arrangement, and differences between 18S rRNA and mitochondrial gene phylogenies. To address these gaps, we reconstructed two complete mitogenomes-from Cavenderia subdiscoidea and Dictyostelium sp. (TH18CC)-and analyzed mitochondrial genes from ten genera and six additional complete mitogenomes from public databases. A comparison of eight complete mitogenomes revealed a conserved core of 39 protein-coding genes, 17 tRNA genes, and three rRNA genes. Two distinct segmental arrangements were identified: Dictyostelium (except D. purpureum) exhibits an A-C-B pattern, while other genera display an A-B-C pattern defined by the clusters nad9-atp1, trnC(GCA)-atp9, and rnl-nad3. Phylogenetic analyses based on 18S rDNA and mitochondrial rns suggest the transposition between segments B and C occurred after D. purpureum diverged from other Dictyostelium species, potentially involving tRNA gene displacement. In contrast, the mitochondrial protein-coding gene phylogeny differs from the rRNA trees, indicating that these gene sets may have evolved independently. These findings advance our understanding of dictyostelid mitogenome structure and evolution.

The landscape of transposable element distribution in the genome of Neotropical fish Apareiodon sp. (Characiformes: Parodontidae)

Transposable elements (TEs) are widely present in eukaryotic genomes, where they can contribute to genome size and functional modifications. As new genomes are sequenced and annotated, more studies can be conducted regarding TE content, distribution, and genome evolution. TEs are extensively diversified in fish genomes resulting in an important role in genome and chromosome evolution. However, curated TE libraries are still scarce in non-model organisms, making it difficult to evaluate TE's impact on genomic modifications thoroughly. Here, we aimed to obtain a curated TE library from the neotropical fish Apareiodon sp. genome. The prospection and curation of the TE library resulted in 244 families from 18 superfamilies of DNA transposons and retrotransposons, which comprise about 10% of the genome, with most insertions fitting in one or a few families. A greater diversity of retrotransposon families is present, especially for Ty3 superfamily. Despite the greater number of retrotransposon families, DNA transposons are the most abundant in the genome, with 37% of all TE insertions belonging to the Tc1-Mariner superfamily. Complete TE copies were observed for almost all superfamilies, with most of the sequences on the Tc1-Mariner group. DNA transposons and SINEs presented older insertions in the genome, followed by LINEs and LTR retrotransposons. TE genome density is highest in the cs25 scaffold, and enriched for Helitron elements. With these data, allied to previous studies on chromosome evolution, we suggest that cs25 bears the W chromosome specific region of the Apareiodon sp. genome, with the presence of significant amount of Helitron insertions.

Critical taxonomic revision of Korean Dictyoteae describing three new species and honoring Haenyeo culture

This study re-evaluates the species diversity and taxonomy of the genera Canistrocarpus, Dictyota, and Rugulopteryx in Korea using an integrative approach combining molecular data and morphological observations. Phylogenetic analyses based on psbA, cox1, and rbcL gene sequences identified nine lineages including eight Dictyota and one Rugulopteryx. Morphological assessments corroborated these molecular findings. Of the seven species listed in recent national checklists, only two were confirmed, while the remaining species were misidentifications. Three novel species are described: Dictyota haenyeosa sp. nov., Dictyota sumbisoria sp. nov., and Dictyota taewakia sp. nov. Additionally, molecular evidence confirmed that the species historically identified as D. dichotoma in Korea corresponds to D. spathulata, a species described from Japan. This revision of Dictyota taxonomy highlights the importance of molecular tools in resolving long-standing misidentifications. The updated checklist for Korean Dictyota and Rugulopteryx includes D. bartayresiana, D. coriacea, D. haenyeosa sp. nov., D. pfaffii, D. spathulata, D. sumbisoria sp. nov., D. taewakia sp. nov., and R. okamurae. The genus Canistrocarpus is absent from the Korean flora. The Korean Dictyota and Rugulopteryx flora is predominantly endemic to the Eastern Asian region (Korea and Japan), with species such as D. coriacea, D. haenyeosa sp. nov., D. spathulata, D. sumbisoria sp. nov., D. taewakia sp. nov., and R. okamurae. Exceptions include the widely distributed, potentially introduced species D. pfaffii and D. bartayresiana, both originally described from the Caribbean. Rugulopteryx okamurae, while endemic to Korea and Japan, has also been introduced to the Atlantic and Mediterranean regions over the past two decades.

Five new species in Piloderma (Atheliales, Basidiomycota) and epitypification of P. byssinum

Piloderma constitutes a small genus of soft, corticioid, ectomycorrhizal, widely distributed and mostly very common species. Microscopically, its members have traditionally been recognised by their simple-septate hyphae and by their small, thick-walled, colourless to pale yellow spores. We describe five new species from northern Europe based on molecular and morphological data: P. frondosum sp. nov., P. fugax sp. nov., P. lamprolithum sp. nov., P. luminosum sp. nov. and P. mirabile sp. nov. All the new species, except P. luminosum seem to be more or less rare. Piloderma fugax has a strong preference for old-growth forest - a lifestyle seemingly deviating from the rest of the genus. Piloderma mirabile is a sister species to P. sphaerosporum and the first known species with clamped hyphae. Piloderma lamprolithum is closely related to P. exiguum and distinguished by its large encrusting crystals. Piloderma luminosum is very closely related to, and morphologically semicryptic with, P. byssinum. To clarify its distinction from P. byssinum, an epitype is designated for the latter. Piloderma frondosum also belongs to the P. byssinum cluster and is distinguished by its association to broadleaved trees. An updated key to all Piloderma species is provided.