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Morpho-phylogenetic evidence reveals Pseudolomaanthathailandica gen. et sp. nov. and Submultiguttulisporamultiseptata gen. et sp. nov. in Chaetosphaeriaceae

Anamorphic chaetosphaeriaceous fungi exhibit high morphological variability and are distributed worldwide across terrestrial and aquatic habitats. During an ongoing taxonomic study of microfungi, two intriguing chaetosphaeriaceous hyphomycetes were collected from dead wood and dead bamboo stems in China and Thailand. A polyphasic approach, combining morphological characteristics and phylogenetic analysis of LSU and ITS sequence data, revealed that these fungi represent two new genera within Chaetosphaeriaceae. Pseudolomaantha and Submultiguttulispora are proposed for these new genera, and they exhibit non-phialidic and phialidic asexual morphs, respectively. Pseudolomaanthathailandica gen. et sp. nov. is characterized by a sporidesmium-like asexual morph with macronematous, mononematous conidiophores; monoblastic conidiogenous cells, and pyriform to obclavate, rostrate conidia bearing an apical appendage. Submultiguttulisporamultiseptata gen. et sp. nov. is distinguished by macronematous, mononematous conidiophores, mono- to polyphialidic conidiogenous cells, and fusiform or ellipsoidal-fusiform, pale brown to olive green to brown conidia with filiform, hyaline appendages at both ends. Detailed descriptions, illustrations, and notes on the new collections are provided, along with a key to non-phialidic hyphomycetous genera in Chaetosphaeriaceae.

Genetic Diversity and Spatiotemporal Distribution of SARS-CoV-2 Variants in Guinea: A Meta-Analysis of Sequence Data (2020-2023)

In Guinea, genomic surveillance has been established to generate sequences of and to identify locally circulating SARS-CoV-2 variants. This study aims to describe the distributions, genetic diversity, and origins of SARS-CoV-2 lineages circulating in Guinea during the COVID-19 pandemic. A migration analysis was performed by selecting all sequences generated in Guinea for variants of concern and interest. From March 2020 to December 2023, 1038 sequences were generated in Guinea and submitted to the Global Initiative on Sharing All Influenza Data (GISAID) database. Of these, 73.1% corresponded to SARS-CoV-2 variants of concern, which were further grouped into Omicron (69.4%), Delta (21.9%), Alpha (6.6%), and Eta (2.1%). Other variants accounted for 26.9% of the total. Among the total variants analyzed, 75 importations into Guinea from various countries worldwide were identified. Most of the importations (40%) originated from African countries, followed in significance by those from European countries (25.3%) and Asia (18.6%). A significant migratory flow was observed within Guinea. The genomic surveillance reported in this study revealed the diversity of SARS-CoV-2 variants circulating in Guinea, emphasizing the importance of large-scale sequencing analyses in understanding the dynamics of the pandemic.

Two novel hyphomycetes associated with ferns from China

During an ongoing investigation of fungi associated with ferns in southwestern China, three hyphomycetes were discovered on the dead rachises of Angiopterisfokiensis and an unidentified fern. Based on morphology and multi-gene phylogenetic analyses, Arthrobotrysangiopteridis and Corynesporaseptata are introduced as new species. Arthrobotrysangiopteridis is a nematode-trapping fungus characterized by macronematous, mononematous, hyaline conidiophores, conidiogenous cells with polyblastic denticles at each node, and 0-1-septate, clavate to elongate pyriform, hyaline conidia. Corynesporaseptata features macronematous, mononematous, pale brown to dark brown conidiophores, integrated, monotretic conidiogenous cells and up to 7-distoseptate with one true septum, subcylindrical to obclavate, hyaline to pale brown conidia. Detailed descriptions and illustrations of these two new species are provided, along with morphological comparisons of the new taxa with closely related species.

Morphology and multigene phylogeny revealed four new species of Geastrum (Geastrales, Basidiomycota) from China

In the present study, four new species, Geastrumartocarpicola, G.fibulatum, G.sinense and G.trachelium collected from China, are proposed based on a combination of morphological characteristics and molecular evidence. Geastrumartocarpicola is characterized by shallowly saccate to deep saccate exoperidium, bubble-shaped to flask shaped basidia, spherical basidiospores. G.fibulatum is characterized by shallowly saccate to deep saccate exoperidium, spherical basidiospores, generative hyphae with clamp connections in the mycelium layer. G.sinense has arched exoperidium, long stipe expanded basidiomata, and spherical basidiospores. G.trachelium has deep saccate exoperidium, flask-shaped basidia, and spherical basidiospores. Sequences of the internal transcribed spacers (ITS), large subunit (nrLSU), the largest subunit of ribosomal polymerase II (RPB1), and subunit 6 of ATP synthase (ATP6) of the nuclear ribosomal DNA (rDNA) markers of the studied samples were generated, and the phylogenetic analyses were performed with maximum likelihood, maximum parsimony and Bayesian inference methods. The results showed that our collection clustered within Geastrum but distinctly from the others. Full morphological descriptions, illustrations, and phylogenetic analyses results for the four new species are provided. In addition, G.sanglinense is treated as a synonym of beijingense.

Dispersal dynamics and introduction patterns of SARS-CoV-2 lineages in Iran

Understanding the dispersal patterns of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) lineages is crucial to public health decision-making, especially in countries with limited access to viral genomic sequencing. This study provides a comprehensive epidemiological and phylodynamic perspective on SARS-CoV-2 lineage dispersal in Iran from February 2020 to July 2022. We explored the genomic epidemiology of SARS-CoV-2 combining 1281 genome sequences with spatial data in a phylogeographic framework. Our analyses shed light on multiple international imports seeding subsequent waves and on domestic dispersal dynamics. Lineage B.4 was identified to have been circulating in Iran, 29 days (95% highest probability density interval: 21-47) before non-pharmaceutical interventions were implemented. The importation dynamics throughout subsequent waves were primarily driven from the country or region where the variant was first reported and gradually shifted to other regions. At the national level, Tehran was the main source of dissemination across the country. Our study highlights the crucial role of continuous genomic surveillance and international collaboration for future pandemic preparedness and efforts to control viral transmission.

Limitations of 18S rDNA Sequence in Species-Level Classification of Dictyostelids

Dictyostelid species classification has traditionally relied on morphology, a time-intensive method requiring expert knowledge. This study evaluated the potential and limitations of using the 18S rDNA sequence for species-level classification. 18S rDNA sequences of 16 samples from the Dicty stock center, including 14 samples found in Thailand, were analyzed. Signature sequence analyses confirmed genus-level identification with high accuracy. These sequences were analyzed alongside 309 database entries retrieved from the GenBank database. The analyses confirmed genus-level identification accuracy but highlighted challenges in distinguishing species due to overlapping intraspecific and interspecific variations, negative barcoding gaps, and incorrectly grouped samples to putative taxa by species delimitation analyses. Species delimitation methods, including maximum likelihood (ML) phylogenetic analysis, achieved limited success, with ML showing the highest accuracy but not exceeding 50%. However, species with high barcoding gaps, such as Raperostelium and Rostrostelium, demonstrated potential for accurate classification. These findings support using 18S rDNA for genus-level identification and suggest its possible application for certain species. Expanded sampling is needed to improve species-level classification and to identify more robust DNA markers for dictyostelid diversity studies.

Phylogenetic Analysis of Chandipura virus: Insights from a Preliminary Genomic Study

Chandipura virus (CHPV) is an arthropod-borne virus linked to encephalitis in humans, primarily in India. Its evolutionary dynamics and transmission pathways remain poorly understood due to limited genomic data. This study analyzed 23 publicly available CHPV genomes, including isolates from humans, sandflies, and a hedgehog, retrieved from GenBank. Phylogenetic analyses were conducted to explore host-specific and geographic evolutionary patterns. Phylogenetic analysis revealed distinct evolutionary lineages. Human-derived genomes collected in India between 2003 and 2024 formed a well-supported monophyletic clade, suggesting a unique evolutionary lineage. In contrast, sandfly-derived genomes exhibited diverse clustering patterns. Notably, Kenyan sandfly isolates from 2016-2017 were phylogenetically closer to human-derived sequences, suggesting possible shared evolutionary pressures. These findings provide preliminary insights into CHPV evolution and emphasize the need for enhanced genomic surveillance in both human and non-human populations. Expanding genomic data is essential to validate these observations and inform public health strategies.

Phylogenetic relationships within western African Torrent Toads (Anura: Bufonidae: Werneria) with focus on the taxonomic status of Werneria preussi and Atelopus africanus

Bufo preussi Matschie, 1893 from Mt. Cameroon was the first African Torrent toad to be described, soon followed by Atelopus africanus Werner, 1898 from Bismarkburg in Togo. Shortly after, both species were considered conspecific and, currently, both fall under the name Werneria preussi following taxonomic revisions. The type locality of A. africanus was consequently believed to be an error, especially due to the absence of reports of Werneria individuals in Togo in subsequent years. However, it remained uncertain if this synonymy is justified or if A. africanus may indeed represent a valid but potentially extinct species. To answer this question, we generated the first mitochondrial data (12S, 16S and COI) for name-bearing types of W. preussi and A. africanus using a museomic approach. This was further complemented by mitochondrial and nuclear data of contemporary relatives. Our multi-gene phylogeny inferred from mitochondrial data showed that W. preussi and A. africanus constitute a well-supported monophyletic group, which further includes W. submontana. Together with distance values falling below the commonly used species threshold of 3% for 16S and 6% for COI, this result provides strong evidence for A. africanus being a junior synonym of W. preussi, and the absence of this genus in Togo. It further indicates that W. submontana does not represent a species distinct from W. preussi, but rather a geographic variety differing morphologically from topotypic W. preussi. Due to this morphological differentiation, we propose to consider the W. submontana populations as a distinct subspecies and herein introduce the new name Werneria preussi submontana comb. nov. We further designate a lectotype for W. preussi, in order to increase nomenclatural stability and facilitate future research focusing on African Torrent Toads.

Additions to the saprobic fungi (Ascomycota) associated with macadamia trees from the Greater Mekong Subregion

Macadamia trees, the most economically important Proteaceae perennial crop, are globally renowned for their edible nuts. During our surveys of microfungi associated with macadamia in China and Thailand, we isolated three saprobic fungi from dead macadamia branches. Our multigene phylogenetic analyses (ITS, LSU, SSU, tef1-α, TUB2, and ACT loci), genealogical concordance phylogenetic species recognition (GCPSR) with a pairwise homoplasy index (PHI) test, and morphological characteristics led to the discovery of two new species, Dothiorellamacadamiae and Phaeoacremoniumchiangmaiense, and one new record, Melomastiapuerensis. We provide morphological descriptions, photo plates, phylogenetic analysis results, and PHI test results of the two new species, along with comparisons with closely related taxa. These findings have global implications for understanding the diversity of microfungi associated with macadamia trees.

Impact of Viral Co-Detection on the Within-Host Viral Diversity of Influenza Patients

Numerous studies have documented the evidence of virus-virus interactions at the population, host, and cellular levels. However, the impact of these interactions on the within-host diversity of influenza viral populations remains unexplored. Our study identified 13 respiratory viral pathogens from the nasopharyngeal swab samples (NPSs) of influenza-like-illness (ILI) patients during the 2012/13 influenza season using multiplex RT-PCR. Subsequent next-generation sequencing (NGS) of RT-PCR-confirmed influenza A infections revealed all samples as subtype A/H3N2. Out of the 2305 samples tested, 538 (23.3%) were positive for the influenza A virus (IAV), while rhinovirus (RV) and adenoviruses (Adv) were detected in 264 (11.5%) and 44 (1.9%) samples, respectively. Among these, the co-detection of more than one virus was observed in ninety-six samples, and five samples showed co-detections involving more than two viruses. The most frequent viral co-detection was IAV-RV, identified in 48 out of the 96 co-detection cases. Of the total samples, 150 were processed for whole-genome sequencing (WGS), and 132 met the criteria for intra-host single-nucleotide variant (iSNV) calling. Across the genome, 397 unique iSNVs were identified, with most samples containing fewer than five iSNVs at frequencies below 10%. Seven samples had no detectable iSNVs. Notably, the majority of iSNVs (86%) were unique and rarely shared across samples. We conducted a negative binomial regression analysis to examine factors associated with the number of iSNVs detected within hosts. Two age groups-elderly individuals (>64 years old) and school-aged children (6-18 years old)-were significantly associated with higher iSNV counts, with incidence rate ratios (IRR) of 1.80 (95% confidence interval [CI]: 1.09-3.06) and 1.38 (95% CI: 1.01-1.90), respectively. Our findings suggest a minor or negligible contribution of these viral co-detections to the evolution of influenza viruses. However, the data available in this study may not be exhaustive, warranting further, more in-depth investigations to conclusively determine the impact of virus-virus interactions on influenza virus genetic diversity.

Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes

BACKGROUND

East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. We set out to bridge this gap and to understand the interactions between TEs and their cichlid hosts.

RESULTS

Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed strong conservation of TE silencing factors in cichlids, and an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that targets TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci.

CONCLUSIONS

Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity.

Atypical hyperendemicity of Rift Valley fever in Southwestern Uganda associated with the rapidly evolving lineage C viruses

Introduction

Recent Rift Valley fever (RVF) epidemiology in eastern Africa region is characterized by widening geographic range and increasing frequency of small disease clusters. Here we conducted studies in southwestern (SW) Uganda region that has since 2016 reported increasing RVF activities.

Methods

A 22-month long hospital-based study in three districts of SW Uganda targeting patients with acute febrile illness (AFI) or unexplained bleeding was followed by a cross-sectional population-based human-animal survey. We then estimated RVFV force of infection (FOI) and yearly cases using the age-structured seroprevalence data and conducted genomic phylodynamic modelling of RVFV isolates.

Results

Overall RVF prevalence was 10.5% (205 of 1,968) among febrile or hemorrhagic cases, including 5% with acute (PCR or IgM positive) infection, averaging 5 cases per month. Community-based serosurvey recorded prevalence of 11.8% (88 of 743) among humans and 14.6% (347 of 2,383) in livestock. Expected yearly human RVF cases were 314-2,111 per 1,369 km 2 in SW Uganda versus 0-711 in comparable regions of Kenya and Tanzania. Viral genomic studies identified RVFV lineage C, sub-clade C.2.2, as the circulating strain in SW Uganda since 2019. Lineage C strain has undergone recent rapid evolution and clonal expansion resulting in four sub-clades, C.1.1, C.1.2, C.2.1, and C.2.2, that are more adept at establishing endemicity in new territories.

Conclusions

We demonstrate an atypical RVF hyperendemic region in SW Uganda characterized by sustained human clinical RVF cases, unusually high population prevalence, and high number of expected yearly human cases, associated in part with emergence of new RVFV sub-lineages.

Key points

Rift Valley fever (RVF) studies in SW Uganda found atypical sustained human cases averaging 5 cases/month, >10% population prevalence, and expected yearly cases >3-fold higher (314-2,111 vs 0-711) than comparable regions in East Africa, associated with emerging RVFV sub-lineages.

Molecular Epidemiological Characteristics of Staphylococcus pseudintermedius, Staphylococcus coagulans, and Coagulase-Negative Staphylococci Cultured from Clinical Canine Skin and Ear Samples in Queensland

Background/Objectives: Infections in dogs caused by methicillin-resistant staphylococci (MRS) present limited treatment options. This study's objective was to investigate the molecular epidemiology of Staphylococcus spp. cultured exclusively from clinical canine skin and ear samples in Queensland, Australia, using whole-genome sequencing (WGS). Methods: Forty-two Staphylococcus spp. isolated from clinical canine skin and ear samples, from an unknown number of dogs, were sourced from two veterinary diagnostic laboratories between January 2022 and May 2023. These isolates underwent matrix-assisted laser desorption ionisation- time of flight bacterial identification, minimum inhibitory concentration testing using SensititreTM plates and WGS. Phylogenetic trees and core genome multilocus sequence typing (cgMLST) minimum spanning trees (MSTs) were constructed. Results: The isolates included methicillin-resistant and -sensitive S. pseudintermedius (MRSP: 57.1%, 24/42; and MSSP: 19.1%, 8/42), methicillin-resistant and -sensitive S. coagulans (MRSC: 14.3%, 6/42; and MSSC: 2.4%, 1/42) and methicillin-resistant coagulase-negative staphylococci (MR-CoNS: 7.1%, 3/42). Thirty-nine isolates were included after WGS, where all MRS harboured the mecA gene. Eighteen sequence types (STs) were identified, including three novel MRSP and six novel MSSP STs. MRSP ST496-V-VII (23%; 9/39) and MRSP ST749-IV-(IVg) (12.8%; 5/39) were commonly isolated. Phylogenetic analysis of single nucleotide polymorphisms showed that MRSP, MRSC and MSSC were similar to globally isolated staphylococci from canine skin and ear infections. Using cgMLST MSTs, MRSP isolates were not closely related to global strains. Conclusions: Our findings revealed a genotypically diverse geographical distribution and phylogenetic relatedness of staphylococci cultured from clinical canine skin and ear samples across Queensland. This highlights the importance of ongoing surveillance to aid in evidence-based treatment decisions and antimicrobial stewardship.

First Detection of Alphacoronavirus in Bats from the World's Largest Wetland, the Pantanal, Brazil

Coronaviruses (CoV) infect a wide variety of hosts, causing epidemics in humans, birds, and mammals over the years. Bats (order Chiroptera) are one of the natural hosts of the Coronaviridae family. They represent 40% of the total number of mammal species in the Pantanal, a biodiversity hotspot in South America. Given the recent SARS-CoV-2 pandemic, we investigated the presence of CoV in bats captured in the Brazilian Pantanal. Oral and rectal swabs collected in 2021 from 419 bats were analyzed using Pancoronavirus-nested PCR targeting the RNA-dependent RNA-polymerase (RdRp) gene. Orthocoronavirinae was detected in 16.7% (70/419) of the bats; nine samples were sequenced, confirming that Carollia perspicillata (4), Phyllostomus hastatus (2), Desmodus rotundus (1), Molossus rufus (1), and Myotis cf. nigricans (1) collected in buildings formally used by humans were infected by Alphacoronavirus genera. This is the first description of Alphacoronavirus in bats from the Pantanal. As they are natural reservoirs of CoVs, constant monitoring of bats is important to comprehend the epidemiology of emerging viruses, especially in the Pantanal biome.

Identification and Pathogenicity of Fusarium Species from Herbaceous Plants on Grassland in Qiaojia County, China

The Fusarium species is an important plant pathogen that can cause plant diseases in grassland, leading to the degradation of grassland quality. However, the morphology of Fusarium is greatly affected by environmental factors, which makes it difficult to identify its species. In addition, the pathogenic ability of different Fusarium species in plants has not been fully studied. In this study, Fusarium isolates were obtained from grassland herbaceous plants via tissue separation. Through morphological means and based on ITS, RPB2, and TEF-1 gene sequences, we compared and constructed polygenic phylogenetic trees to classify and identify the Fusarium species. In addition, the pathogenicity of different Fusarium species was also analyzed. The results showed that a total of 24 Fusarium strains were successfully isolated from grassland, from which ten species were identified: F. flagelliforme, F. longifundum, F. clavum, F. scirpi, F. ipomoeae, F. oxysporum, etc. and were included in four complexes: Fusarium incarnatum-equiseti species complex (FIESC), Fusarium oxysporum species complex (FOSC), Fusarium tricinctum species complex (FTSC), and Fusarium sambucinum species complex (FSAMSC). Pathogenicity tests demonstrated that except for F. ipomoeae QJ5211, F. sambucinum QJ203, and F. acuminatum QJ1662, other Fusarium species had different degrees of pathogenic ability. This is the first study that discusses the effect of Fusarium on grassland disease control in this area. This study further provides clear pathogen information for the prevention and control of grassland diseases.

Somy evolution in the honey bee infecting trypanosomatid parasite Lotmaria passim

Lotmaria passim is a ubiquitous trypanosomatid parasite of honey bees nestled within the medically important subfamily Leishmaniinae. Although this parasite is associated with honey bee colony losses, the original draft genome-which was completed before its differentiation from the closely related Crithidia mellificae-has remained the reference for this species despite lacking improvements from newer methodologies. Here, we report the updated sequencing, assembly, and annotation of the BRL-type (Bee Research Laboratory) strain (ATCC PRA-422) of Lotmaria passim. The nuclear genome assembly has been resolved into 31 complete chromosomes and is paired with an assembled kinetoplast genome consisting of a maxicircle and 30 minicircle sequences. The assembly spans 33.7 Mb and contains very little repetitive content, from which our annotation of both the nuclear assembly and kinetoplast predicted 10,288 protein-coding genes. Analyses of the assembly revealed evidence of a recent chromosomal duplication event within chromosomes 5 and 6 and provided evidence for a high level of aneuploidy in this species, mirroring the genomic flexibility employed by other trypanosomatids as a means of adaptation to different environments. This high-quality reference can therefore provide insights into adaptations of trypanosomatids to the thermally regulated, acidic, and phytochemically rich honey bee hindgut niche, which offers parallels to the challenges faced by other Leishmaniinae during the challenges they undergo within insect vectors, during infection of mammals, and exposure to antiparasitic drugs throughout their multi-host life cycles. This reference will also facilitate investigations of strain-specific genomic polymorphisms, their role in pathogenicity, and the development of treatments for pollinator infection.

Molecular phylogeny and morphology reveal four new wood-inhabiting fungi of Asterostroma and Radulomyces (Basidiomycota) from Southwestern China

In the ecosystem, wood-inhabiting fungi play an indispensable role in wood degradation and the cycle of substances. They are regarded as the "key player" in the process of wood decomposition because of their ability to produce various enzymes that break down woody lignin, cellulose, and hemicellulose. In this study, four new wood-inhabiting fungal species, Asterostromaparamuscicola, Radulomycesbambusinus, R.fissuratus, and R.sinensis, were collected from southwestern China and were proposed based on the morphological and molecular evidence. Asterostromaparamuscicola is characterised by the felted-membranous to pellicular basidiomata with pinkish to slightly salmon-buff, a smooth hymenial surface, a monomitic hyphal system, and generative hyphae bearing simple-septate and subglobose, thin-walled, echinulate basidiospores measuring as 8-8.8 × 7-8 µm. Radulomycesbambusinus is characterised by the resupinate basidiomata with pinkish-white to pink, a tuberculate hymenial surface, a monomitic hyphal system and generative hyphae bearing clamp connections, and subglobose, slightly thick-walled, smooth basidiospores measuring as 6-7.5 × 5.5-7.3 µm. Radulomycesfissuratus is characterised by the coriaceous basidiomata with grey to grey-buff, a tuberculate hymenial surface, a monomitic hyphal system and generative hyphae bearing clamp connections, and globose, slightly thick-walled, smooth basidiospores measuring as 7-9.5 × 6.5-8.5 µm. Radulomycessinensis is characterised by the coriaceous basidiomata with straw to cinnamon to ocherous, a tuberculate hymenial surface, a monomitic hyphal system and generative hyphae bearing clamp connections, and broadly ellipsoid, slightly thick-walled, smooth basidiospores measuring as 7.5-9 × 6.2-7.5 µm. Sequences of the internal transcribed spacer (ITS) and large subunit (nrLSU) markers of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony, and Bayesian inference methods. Phylogenetic analyses of ITS+nrLSU nuclear RNA gene regions showed that four new species were assigned to the genera Asterostroma and Radulomyces. The phylogenetic tree inferred from the ITS sequences revealed that A.paramuscicola was closely associated with A.macrosporum and A.muscicola. Based on the ITS sequences, the topology showed that Radulomycesbambusinus was retrieved as a sister to R.zixishanensis. The taxon R.fissuratus forms a monophyletic lineage. The other one species, R.sinensis, was closely associated with R.molaris and R.yunnanensis.

Novel High-Quality Amoeba Genomes Reveal Widespread Codon Usage Mismatch Between Giant Viruses and Their Hosts

The need for high-quality protist genomes has prevented in-depth computational and experimental studies of giant virus-host interactions. In addition, our current knowledge of host range is highly biased due to the few hosts used to isolate novel giant viruses. This study presents 6 high-quality amoeba genomes from known and potential giant virus hosts belonging to 2 distinct eukaryotic clades: Amoebozoa and Discoba. We employ their genomic data to investigate the predictability of giant virus host range. Using a combination of long- and short-read sequencing, we obtained highly contiguous and complete genomes of Acanthamoeba castellanii, Acanthamoeba griffini, Acanthamoeba terricola, Naegleria clarki, Vermamoeba vermiformis, and Willaertia magna, contributing to the collection of sequences for the eukaryotic tree of life. We found that the 6 amoebae have distinct codon usage patterns and that, contrary to other virus groups, giant viruses often have different and even opposite codon usage with their known hosts. Conversely, giant viruses with matching codon usage are frequently not known to infect or replicate in these hosts. Interestingly, analyses of integrated viral sequences in the amoeba host genomes reveal potential novel virus-host associations. Matching of codon usage preferences is often used to predict virus-host pairs. However, with the broad-scale analyses performed in this study, we demonstrate that codon usage alone appears to be a poor predictor of host range for giant viruses infecting amoeba. We discuss the potential strategies that giant viruses employ to ensure high viral fitness in nonmatching hosts. Moreover, this study emphasizes the need for more high-quality protist genomes. Finally, the amoeba genomes presented in this study set the stage for future experimental studies to better understand how giant viruses interact with different host species.

Phylogenomics of neglected flagellated protists supports a revised eukaryotic tree of life

Eukaryotes evolved from prokaryotic predecessors in the early Proterozoic1,2 and radiated from their already complex last common ancestor,3 diversifying into several supergroups with unresolved deep evolutionary connections.4 They evolved extremely diverse lifestyles, playing crucial roles in the carbon cycle.5,6 Heterotrophic flagellates are arguably the most diverse eukaryotes4,7,8,9 and often occupy basal positions in phylogenetic trees. However, many of them remain undersampled4,10 and/or incertae sedis.4,11,12,13,14,15,16,17,18 Progressive improvement of phylogenomic methods and a wider protist sampling have reshaped and consolidated major clades in the eukaryotic tree.13,14,15,16,17,18,19 This is illustrated by the Opimoda,14 one of the largest eukaryotic supergroups (Amoebozoa, Ancyromonadida, Apusomonadida, Breviatea, CRuMs [Collodictyon-Rigifila-Mantamonas], Malawimonadida, and Opisthokonta-including animals and fungi).4,14,19,20,21,22 However, their deepest evolutionary relationships still remain uncertain. Here, we sequenced transcriptomes of poorly studied flagellates23,24 (14 apusomonads,25,26 7 ancyromonads,27 and 1 cultured Mediterranean strain of Meteora sporadica17) and conducted comprehensive phylogenomics analyses with an expanded taxon sampling of early-branching protists. Our findings support the monophyly of Opimoda, with CRuMs being sister to the Amorphea (amoebozoans, breviates, apusomonads, and opisthokonts) and ancyromonads and malawimonads forming a moderately supported clade. By mapping key complex phenotypic traits onto this phylogenetic framework, we infer an opimodan biflagellate ancestor with an excavate-like feeding groove, which ancyromonads subsequently lost. Although breviates and apusomonads retained the ancestral biflagellate state, some early-diverging Amorphea lost one or both flagella, facilitating the evolution of amoeboid morphologies, novel feeding modes, and palintomic cell division resulting in multinucleated cells. These innovations likely facilitated the subsequent evolution of fungal and metazoan multicellularity.

Myxobacteria from soil can substantially reduce the bacterial load in a wound infection model

AIMS

Myxobacteria are non-pathogenic, saprophytic, soil-dwelling predatory bacteria known for their antimicrobial potential. Many pathogenic bacteria form biofilms to protect themselves from antimicrobial agents and the immune system. This study has investigated the predatory activities of myxobacteria against pathogenic bacteria in biofilms.

METHODS AND RESULTS

A total of 50 soil samples were collected in and around Cardiff, South Wales (UK). Using a baiting method with 6 prey organisms, 32 myxobacteria were isolated and identified by 16S rRNA sequencing, of which 18 were Myxococcus spp. and 14 were Corallococcus spp. Predation assays, biofilm inhibition and disruption assays, and a dynamic, polymicrobial wound biofilm model were used with live myxobacteria to assess efficacy of predation. Good activity in predation assays was observed against Escherichia coli, while Enterococcus faecalis was more recalcitrant to myxobacteria. Staphylococcus aureus and Citrobacter freundii were significantly (P < 0.05) reduced in both biofilm inhibition and disruption assays compared to other pathogens. Considerable reductions (>3 log10 CFU) in the wound infection model were seen after 96 h of incubation, particularly for C. freundii and E. coli.

CONCLUSION

Using live predatory bacteria as an alternative therapeutic agent has received attention in the recent past to combat the problem of antimicrobial resistance. Myxobacteria isolated from soil using multiple prey organisms yielded diverse isolates, including strains which exhibited therapeutically promising activities in a variety of infection/biofilm assays.

Phylogenetic inferences reveal multiple intra- and interhost genetic diversity among bat rabies viruses circulating in northeastern Brazil

BACKGROUND

Rabies, a lethal viral zoonotic disease, remains a significant global public health concern. In northeastern Brazil, in particular, its epidemiology is complex and dynamic, characterized by the presence of several reservoirs associated with human rabies infection.

METHODS

This study, conducted from June 2022 to July 2023, was part of a passive epidemiological surveillance initiative under Brazil's National Rabies Surveillance Program. It investigated the presence of Rhabdovirus (RhabV) in 356 postmortem chiropteran brain samples using three diagnostic techniques for rabies and conducted an evolutionary study on both pan-RhabV- and pan-LYSSAV-positive PCR samples. The samples were collected from 20 bat species and different locations in the State of Ceará, an endemic region for the rabies virus (RABV). Rabies-positive samples were further explored through Bayesian, genetic distance mapping and recombination analyses.

RESULTS

From a total of 356 samples collected, 43 (12.07%) were positive for direct immunofluorescence (DIF) and 40 (11.23%) for mouse intracerebral inoculation (MIT) tests. Among the positive results, 40 samples were confirmed by both DIF and MIT, while 13 (3.65%) had inconclusive results for one or both techniques. Molecular assays identified 38 rabies-positive samples (10.67%). Members of the Molossidae and Phyllostomidae families had the highest prevalence, highlighting the role of insectivorous and frugivorous bats in the cycle and dynamics of rabies transmission. Phylogenetic reconstructions revealed three distinct and well-supported clusters and clades, indicating the cocirculation of different RABV lineages in the region and shedding light on both intra- and interhost diversity. We also demonstrated genetic distance among the RABV clusters and inferred that their common ancestor originated in Europe, later diversifying across continents. No recombination breakpoints were identified.

CONCLUSIONS

This study highlights the dynamic nature of RABV evolution within individual bat hosts, contributing to the understanding of the genetic diversity of RABV variants found in several bat species in northeastern Brazil. This study provides crucial insights into viral transmission dynamics within and between different host species and is essential for designing effective rabies control and prevention strategies tailored to endemic regions.

Less, but More: New Insights From Appendicularians on Chordate Fgf Evolution and the Divergence of Tunicate Lifestyles

The impact of gene loss on the diversification of taxa and the emergence of evolutionary innovations remains poorly understood. Here, our investigation on the evolution of the Fibroblast Growth Factors (FGFs) in appendicularian tunicates as a case study reveals a scenario of "less, but more" characterized by massive losses of all Fgf gene subfamilies, except for the Fgf9/16/20 and Fgf11/12/13/14, which in turn underwent two bursts of duplications. Through phylogenetic analysis, synteny conservation, and gene and protein structure, we reconstruct the history of appendicularian Fgf genes, highlighting their paracrine and intracellular functions. An exhaustive analysis of developmental Fgf expression in Oikopleura dioica allows us to identify four associated evolutionary patterns characterizing the "less, but more" conceptual framework: conservation of ancestral functions; function shuffling between paralogs linked to gene losses; innovation of new functions after the duplication bursts; and function extinctions linked to gene losses. Our findings allow us to formulate novel hypotheses about the impact of Fgf losses and duplications on the transition from an ancestral ascidian-like biphasic lifestyle to the fully free-living appendicularians. These hypotheses include massive co-options of Fgfs for the development of the oikoblast and the tail fin; recruitment of Fgf11/12/13/14s into the evolution of a new mouth, and their role modulating neuronal excitability; the evolutionary innovation of an anterior tail FGF signaling source upon the loss of retinoic acid signaling; and the potential link between the loss of Fgf7/10/22 and Fgf8/17/18 and the loss of drastic metamorphosis and tail absorption in appendicularians, in contrast to ascidians.

Phytophthora Species and Their Associations with Chaparral and Oak Woodland Vegetation in Southern California

Evidence of unintended introductions of Phytophthora species into native habitats has become increasingly prevalent in California. If not managed adequately, Phytophthora species can become devastating agricultural and forest plant pathogens. Additionally, California's natural areas, characterized by a Mediterranean climate and dominated by chaparral (evergreen, drought-tolerant shrubs) and oak woodlands, lack sufficient baseline knowledge on Phytophthora biology and ecology, hindering effective management efforts. From 2018 to 2021, soil samples were collected from Angeles National Forest lands (Los Angeles County) with the objective of better understanding the diversity and distribution of Phytophthora species in Southern California. Forty sites were surveyed, and soil samples were taken from plant rhizospheres, riverbeds, and off-road vehicle tracks in chaparral and oak woodland areas. From these surveys, fourteen species of Phytophthora were detected, including P. cactorum (subclade 1a), P. multivora (subclade 2c), P. sp. cadmea (subclade 7a), P. taxon 'oakpath' (subclade 8e, first reported in this study), and several clade-6 species, including P. crassamura. Phytophthora species detected in rhizosphere soil were found underneath both symptomatic and asymptomatic plants and were most frequently associated with Salvia mellifera, Quercus agrifolia, and Salix sp. Phytophthora species were present in both chaparral and oak woodland areas and primarily in riparian areas, including detections in off-road tracks, trails, and riverbeds. Although these Mediterranean ecosystems are among the driest and most fire-prone areas in the United States, they harbor a large diversity of Phytophthora species, indicating a potential risk for disease for native Californian vegetation.

Unearthing the secrets of Australia's most enigmatic and cryptic mammal, the marsupial mole

The marsupial moles are arguably Australia's most enigmatic marsupials. Almost indistinguishable from placental (eutherian) moles, they provide a striking example of convergent evolution. Exploring the genome of the southern marsupial mole, we provide insights into its unusual biology. We show definitively by retrophylogenomic analysis that marsupial moles are most closely related to bandicoots and bilbies (order Peramelemorphia). We find evidence of a marked decline in marsupial mole effective population size, most likely preceding the arrival of humans in regions near its range, and potentially corresponding to periods of climatic change. Our analysis of loss of eye function-an adaptation to subterranean life-reveals a structured order of loss of gene function associated first with the lens, then cone, and finally rod cells. Last, we identify genetic changes suggestive of adaptation to an oxygen-poor environment and of its evolution of partially descended testes.

The evolution of thermal performance curves in fungi farmed by attine ant mutualists in above-ground or below-ground microclimates

Fungi are abundant and ecologically important at a global scale, but little is known about whether their thermal adaptations are shaped by biochemical constraints (i.e., the hotter is better model) or evolutionary tradeoffs (i.e., the specialist-generalist model). We tested these hypotheses by generating thermal performance curves of fungal cultivars farmed by six species of Panamanian fungus-farming "attine" ants. These fungi represent evolutionary transitions in farming strategies, as four cultivars are farmed by ants below ground at stable temperatures near 25 °C and two cultivars are farmed above ground at variable temperatures. We generated thermal performance curves using a common garden experiment confining fungal isolates to different temperatures and then used a Bayesian hierarchical modelling approach to compare competing temperature sensitivity models. Some thermal performance traits differed consistently across farming strategies, with above-ground cultivars having: (1) higher tolerance to low temperatures (CTLmin) and (2) higher maximum growth rate at the optimal temperature (rmax). However, two core assumptions shared by the hotter is better model or specialist-generalist model were not supported as above-ground cultivars did not show systematic increases in either their optimal temperature (Topt) or thermal tolerance breadth. These results harness ant farming systems as long-term natural experiments to decouple the effects of environmental thermal variation and innate physiological temperature sensitivity on fungal thermal evolution. The results have clear implications for predicting climate warming-induced breaking points in animal-microbe mutualisms.

Application of a targeted amplicon sequencing panel to screen for insecticide resistance mutations in Anopheles darlingi populations from Brazil

Large-scale surveillance and informed vector control approaches are urgently needed to ensure that national malaria programs remain effective in reducing transmission and, ultimately, achieving malaria elimination targets. In South America, Anopheles darlingi is the primary malaria vector and is responsible for the majority of Plasmodium species transmission. However, little is known about the molecular markers associated with insecticide resistance in this species. In this study, we developed a low-cost, high throughput amplicon sequencing ("amp-seq") panel, consisting of 11 amplicons targeting genes linked to mosquito species identification (cox-1 and its2) and insecticide resistance (ace-1, GSTe2, vgsc and rdl). When used in tandem with dual-index barcoding of amplicons, this approach permits high numbers of loci and samples to be sequenced in single runs, thereby decreasing costs and increasing efficiency. By screening 200 An. darlingi mosquitoes collected in Brazil, our amp-seq approach identified 10 point mutations leading to amino acid changes in ace-1 (V243I, N294H, S673N, S674N/T) and GSTe2 genes (I114V, D128E, T166I, T179I, and T205A). Overall, our work has demonstrated the utility of amp-seq to provide insights into the genetic diversity of An. darlingi mosquitoes. The amp-seq approach can be applied as a wide-scale insecticide-resistance surveillance technique to better inform vector-control methods.

PathCrisp: an innovative molecular diagnostic tool for early detection of NDM-resistant infections

The rapid and early detection of infections and antibiotic resistance markers is a critical challenge in healthcare. Currently, most commercial diagnostic tools for analyzing antimicrobial resistance patterns of pathogens require elaborate culture-based testing. Our study aims to develop a rapid, accurate molecular detection system that can be used directly from culture, thereby introducing molecular testing in conjunction with culture tests to reduce turnaround time and guide therapy. PathCrisp assay, a combination of loop-mediated isothermal amplification and CRISPR-based detection, maintained at a single temperature, was designed and tested on clinical isolates. The specificity and sensitivity of the assay was analyzed, post which the assay was compared with the polymerase chain reaction (PCR) method to detect the New Delhi metallo-beta-lactamase (NDM) gene in carbapenem-resistant enterobacteriaceae clinical samples. Our PathCrisp assay demonstrated the ability to detect as few as 700 copies of the NDM gene from clinical isolates. Our assay demonstrated 100% concordance with the PCR-Sanger sequencing method, more commonly used. Additionally, the lack of the need for a kit-based DNA purification step, rather a crude extraction via heating, enables the direct use of culture samples. The PathCrisp assay is precise, specific and rapid, providing results in approximately 2 h, and operates at a constant temperature, reducing the need for complex equipment handling. In the near future, we hope that this assay can be further optimized and designed as a point-of-care test kit, facilitating its use in various healthcare settings and aiding clinicians in the choice of antibiotics for therapy.

Different orthology inference algorithms generate similar predicted orthogroups among Brassicaceae species

Premise

Orthology inference is crucial for comparative genomics, and multiple algorithms have been developed to identify putative orthologs for downstream analyses. Despite the abundance of proposed solutions, including publicly available benchmarks, it is difficult to assess which tool is most suitable for plant species, which commonly have complex genomic histories.

Methods

We explored the performance of four orthology inference algorithms-OrthoFinder, SonicParanoid, Broccoli, and OrthNet-on eight Brassicaceae genomes in two groups: one group comprising only diploids and another set comprising the diploids, two mesopolyploids, and one recent hexaploid genome.

Results

The composition of the orthogroups reflected the species' ploidy and genomic histories, with the diploid set having a higher proportion of identical orthogroups. While the diploid + higher ploidy set had a lower proportion of orthogroups with identical compositions, the average degree of similarity between the orthogroups was not different from the diploid set.

Discussion

Three algorithms-OrthoFinder, SonicParanoid, and Broccoli-are helpful for initial orthology predictions. Results produced using OrthNet were generally outliers but could still provide detailed information about gene colinearity. With our Brassicaceae dataset, slight discrepancies were found across the orthology inference algorithms, necessitating additional analyses such as tree inference to fine-tune results.

Molecular Detection and Phylogenetic Analysis of Orf Virus From Dermatological Lesions in the Teats of Goats

BACKGROUND

The orf virus (ORFV) is a viral pathogen that primarily causes contagious ecthyma in humans and different ruminants. The infection, which is common worldwide, causes large-scale economic losses to animal breeders.

OBJECTIVE AND METHODS

In this study, tissue samples collected from eight randomly selected goats with dermatological lesions on the teats were examined in different goat herds. B2L gene-specific primer pairs (PP1, PP3 and PP4) were used to reveal the presence of ORFV by molecular methods and for phylogenetic analysis.

RESULTS

Viral DNA was detected in four of eight tissues using the semi-nested PCR method. In addition, the data obtained by performing sequence analyses of the amplicons with positive results were compared with the information of different ORFV isolates registered in the GenBank database. Based on the sequence analysis of the field isolates obtained in our study, it was found that the nucleotide similarities among these isolates and those from Asian countries were 100%. Furthermore, ORFV isolates collected from different species and produced in Türkiye over various periods exhibited homologous nucleotide sequences with similarities ranging from 98.1% to 98.8%. In the phylogenetic tree drawn based on the B2L genomic region, it was observed that our field isolates were classified in Group I together with other Turkish and Asian strains.

CONCLUSION

As a result, while other pathogenic agents are considered the cause of disease in goats with dermatological lesions on their mammary tissue, the ORFV should also be evaluated, and protection and control programs should be prepared accordingly.

Ultrastructure of Olkasia polycarbonata (Euglenozoa, Euglenida) demonstrates cytoskeletal innovations associated with the feeding and flagellar apparatuses

Euglenids are flagellates with diverse modes of nutrition, including the photosynthetic Euglenophyceae, which acquired plastids via secondary endosymbiosis with green algae, and a diverse assemblage of predators of bacteria and other microeukaryotes. Most heterotrophic euglenids have never been cultivated, so their morphology remains poorly characterized and limited to only a few studies. "Ploeotids" are a paraphyletic group representing much of the diversity of heterotrophic euglenids and are characterized by their feeding apparatus and a rigid pellicle of 10-12 longitudinally arranged strips. Ploeotid-like euglenids gave rise to the Spirocuta, a large clade of heterotrophic and photosynthetic euglenids defined by a flexible pellicle of helically arranged strips. Using single-cell approaches, we report the first ultrastructural characterization of Olkasia polycarbonata, a ploeotid that is consistently positioned as the sister lineage to the Spirocuta in multigene phylogenetic analyses. O. polycarbonata shares several morphological characteristics with members of Spirocuta, such as prominent swellings on the paraxonemal rods and a robust feeding apparatus consisting of rods and vanes. These morphological traits are consistent with the phylogenetic position of O. polycarbonata and demonstrate an increase in cytoskeletal complexity that occurred prior to the key strip duplication event in the most recent common ancestor of Spirocuta.

Genome-wide association studies unveils the genetic basis of cell wall composition and saccharification of cassava pulp

Cassava (Manihot esculenta Crantz) is a key crop for starch and biofuels production. This study focuses on the polysaccharide composition and saccharification efficiency in cassava pulp through genome-wide association studies (GWAS), targeting the improvement of root characteristics for industrial use. We analyzed 135 partially inbred lines population, performing monosaccharide composition and saccharification analyses to reveal substantial variability in storage root biomass. Among 33 traits examined, 128 significant SNPs were associated with 23 biomass traits, highlighting a complex genetic architecture. Saccharification potential varied from 39 to 95 nmol Glu mg-1 h-1, with high broad-sense heritability for saccharification and several monosaccharide traits, indicating a strong genetic control. Our findings revealed that cassava pulp comprises similar proportions of pectin, hemicellulose, and cellulose in all genotypes. Correlation analysis showed significant associations between cellulose content and saccharification, suggesting that enhancing these traits can improve bioconversion efficiency. Negative correlations with glucose and glucuronic acid in hemicellulose and pectin fractions imply these components may inhibit saccharification. We identified 118 candidate genes associated with 21 traits, with many involved in stress responses affecting cell wall composition. This study verified 12 key candidate genes through sequence and expression analysis, including MANES_07G081200, a YTH domain-containing protein associated with saccharification. Several stress-response genes, such as MANES_04G118600 and MANES_09G174600, were linked to monosaccharide traits, suggesting that adaptive stress pathways influence biomass characteristics. This study provides insights into the genetic determinants of cassava pulp's saccharification and polysaccharide composition, aiding breeding efforts to develop cassava varieties optimized for industrial applications.

Using PSICalc to Identify Protein Sequence Interdependencies

Protein sequence analysis has been utilized to explore features of protein structure, protein interactions, and enzyme mechanism. One approach is to compare sequences using multiple sequence alignment (MSA) and identify relationships or interdependencies within a protein sequence. This chapter will describe the Protein Sequence Interdependency Calculator (PSICalc) software tool. PSICalc is a GUI tool for analyzing protein MSAs to identify sequence interdependencies using a K modes algorithm approach. The software outputs information about sequence clusters both in graphical and in CSV format. In addition, the tool identifies sites that are invariant and nearly invariant within a group of sequences. Finally, the tool also has the ability to compare separate MSAs of two or more proteins to identify interdependencies between or among proteins.

Secondary contact erodes Pleistocene diversification in a wide-ranging freshwater mussel (Quadrula)

The isolated river drainages of eastern North America serve as a natural laboratory to investigate the roles of allopatry and secondary contact in the evolutionary trajectories of recently diverged lineages. Drainage divides facilitate allopatric speciation, but due to their sensitivity to climatic and geomorphological changes, neighboring rivers frequently coalesce, creating recurrent opportunities of isolation and contact throughout the history of aquatic lineages. The freshwater mussel Quadrula quadrula is widely distributed across isolated rivers of eastern North America and possesses high phenotypic and molecular variation across its range. We integrate sequence data from three genomes, including female- and male-inherited mitochondrial markers and thousands of nuclear encoded SNPs with morphology and geography to illuminate the group's divergence history. Across contemporary isolated rivers, we found continuums of molecular and morphological variation, following a pattern of isolation by distance. In contact zones, hybridization was frequent with no apparent fitness consequences, as advanced hybrids were common. Accordingly, we recognize Q. quadrula as a single cohesive species with subspecific variation (Q. quadrula rumphiana). Demographic modeling and divergence dating supported a divergence history characterized by allopatric vicariance followed by secondary contact, likely driven by river rearrangements and Pleistocene glacial cycles. Despite clinal range-wide variation and hybridization in contact zones, the process-based species delimitation tool delimitR, which considers demographic scenarios like secondary contact, supported the delimitation of the maximum number of species tested. As such, when interpreting species delimitation results, we suggest careful consideration of spatial sampling and subsequent geographic patterns of biological variation, particularly for wide-ranging taxa.

Evolution of a bipolar sexual compatibility system in Marasmius

Sexual compatibility in the Basidiomycota is governed by genetic identity at one or two loci, resulting in compatibility systems called bipolar and tetrapolar. The loci are known as HD and P/R, encoding homeodomain transcription factors and pheromone precursors and receptors, respectively. Bipolarity is known to evolve either by linkage of the two loci or by loss of mating-type determination of either the HD or the P/R locus. The ancestor to basidiomycete fungi is thought to have been tetrapolar, and many transitions to bipolarity have been described in different lineages. In the diverse genus Marasmius (Agaricales), both compatibility systems are found, and the system has been shown to follow the infrageneric sections of the genus, suggesting a single origin of bipolarity. Here, we tested this hypothesis using a comprehensive phylogenetic framework and investigated the mode by which bipolarity has evolved in this group. We utilized available genomic data and marker sequences to investigate evolution of sexual compatibility in Marasmius and allied genera. By generating a concatenated multilocus phylogeny, we found support for a single transition to known bipolarity within Marasmius. Furthermore, utilizing genomic data of the bipolar species Marasmius oreades, we found that the HD and P/R loci likely have remained unlinked through this transition. By comparing nucleotide diversity at the HD and P/R loci in Ma. oreades, we show that the HD locus has retained high diversity, and thus likely the function of determining sexual identity, as similarly in other bipolar mushroom-forming fungi. Finally, we describe the genomic architecture of the MAT loci of species of both sexual compatibility systems in Marasmiaceae and related families.

Recombination Analysis of Geminiviruses Using Recombination Detection Program (RDP)

Geminiviruses are recombination-prone, and characterizing this evolutionary process within their genomes is a frequent goal of researchers. RDP is a stand-alone Windows program combining many algorithms that detect and characterize recombination. It has been widely used by the geminivirus community (and beyond). Here we describe the use of RDP4 and RDP5 for analysis of geminiviral nucleotide sequences including: (i) obtaining a reasonable dataset for analysis, (ii) making a credible multiple sequence alignment and (iii) analyzing an alignment with RDP on that alignment. RDP to both characterize recombination events and to produce statistically recombination-free datasets for other molecular evolution analyses.

Taxonomy and Biopharmaceutical Properties of a Newly Discovered Variety of Lentinus squarrosulus (Agaricomycetes) from West Bengal, India

In the present study, a unique mushroom belonging to the genus Lentinus was collected from the Lateritic region of West Bengal, India. The purpose of our investigation is to determine its taxonomic identity and evaluate its therapeutic properties, with a particular emphasis on its antioxidant and antimicrobial properties. A thorough morpho-molecular investigation revealed that the collected mushroom is a novel variety that has been named Lentinus squarrosulus var. odoratus in recognition of its potent, rotting banana-like aroma. The methanolic extract of the desiccated basidiocarps exhibits potent antioxidant properties, as evidenced by the EC50 values that range from 314.201 ± 3.12 to 933.48 ± 3.58 μg/mL, contingent upon the type of free radicals employed. The extracted fraction was also discovered to be effective in inhibiting the growth of human-pathogenic bacterial strains in a dose-responsive manner, as evidenced by the low MIC50 values, which varied from 281.61 ± 1.64 to 680.31 ± 4.12 μg/mL depending on the strains under investigation. The inhibitory effect was shown to be potentially caused by an increase in membrane porosity and damage to the cell wall, resulting in the leaking of intracellular components. The findings of this research indicate that there is a significant therapeutic potential encased in this mushroom, necessitating further comprehensive investigation.

Molecular phylogeny and morphology reveal three new plant pathogenic fungi species (Septobasidiales, Basidiomycota) from China

Three new fungal species, Septobasidiummacrobasidium, S.puerense and S.wuliangshanense, are proposed based on a combination of the morphological features and molecular evidence. The taxon S.macrobasidium is characterized by the coriaceous basidiomata with a cream surface, cylindrical basidia, straight, 4-celled, subglobose or ovoid probasidia and thin-walled, narrowly cylindrical basidiospores with septa, measuring as 7-9 × 3.5-4.5 µm, the haustoria consisting of irregularly coiled hyphae; in addition, this fungus was found associated with the insect of Diaspididae. The species S.puerense is characterised by resupinate coriaceous basidiomata with a cinnamon brown to chestnut brown surface, cylindrical or slightly irregular basidia, 2-3-celled, slightly curved, subglobose to pyriform probasidia, probasidia cell persistent after the formation of the basidia and the haustoria with two types consisting of irregularly coiled hyphae and spindle-shape. The fungus was found associated with the insect species Pseudaulacaspispentagona. The species S.wuliangshanense is characterised by the coriaceous basidiomata with a slightly brown surface, cylindrical or slightly irregular basidia, 2-3-celled, straight or slightly curved, pyriform, subglobose or ovoid and probasidia, haustoria consisting of irregularly coiled hyphae, associated with the insect genus Aulacaspis. Sequences of internal transcribed spacer region (ITS) were analysed maximum likelihood, maximum parsimony and Bayesian inference methods. The new species S.macrobasidium was clustered with S.maesae. Furthermore, S.puerense was retrieved as a sister to S.carestianum. The phylogenetic tree, inferred from the ITS sequences, highlighted that S.wuliangshanense was the sister to S.aquilariae with strong supports. Application of PHI test to the ITS tree-locus sequences revealed no recombination level within phylogenetically related species.

Zoonotic transmission of novel Influenza A variant viruses detected in Brazil during 2020 to 2023

Zoonotic infections (swine-human) caused by influenza A viruses (IAVs) have been reported and linked to close contact between these species. Here, we describe eight human IAV variant infections (6 mild and 2 severe cases, including 1 death) detected in Paraná, Brazil, during 2020-2023. Genomes recovered were closely related to Brazilian swIAVs of three major lineages (1 A.3.3.2/pdm09, 1B/human-like, and H3.1990.5), including three H1N1v, two H1N2v, two H3N2v and one H1v. Five H1v were closely related to pdm09 lineage, one H1v (H1N2v) grouped within 1B.2.3 clade, and the two H3v grouped within a clade composed exclusively of Brazilian H3 swIAV (clade H3.1990.5.1). Internal gene segments were closely related to H1N1pdm09 isolated from pigs. IAV variant rarely result in sustained transmission between people, however the potential to develop such ability is of concern and must not be underestimated. This study brings into focus the need for continuous influenza surveillance and timely risk assessment.

Microtoenawawushanensis (Lamiaceae, Lamioideae): A new species from Sichuan, China

Microtoenawawushanensis, a new species from Sichuan, China, is described and illustrated here. The new species is closely related to M.moupinensis and M.prainiana, but differs distinctly from both in leaf, calyx and bract morphology. It is further distinguished by its highly variable and unstable calyx tooth ratio (1.36-2.13), red-marked lateral lobes on the lower corolla and filaments that are barbate at both the upper and basal parts, with nearly imperceptible hairs in the middle section. Phylogenetic analyses, based on 81 coding regions of the chloroplast genome, suggest that M.wawushanensis belongs to sect. Delavayana and is sister to a clade formed by M.urticifolia, M.prainiana and M.megacalyx.

Geographic origin and evolution of dengue virus serotypes 1 and 3 circulating in Africa

Despite the increasing burden of dengue in Kenya and Africa, the introduction and expansion of the virus in the region remain poorly understood. The objective of this study is to examine the genetic diversity and evolutionary histories of dengue virus (DENV) serotypes 1 and 3 in Kenya and contextualize their circulation within circulation dynamics in the broader African region. Viral RNA was extracted from samples collected from a cohort of febrile patients recruited at clinical sites in Kenya from 2013 to 2022. Samples were tested by polymerase chain reaction (PCR) for DENV presence. Five DENV-positive samples were serotyped, and complete viral genomes for phylogenetic inference were obtained via sequencing on Illumina platforms. Sequences generated in our study were combined with global datasets of sequences, and Bayesian and maximum likelihood methods were used to infer phylogenetic trees and geographic patterns of spread with a focus on Kenya and Africa as a whole. Four new DENV-1 and one new DENV-3 genomes were successfully sequenced and combined with 328 DENV-1 and 395 DENV-3 genomes from elsewhere for phylogenetic analyses. The DENV-1 sequences from our study formed a monophyletic cluster with an inferred common ancestor in 2019 (most recent common ancestor 2019 and 95% high posterior density 2018-19), which was closely related to sequences from Tanzania. The single DENV-3 sequence clustered with sequences from Tanzania and Kenya, was collected between 2017 and 2019 and was related to recent outbreaks in the region. Phylogenetic trees resolved multiple clades of DENV-1 and DENV-3 concurrently circulating in Africa, introduced in the early-to mid-2000s. Three DENV-1 and four DENV-3 clades are highlighted, introduced between 2000 and 2015. Phylogeographic models suggest frequent, independent importations of DENV lineages into Kenya and Africa from East and South-East Asia via distinct geographic pathways. DENV-1 and DENV-3 evolutionary dynamics in Africa are characterized by the cocirculation of multiple recently introduced lineages. Circulating lineages are introduced via distinct geographic pathways that may be centered around regional nexus locations. Increased surveillance is required to identify key regional locations that drive spread, and dengue interventions should focus on interrupting spread at these locations.

Analysis of complete genomes of Mycobacterium tuberculosis sublineage 2.1 (Proto-Beijing) revealed the presence of three pe_pgrs3-pe_pgrs4-like genes

Mycobacterium tuberculosis Complex (MTBC), the etiological agent of tuberculosis (TB), demonstrates considerable genotypic diversity with distinct geographic distributions and variable virulence profiles. The pe-ppe gene family is especially noteworthy for its extensive variability and roles in host immune response modulation and virulence enhancement. We sequenced an Mtb genotype L2.1 isolate from Chiangrai, Northern Thailand, using second and third-generation sequencing technologies. Comparative genomic analysis with two additional L2.1 isolates and two L2.2.AA3 (Asia Ancestral 3 Beijing) isolates revealed significant pe-ppe gene variations. Notably, all L2.1 isolates harbored three copies of pe_pgrs3-pe_pgrs4-like genes (pe_pgrs3*, pe_pgrs4*, and pe_pgrs4), different from L2.2.AA3 and H37Rv strains. Additionally, ppe53 was duplicated in all but H37Rv, and ppe50 was deleted in L2.1 isolates, contrasting with an extended ppe50 in an L2.2 isolate (Mtb 18b), which contains an additional SVP motif. Complete deletion of ppe66 and loss of wag22 were observed in L2.1 isolates. These findings highlight the high structural variability of the pe-ppe gene family, emphasizing its complex roles in Mtb-host immune interactions. This genetic complexity offers potentially critical insights into mycobacterial pathogenesis, with significant implications for vaccine development and diagnostics.

Regulation of human interferon signaling by transposon exonization

Innate immune signaling is essential for clearing pathogens and damaged cells and must be tightly regulated to avoid excessive inflammation or autoimmunity. Here, we found that the alternative splicing of exons derived from transposable elements is a key mechanism controlling immune signaling in human cells. By analyzing long-read transcriptome datasets, we identified numerous transposon exonization events predicted to generate functional protein variants of immune genes, including the type I interferon receptor IFNAR2. We demonstrated that the transposon-derived isoform of IFNAR2 is more highly expressed than the canonical isoform in almost all tissues and functions as a decoy receptor that potently inhibits interferon signaling, including in cells infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our findings uncover a primate-specific axis controlling interferon signaling and show how a transposon exonization event can be co-opted for immune regulation.

Mitochondrial Splicing Efficiency Is Lower in Holoparasites Than in Free-Living Plants

Mitochondria play a crucial role in eukaryotic organisms, housing their own genome with genes vital for oxidative phosphorylation. Coordination between nuclear and mitochondrial genomes is pivotal for organelle gene expression. Splicing, editing and processing of mitochondrial transcripts are regulated by nuclear-encoded factors. Splicing efficiency (SEf) of the many group II introns present in plant mitochondrial genes is critical for mitochondrial function since a splicing defect or splicing deficiency can severely impact plant growth and development. This study investigates SEf in free-living and holoparasitic plants, focusing on 25 group II introns from 15 angiosperm species. Our comparative analyses reveal distinctive splicing patterns with holoparasites exhibiting significantly lower SEf, potentially linked to their unique evolutionary trajectory. Given the preponderance of horizontal gene transfer (HGT) in parasitic plants, we investigated the effect of HGT on SEf, such as the presence of foreign introns or foreign nuclear-encoded splicing factors. Contrary to expectations, the SEf reductions do not correlate with HGT events, suggesting that other factors are at play, such as the loss of photosynthesis or the transition to a holoparasitic lifestyle. The findings of this study broaden our understanding of the molecular evolution in parasitic plants and shed light on the multifaceted factors influencing organelle gene expression.

The Complete Mitochondrial Genome of the Luciocyprinus langsoni (Cypriniformes: Cyprinidae): Characterization, Phylogeny, and Genetic Diversity Analysis

Background: Luciocyprinus langsoni is a species belonging to the Cyprinidae family. The objective of this study is to gain a comprehensive understanding of its evolutionary history and genetic characteristics. Methods: The complete mitochondrial genome of L. langsoni was determined using overlapping PCR. A phylogenetic analysis was conducted based on 13 protein-coding genes from 48 species. A population genetic diversity analysis using the COI gene and a selection analysis of 13 protein-coding genes were also performed. Results: The mitogenome is 16,586 base pairs long and consists of 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and two control regions. It has a high adenine-thymine (A + T) content. The phylogenetic analysis confirms the placement of L. langsoni within the subfamily Cyprininae. The population genetic diversity analysis reveals low variability in the Hechi Longjiang population. The selection analysis shows that all 13 protein-coding genes have evolved under purifying selection with Ka/Ks ratios below 1. Conclusions: These results enhance our understanding of L. langsoni's evolutionary history and lay a genetic foundation for future studies in population genetics and phylogenetics.

Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses

Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum, C. pseudodiphtheriticum, C. accolens, and C. tuberculostearicum. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the United States. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution spanning Africa and North America. All species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent versus accessory genome of each species indicating limited strain-level variability in metabolic capacity. Based on prevalence data, at least two Corynebacterium species likely coexist in the nasal microbiota of 82% of adults. So, it was surprising that core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the U.S. clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in most of the strains in the Botswana clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.

IMPORTANCE

Pangenomic analysis with estimation of functional capabilities facilitates our understanding of the full biologic diversity of bacterial species. We performed systematic genomic, phylogenomic, and pangenomic analyses with qualitative estimation of the metabolic capabilities of four common human nasal Corynebacterium species, along with focused experimental validations, generating a foundational resource. The prevalence of each species in human nasal microbiota is consistent with the common coexistence of at least two species. We identified a notably high level of metabolic conservation within and among species indicating limited options for species to occupy distinct metabolic niches, highlighting the importance of investigating interactions among nasal Corynebacterium species. Comparing strains from two continents, C. pseudodiphtheriticum had restricted geographic strain distribution characterized by an evolutionarily recent loss of assimilatory sulfate reduction in U.S. strains. Our findings contribute to understanding the functions of Corynebacterium within human nasal microbiota and to evaluating their potential for future use as biotherapeutics.

Genomic Diversity and Antimicrobial Susceptibility of Invasive Neisseria meningitidis in South Africa, 2016-2021

BACKGROUND

Invasive meningococcal isolates in South Africa have in previous years (<2008) been characterized by serogroup B, C, W, and Y lineages over time, with penicillin intermediate resistance (peni) at 6%. We describe the population structure and genomic markers of peni among invasive meningococcal isolates in South Africa, 2016-2021.

METHODS

Meningococcal isolates were collected through national, laboratory-based invasive meningococcal disease (IMD) surveillance. Phenotypic antimicrobial susceptibility testing and whole-genome sequencing were performed, and the mechanism of reduced penicillin susceptibility was assessed in silico.

RESULTS

Of 585 IMD cases reported during the study period, culture and PCR-based capsular group was determined for 477/585 (82%); and 241/477 (51%) were sequenced. Predominant serogroups included NmB (210/477; 44%), NmW (116/477; 24%), NmY (96/477; 20%), and NmC (48/477; 10%). Predominant clonal complexes (CC) were CC41/44 in NmB (27/113; 24%), CC11 in NmW (46/56; 82%), CC167 in NmY (23/44; 53%), and CC865 in NmC (9/24; 38%). Peni was detected in 16% (42/262) of isolates, and was due to the presence of a penA mosaic, with the majority harboring penA7, penA9, or penA14.

CONCLUSIONS

IMD lineages circulating in South Africa were consistent with those circulating prior to 2008; however, peni was higher than previously reported, and occurred in a variety of lineages.

A newly bat-borne hantavirus detected in Seba's short-tailed bats (Carollia perspicillata) in the Brazilian Atlantic Rainforest

BACKGROUND

Bat-borne hantaviruses have been identified worldwide but little is known about neotropical bats in the megadiverse biomes of the American continent. Although serological evidence has hinted at hantavirus circulation in Brazil, the scarce number of genomic detection represents a gap to understand viral diversity, prevalence, and ecology of bat-borne hantaviruses.

OBJECTIVE

We aim to investigate and evaluate the presence and prevalence of bat-borne hantavirus in the Brazilian Atlantic Forest.

METHODS

Here in, 97 lung and kidney tissue samples from bats captured in the Brazilian Atlantic Rainforest were submitted to hantavirus-specific nested reverse transcription-polymerase chain reaction (RT-PCR) targeted the hantaviral L segment and metagenomic analysis.

FINDINGS

Hantavirus RNA was detected in five tissue fragments of 20 Seba's short-tailed bats (Carollia perspicillata). Phylogenetic analysis, based on partial L-segment sequence using maximum likelihood method, demonstrated that the identified virus formed a monophyletic clade and a highly divergent bat-borne lineage comprising other recent strains found in the genus Carollia from South America.

MAIN CONCLUSIONS

Our findings suggest the presence of a novel bat-borne hantavirus in Brazil, tentatively named Mamanguape virus (MGPV). Additional genomic data will help to extend our knowledge about the classification of MGPV within the Hantaviridae family and the evolution origins of new world bat-borne hantaviruses.

Additions to Dictyosporiaceae: Neoxylochrysis typhicola comb. et gen. nov., Two New Species and Four New Host Records from Medicinal Plants in Southwestern China

Medicinal plants serve as vital resources for preventing and treating diseases, with their flowers, fruits, leaves, roots, or entire plants being utilized in the pharmaceutical industry or as direct therapeutic agents. During our investigation of microfungi associated with medicinal plants in Guizhou and Sichuan Provinces, China, several asexual and sexual fungal morphs were collected. Multi-locus phylogenetic analysis based on combined ITS, LSU, SSU and TEF1-α datasets revealed that these taxa are related to the family Dictyosporiaceae. Morphological characteristics, along with multi-locus phylogenetic analysis, supported the establishment of Dictyocheirospora alangii sp. nov. and Pseudocoleophoma rosae sp. nov., as well as the introduction of a novel genus Neoxylochrysis, which accommodates Neoxylochrysis typhicola comb. nov. (≡Pseudocoleophoma typhicola). In addition, four new host records are introduced for Aquadictyospora lignicola from Periploca forrestii, Dendryphiella eucalyptorum from Leonurus japonicus, Ophiopogon japonicus and Sambucus javanica, D. vinosa from Phytolacca americana, and Dictyocheirospora rotunda from Euonymus japonicus and Prinsepia utilis. Detailed descriptions, micrographs of the new taxa and a phylogenetic tree are provided.

Over 400 food resources from Brazil: evidence-based records of wild edible mushrooms

Many species of mushroom-forming fungi have been harvested in the wild and used for food and medicine for thousands of years. In Brazil, the knowledge of the diversity of wild edible mushrooms remains scattered and poorly studied. Based on new samples, bibliographic records revision, and searches through the GenBank, we recorded 409 species of wild edible mushrooms in Brazil, of which 350 can be safely consumed and 59 are edible but with conditions. Additionally, other 150 species represent taxa with unclear evidence of consumption or unconfirmed edibility status. A total of 86 of the 409 edible species represents consistent records in Brazil based on molecular data and/or Brazilian nomenclatural types. Other 323 names represent species that need further taxonomic investigations to confirm their identity and occurrence in the country, with 41 of them having some record of consumption by part of the Brazilian population. The remaining 282 species can represent new food resources for the country. We generated 143 DNA sequences, representing 40 species within 29 genera. Edible mushrooms are an important non-wood forest product and the knowledge about them adds value to the local biodiversity and the population, increasing the incentive to conservation allied to sustainable rural development.