AliView: a fast and lightweight alignment viewer and editor for large datasets

The Diversity and Taxonomy of Thelephoraceae (Basidiomycota) with Descriptions of Four Species from Southwestern China

Taxonomy plays a central role in understanding the diversity of life, translating the products of biological exploration and discovery specimens and observations into systems of names that settle a "classification home" to taxa. The ectomycorrhizal basidiomycetes family Thelephoraceae has been understudied in subtropical ecosystems. Many species of Thelephoraceae are important edible and medicinal fungi, with substantial economic value. Four new species, Thelephora resupinata, T. subtropica, T. yunnanensis, and Tomentella tenuifarinacea, are proposed based on a combination of the morphological features and molecular evidence. Thelephora resupinata is characterized by the resupinate basidiomata having a tuberculate pileal surface hymenial, and the presence of the subglobose to globose basidiospores (9-12 × 7-9 µm). T. subtropica is solitary coriaceous infundibuliform gray-brown basidiomata with a presence of the subclavate basidia and subglobose to globose basidiospores (6-8 × 5-7 µm). T. yunnanensis is typical of the laterally stipitate basidiomata having a smooth, umber to coffee hymenial surface, a monomitic hyphal system with clamped generative hyphae, and the presence of the subglobose basidiospores (7-10 × 6-8 µm). Tomentella tenuifarinacea is typical of the arachnoid basidiomata having a smooth, gray, or dark gray hymenial surface, a monomitic hyphal system with clamped generative hyphae, and the presence of the subglobose to globose basidiospores (7-9 × 6-8 µm). Sequences of ITS+nLSU+mtSSU genes were used for the phylogentic analyses using maximum likelihood, maximum parsimony, and Bayesian inference methods. The three genes' (ITS+nLSU+mtSSU) phylogenetic analysis showed that the genera Thelephora and Tomentella grouped together within the family Thelephoraceae and three new species were nested into the genus Thelephora, and one new species was nested into the genus Tomentella.

A new monopartite begomovirus infecting Melochia tomentosa in Burkina Faso

This is the first description of the complete genome sequence of a newly characterized monopartite begomovirus isolated from an asymptomatic uncultivated plant, Melochia tomentosa, collected in Burkina Faso. The sequence was obtained through rolling-circle amplification, cloning, and Sanger sequencing. The provisional species name "Begomovirus melochiae" and common virus name "melochia associated virus" (MeAV) are proposed. The MeAV genome was found to share the most nucleotide sequence similarity with three African monopartite begomoviruses: tomato curly stunt virus (74%), pepper yellow vein Mali virus (73%), and tomato leaf curl Cameroon virus (73%). Phylogenetic analysis confirmed its relationship to Old World monopartite begomoviruses. The discovery of MeAV in an uncultivated and asymptomatic plant provides a further example of the high diversity of begomoviruses in sub-Saharan African ecosystems.

Molecular evolution of toothed whale genes reveals adaptations to echolocating in different environments

BACKGROUND

Echolocation was a key development in toothed whale evolution, enabling their adaptation and diversification across various environments. Previous bioacoustic and morphological studies suggest that environmental pressures have influenced the evolution of echolocation in toothed whales. This hypothesis demands further investigation, especially regarding the molecular mechanisms involved in the adaptive radiation of toothed whales across multiple habitats. Here we show that the coding sequences of four hearing genes involved in echolocation (CDH23, prestin, TMC1, and CLDN14) have different signatures of molecular evolution among riverine, coastal, and oceanic dolphins, suggesting that the evolutionary constraints of these habitats shaped the underlying genetic diversity of the toothed whale sonar.

RESULTS

Our comparative analysis across 37 odontocete species revealed patterns of accelerated evolution within coastal and riverine lineages, supporting the hypothesis that shallow habitats pose specific selective pressures to sonar propagation, which are not found in the deep ocean. All toothed whales with genes evolving under positive selection are shallow coastal species, including three species that have recently diverged from freshwater lineages (Cephalorhynchus commersonii, Sotalia guianensis, and Orcaella heinsohni - CDH23), and three species that operate specialized Narrow Band High Frequency (NBHF) Sonars (Phocoena sinus - prestin, Neophocaena phocaenoides - TMC1 and Cephalorhynchus commersonii - CDH23). For river dolphins and deep-diving toothed whales, we found signatures of positive selection and molecular convergence affecting specific sites on CDH23, TMC1, and prestin. Positively selected sites (PSS) were different in number, identity, and substitution rates (dN/dS) across riverine, coastal, and oceanic toothed whales.

CONCLUSION

Here we shed light on potential molecular mechanisms underlying the diversification of toothed whale echolocation. Our results suggest that toothed whale hearing genes changed under different selective pressures in coastal, riverine, and oceanic environments.

Mercury Immobilization without Methylation in Sulfidogenic Systems Dominated by Sulfur Disproportionating Bacteria

The sulfidogenic process mediated by sulfate-reducing bacteria (SRB) is not ideal for treating mercury (Hg)-bearing wastewater due to the risk of methylmercury (MeHg) production. Addressing this challenge, our study demonstrated that, under S0-rich conditions and without organic additives, sulfidogenic communities dominated by sulfur-disproportionating bacteria (SDB) can effectively remove Hg(II) and prevent MeHg production. Using various inocula, we successfully established biological sulfidogenic systems driven separately by SDB and SRB. Batch experiments revealed that SDB cultures completely removed Hg(II) from the solution as HgS. Remarkably, no MeHg production was observed in the SDB cultures, while an average concentration of 0.32 μg/L of MeHg was detected in the SRB cultures. The absence of MeHg production in the SDB cultures could be mainly attributed to the cultivation conditions that reshaped the microbial community, resulting in a rapid decline of SRB-dominated Hg-methylating microorganisms. Consequently, the average abundance of the hgcA gene was 28 times lower than the levels before cultivation. Additionally, we found that the enriched Dissulfurimicrobium sp. bin121 can produce biogenic sulfide through sulfur disproportionation but lacks the hgcA gene, rendering it incapable of methylating Hg. Overall, we propose a novel biotechnology driven by SDB that can safely and sustainably treat Hg-bearing wastewater.

A molecular phylogeny of the Petaluridae (Odonata: Anisoptera): A 160-Million-Year-Old story of drift and extinction

Petaluridae (Odonata: Anisoptera) is a relict dragonfly family, having diverged from its sister family in the Jurassic, of eleven species that are notable among odonates (dragonflies and damselflies) for their exclusive use of fen and bog habitats, their burrowing behavior as nymphs, large body size as adults, and extended lifespans. To date, several nodes within this family remain unresolved, limiting the study of the evolution of this peculiar family. Using an anchored hybrid enrichment dataset of over 900 loci we reconstructed the species tree of Petaluridae. To estimate the temporal origin of the genera within this family, we used a set of well-vetted fossils and a relaxed molecular clock model in a divergence time estimation analysis. We estimate that Petaluridae originated in the early Cretaceous and confirm the existence of monophyletic Gondwanan and Laurasian clades within the family. Our relaxed molecular clock analysis estimated that these clades diverged from their MRCA approximately 160 mya. Extant lineages within this family were identified to have persisted from 6 (Uropetala) to 120 million years (Phenes). Our biogeographical analyses focusing on a set of key regions suggest that divergence within Petaluridae is largely correlated with continental drift, the exposure of land bridges, and the development of mountain ranges. Our results support the hypothesis that species within Petaluridae have persisted for tens of millions of years, with little fossil evidence to suggest widespread extinction in the family, despite optimal conditions for the fossilization of nymphs. Petaluridae appear to be a rare example of habitat specialists that have persisted for tens of millions of years.

Environmental selection and advective transport shape the distribution of two cyst-forming Acantharia clades in the Canadian Arctic

Anthropogenic induced climate perturbations are seen in changes in oceanic circulation patterns, and Arctic water masses defined by salinity are vulnerable to change. Biogeography of marine microbial eukaryotes is expected to be impacted by changes in local environmental conditions and advective processes, but tracking the extent of plankton distribution requires understanding routes for both active and passive tracers. To identify such tracers, we focused on samples collected in the western (Canada Basin) and eastern (Nares Strait); extremes of the Canadian High Arctic that are connected by an east flowing current north of Canada. Sequencing of the V4 region of 18S rRNA revealed that Acantharia, a taxonomically and functionally diverse group of large planktonic protists, were particularly common. Arctic acantharians in our study were dominated by two clades belonging to cyst-forming groups. The distribution of one clade suggested successful advective transport from the Pacific sourced water in the Beaufort Gyre to southern Nares Strait, with cells transported along the northern shelf of the Canadian Arctic. A second clade appeared to be a resident taxon of the Canada Basin whose distribution correlated to local environmental conditions, and detection in deeper samples would be consistent with swarmer formation enabling reestablishment the following year.

Inter- and intra-specific metal tolerance variation in ectomycorrhizal fungal Suillus species

Soil metal contamination can affect growth, metabolism, and reproduction of organisms, and can lead to death. However, some fungi have evolved metal tolerance and are able to live in contaminated soils. Species in the ectomycorrhizal genus Suillus from Europe and Asia display variation in metal tolerance, yet it is unknown whether this is a widespread trait in the genus and whether it occurs in North America. Here we investigate cadmium (Cd) and zinc (Zn) tolerance in S. brevipes and S. tomentosus isolates collected from sites in the Rocky Mountains of Colorado displaying different metal content. In line with previous findings for other Suillus species, we hypothesized (1) S. brevipes and S. tomentosus to display intra-specific metal tolerance variation, (2) Zn and Cd tolerance to be correlated to soil metal content, and (3) tolerant isolates to show lower metal tissue content compared to sensitive isolates (due to increased metal exclusion). We found ample intra- and inter-specific Zn and Cd tolerance variation in both S. brevipes and S. tomentosus, but no correlation between soil metal content and tolerance. There was a negative correlation between tolerance level and Zn uptake, indicating an exclusion-based Zn tolerance strategy. Sensitive and tolerant isolates showed no difference in Cd accumulation, indicating that Cd tolerance in these species is likely not dependent on exclusion. Our study sets the groundwork for further investigation into the genetic basis of Suillus metal tolerance and whether and how it impacts pine mycorrhizal partners.

Data-driven guidelines for phylogenomic analyses using SNP data

Premise

There is a general lack of consensus on the best practices for filtering of single-nucleotide polymorphisms (SNPs) and whether it is better to use SNPs or include flanking regions (full "locus") in phylogenomic analyses and subsequent comparative methods.

Methods

Using genotyping-by-sequencing data from 22 Glycine species, we assessed the effects of SNP vs. locus usage and SNP retention stringency. We compared branch length, node support, and divergence time estimation across 16 datasets with varying amounts of missing data and total size.

Results

Our results revealed five aspects of phylogenomic data usage that may be generally applicable: (1) tree topology is largely congruent across analyses; (2) filtering strictly for SNP retention (e.g., 90-100%) reduces support and can alter some inferred relationships; (3) absolute branch lengths vary by two orders of magnitude between SNP and locus datasets; (4) data type and branch length variation have little effect on divergence time estimation; and (5) phylograms alter the estimation of ancestral states and rates of morphological evolution.

Discussion

Using SNP or locus datasets does not alter phylogenetic inference significantly, unless researchers want or need to use absolute branch lengths. We recommend against using excessive filtering thresholds for SNP retention to reduce the risk of producing inconsistent topologies and generating low support.

Fatal Oropouche Virus Infections in Nonendemic Region, Brazil, 2024

We report acute Oropouche virus infections in 2 previously healthy women from a nonendemic region of Brazil outside the Amazon Basin. Infections rapidly progressed to hemorrhagic manifestations and fatal outcomes in 4-5 days. These cases highlight the critical need for enhanced surveillance to clarify epidemiology of this neglected disease.

The prevalence and immune response to coinfection by avian haemosporidians in wild Eurasian blackbirds Turdus merula

Coinfection of a host by more than 1 parasite is more common than single infection in wild environments and can have differing impacts, although coinfections have relatively rarely been quantified. Host immune responses to coinfection can contribute to infection costs but are often harder to predict than those associated with single infection, due to the influence of within-host parasite–parasite interactions on infection virulence. To first quantify coinfection in a common bird species, and then to test for immune-related impacts of coinfection, we investigated the prevalence and immune response to avian haemosporidian (genera: Plasmodium, Haemoproteus and Leucocytozoon) coinfection in wild blackbirds. Coinfection status was diagnosed using a 1-step multiplex polymerase chain reaction, immune response was quantified through white blood cell counts and heterophil: lymphocyte ratios, and parasitaemia was quantified for each infected sample. We detected high rates of haemosporidian infection and coinfection, although neither impacted immune activity, despite a significantly higher parasitaemia in individuals experiencing double vs single infection. This suggests that immune-related costs of haemosporidian single and coinfection are low in this system. This could be due to long-term host–parasite coevolution, which has decreased infection virulence, or a consequence of reduced costs associated with chronic infections compared to acute infections. Alternatively, our results may obscure immune-related costs associated with specific combinations of coinfecting haemosporidian genera, species or lineages. Future research should investigate interactions that occur between haemosporidian parasites within hosts, as well as the ways in which these interactions and resulting impacts may vary depending on parasite identity.

Dynamics and ecology of a multi-stage expansion of Oropouche virus in Brazil

In March 2024, the Pan American Health Organization (PAHO) issued an alert in response to a rapid increase in Oropouche fever cases across South America. Brazil has been particularly affected, reporting a novel reassortant lineage of the Oropouche virus (OROV) and expansion to previously non-endemic areas beyond the Amazon Basin. Utilising phylogeographic approaches, we reveal a multi-scale expansion process with both short and long-distance dispersal events, and diffusion velocities in line with human-mediated jumps. We identify forest cover, banana and cocoa cultivation, temperature, and human population density as key environmental factors associated with OROV range expansion. Using ecological niche modelling, we show that OROV circulated in areas of enhanced ecological suitability immediately preceding its explosive epidemic expansion in the Amazon. This likely resulted from the virus being introduced into simultaneously densely populated and environmentally favourable regions in the Amazon, such as Manaus, leading to an amplified epidemic and spread beyond the Amazon. Our study provides valuable insights into the dispersal and ecological dynamics of OROV, highlighting the role of human mobility in colonisation of new areas, and raising concern over high viral suitability along the Brazilian coast.

Morphological and molecular identification for four new wood-inhabiting species of Lyomyces (Basidiomycota) from China

Fungi are one of the most diverse groups of organisms on Earth, in which the wood-inhabiting fungi play an important role in forest ecosystem processes and functions. Four new wood-inhabiting fungi, Lyomyceshengduanensis, L.niveomarginatus, L.wumengshanensis and L.zhaotongensis, are proposed, based on morphological features and molecular evidence. Lyomyceshengduanensis differs in the brittle basidiomata with pruinose hymenial surface, a monomitic hyphal system and ellipsoid basidiospores (3.5-6 × 3-4.5 µm). Lyomycesniveomarginatus is distinguished by the subceraceous basidiomata with crackled hymenial surface, a monomitic hyphal system and ellipsoid basidiospores (4.5-7 × 3-4 µm). Lyomyceswumengshanensis is distinguished by the grandinioid hymenial surface, a monomitic hyphal system and ellipsoid to broad ellipsoid basidiospores (4-6 × 3-5 µm). Lyomyceszhaotongensis is unique in the grandinioid hymenial surface, a monomitic hyphal system and broadly ellipsoid basidiospores measuring as 2.6-3.5 × 2.5-3 µm. Sequences of ITS and nLSU rRNA markers of the studied samples were generated and phylogenetic analyses were performed using the Maximum Likelihood, Maximum Parsimony and Bayesian Inference methods. The phylogram, based on the ITS+nLSU rDNA gene regions, included three genera within the Schizoporaceae viz. Fasciodontia, Lyomyces and Xylodon, in which the four new species were grouped into Lyomyces. The phylogenetic tree inferred from the ITS sequences highlighted that L.hengduanensis group with L.zhaotongensis and then closely grouped with L.crustosus, L.ochraceoalbus, and L.vietnamensis. The new taxon L.niveomarginatus was retrieved as a sister to L.juniperi. The new species L.wumengshanensis was sister to L.macrosporus. The new taxon L.zhaotongensis grouped with L.hengduanensis and then closely grouped with L.crustosus, L.ochraceoalbus and L.vietnamensis.

Into the Cauldron of the Variant Soup: Insights into the Molecular Epidemiology and Transition to Endemicity of SARS-CoV-2 in Cyprus (November 2022-February 2024)

The coronavirus disease 2019 (COVID-19) pandemic, driven by the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been characterized by the virus's ongoing evolution, leading to the appearance of more transmissible variants that have often triggered infection surges. In this study, we analyzed the SARS-CoV-2 epidemic in Cyprus, utilizing 1627 viral sequences from infected individuals between November 2022 and February 2024. Over this period, 251 distinct lineages and sublineages were identified, predominantly categorized into three groups: Omicron 5, XBB, and JN.1 (parental lineage BA.2.86), all of which harbor S protein mutations linked to enhanced transmissibility and immune escape. Despite the relatively low numbers of new infections during this period, and the lack of any major waves, unlike earlier phases of the pandemic, these lineages demonstrated varying periods of dominance, with Omicron 5 prevailing from November 2022 to February 2023, XBB variants leading from March to November 2023, and JN.1 generating a wavelet from December 2023 to February 2024. These findings suggest that the SARS-CoV-2 epidemic in Cyprus has reached endemicity, with new variants gradually replacing previously circulating variants irrespective of seasonal patterns. This study highlights the critical importance of ongoing surveillance of SARS-CoV-2 evolution in Cyprus and emphasizes the role of preventive measures in limiting virus transmission, providing valuable insights for safeguarding public health.

Mitonuclear compatibility is maintained despite relaxed selection on male mitochondrial DNA in bivalves with doubly uniparental inheritance

Mitonuclear coevolution is common in eukaryotes, but bivalve lineages that have doubly uniparental inheritance (DUI) of mitochondria may be an interesting example. In this system, females transmit mtDNA (F mtDNA) to all offspring, while males transmit a different mtDNA (M mtDNA) solely to their sons. Molecular evolution and functional data suggest oxidative phosphorylation (OXPHOS) genes encoded in M mtDNA evolve under relaxed selection due to their function being limited to sperm only (vs. all other tissues for F mtDNA). This has led to the hypothesis that mitonuclear coevolution is less important for M mtDNA. Here, we use comparative phylogenetics, transcriptomics, and proteomics to understand mitonuclear interactions in DUI bivalves. We found nuclear OXPHOS proteins coevolve and maintain compatibility similarly with both F and M mtDNA OXPHOS proteins. Mitochondrial recombination did not influence mitonuclear compatibility and nuclear-encoded OXPHOS genes were not upregulated in tissues with M mtDNA to offset dysfunction. Our results support that selection maintains mitonuclear compatibility with F and M mtDNA despite relaxed selection on M mtDNA. Strict sperm transmission, lower effective population size, and higher mutation rates may explain the evolution of M mtDNA. Our study highlights that mitonuclear coevolution and compatibility may be broad features of eukaryotes.

Epidemiology and genetic diversity of human respiratory syncytial virus in Belgium between 2011 and 2019

BACKGROUND

Human respiratory syncytial virus (HRSV) is worldwide one of the leading causes of acute respiratory tract infections in young children and the elderly population. Two distinct subtypes of HRSV (A and B) and a multitude of genotypes have been described. The laboratory of Clinical and Epidemiological Virology (KU Leuven/University Hospitals Leuven) has a long-standing history of HRSV surveillance in Belgium.

METHODS

In this study, the seasonal circulation of HRSV in Belgium was monitored during 8 consecutive seasons prior to the SARS-CoV-2 pandemic (2011-2012 until 2018-2019). By use of a multiplex quantitative real time PCR panel, 27,386 respiratory samples were tested for HRSV. Further subtyping and sequencing of the HRSV positive samples was performed by PCR and Sanger sequencing. The prevalence and positivity rate were estimated in 4 distinct age groups and the circulating strains of each subtype were situated in a global context and in reference to the described genotypes in literature.

RESULTS

HRSV circulated in Belgium in a yearly re-occurring pattern during the winter months and both HRSV subtypes co-circulated simultaneously. All HRSV-B strains contained the 60 nt duplication in the HVR2 region of the G gene. Strains of subtype HRSV-A with a 72 nt duplication in the HVR2 region were first observed during the 2011-2012 season and replaced all other circulating strains from 2014 to 2015 onwards.

Global metagenomic survey identifies sewage-derived hgcAB+ microorganisms as key contributors to riverine methylmercury production

Methylmercury (MeHg) in aquatic systems poses a serious public health risk through bioaccumulation in the aquatic food web. In recent years, MeHg has been observed to increase to concerning levels globally in rivers near cities; however, the causes of this increase are not well understood. Here, we demonstrate the significant role of sewage contamination by analyzing over 1,300 publicly available metagenomes in urban rivers worldwide, and conducting experiments with water samples across China. We find that sewage contamination significantly increases the abundance of mercury (Hg)-methylating microorganisms in urban rivers globally. This increase is primarily attributed to the high abundance of active Hg-methylating microorganisms in sewage, which migrate to rivers via direct discharge or combined sewer overflows (CSOs), becoming key contributors to elevated riverine MeHg levels. Our findings underscore the importance of effectively eliminating Hg-methylating microorganisms from sewage to mitigate the public health risks associated with MeHg in urban rivers.

Phylogenomics, Lineage Diversification Rates, and the Evolution of Diadromy in Clupeiformes (Anchovies, Herrings, Sardines, and Relatives)

Migration independently evolved numerous times in animals, with a myriad of ecological and evolutionary implications. In fishes, perhaps the most extreme form of migration is diadromy, the migration between marine and freshwater environments. Key and long-standing questions are: how many times has diadromy evolved in fishes, how frequently do diadromous clades give rise to non-diadromous species, and does diadromy influence lineage diversification rates? Many diadromous fishes have large geographic ranges with constituent populations that use isolated freshwater habitats. This may limit gene flow between some populations, increasing the likelihood of speciation in diadromous lineages relative to nondiadromous lineages. Alternatively, diadromy may reduce lineage diversification rates if migration is associated with enhanced dispersal capacity that facilitates gene flow within and between populations. Clupeiformes (herrings, sardines, shads, and anchovies) is a model clade for testing hypotheses about the evolution of diadromy because it includes an exceptionally high proportion of diadromous species and several independent evolutionary origins of diadromy. However, relationships among major clupeiform lineages remain unresolved, and existing phylogenies sparsely sampled diadromous species, limiting the resolution of phylogenetically informed statistical analyses. We assembled a phylogenomic dataset and used multi-species coalescent and concatenation-based approaches to generate the most comprehensive, highly resolved clupeiform phylogeny to date, clarifying associations among several major clades and identifying recalcitrant relationships needing further examination. We determined that variation in rates of sequence evolution (heterotachy) and base-composition (nonstationarity) had little impact on our results. Using this phylogeny, we characterized evolutionary patterns of diadromy and tested for differences in lineage diversification rates between diadromous, marine, and freshwater lineages. We identified 13 transitions to diadromy, all during the Cenozoic Era (10 origins of anadromy, 2 origins of catadromy, and 1 origin of amphidromy), and 7 losses of diadromy. Two diadromous lineages rapidly generated nondiadromous species, demonstrating that diadromy is not an evolutionary dead end. We discovered considerably faster transition rates out of diadromy than to diadromy. The largest lineage diversification rate increase in Clupeiformes was associated with a transition to diadromy, but we uncovered little statistical support for categorically faster lineage diversification rates in diadromous versus nondiadromous fishes. We propose that diadromy may increase the potential for accelerated lineage diversification, particularly in species that migrate long distances. However, this potential may only be realized in certain biogeographic contexts, such as when diadromy allows access to ecosystems in which there is limited competition from incumbent species.

Dengue virus surveillance in Nepal yields the first on-site whole genome sequences of isolates from the 2022 outbreak

BACKGROUND

The 4 serotypes of dengue virus (DENV1-4) can each cause potentially deadly dengue disease, and are spreading globally from tropical and subtropical areas to more temperate ones. Nepal provides a microcosm of this global phenomenon, having met each of these grim benchmarks. To better understand DENV transmission dynamics and spread into new areas, we chose to study dengue in Nepal and, in so doing, to build the onsite infrastructure needed to manage future, larger studies.

METHODS AND RESULTS

During the 2022 dengue season, we enrolled 384 patients presenting at a hospital in Kathmandu with dengue-like symptoms; 79% of the study participants had active or recent DENV infection (NS1 antigen and IgM). To identify circulating serotypes, we screened serum from 50 of the NS1+ participants by RT-PCR and identified DENV1, 2, and 3 - with DENV1 and 3 codominant. We also performed whole-genome sequencing of DENV, for the first time in Nepal, using our new on-site capacity. Sequencing analysis demonstrated the DENV1 and 3 genomes clustered with sequences reported from India in 2019, and the DENV2 genome clustered with a sequence reported from China in 2018.

CONCLUSION

These findings highlight DENV's geographic expansion from neighboring countries, identify China and India as the likely origin of the 2022 DENV cases in Nepal, and demonstrate the feasibility of building onsite capacity for more rapid genomic surveillance of circulating DENV. These ongoing efforts promise to protect populations in Nepal and beyond by informing the development and deployment of DENV drugs and vaccines in real time.

Immune History Modifies Disease Severity to HPAI H5N1 Clade 2.3.4.4b Viral Challenge

The most recent outbreak of highly pathogenic avian H5 influenza (HPAI) virus in cattle is now widespread across the U.S. with spillover events happening to other mammals, including humans. Several human cases have been reported with clinical signs ranging from conjunctivitis to respiratory illness. However, most of those infected report mild to moderate symptoms, while previously reported HPAI H5Nx infections in humans have had mortality rates upwards of 50%. We recently reported that mice with pre-existing immunity to A/Puerto Rico/08/1934 H1N1 virus were protected from lethal challenge from highly pathogenic clade 2.3.4.4b H5N1 influenza virus. Here, we demonstrate that mice infected with the 2009 pandemic H1N1 virus strain A/California/04/2009 (Cal09) or vaccinated with a live-attenuated influenza vaccine (LAIV) were moderately-to-highly protected against a lethal A/bovine/Ohio/B24OSU-439/2024 H5N1 virus challenge. We also observed that ferrets with mixed pre-existing immunity-either from LAIV vaccination and/or from Cal09 infection-showed protection against a HPAI H5N1 clade 2.3.4.4b virus isolated from a cat. Notably, this protection occurred independently of any detectable hemagglutination inhibition titers (HAIs) against the H5N1 virus. To explore factors that may contribute to protection, we conducted detailed T cell epitope mapping using previously published sequences from H1N1 strains. This analysis revealed a high conservation of amino acid sequences within the internal proteins of our bovine HPAI H5N1 virus strain. These data highlight the necessity to explore additional factors that contribute to protection against HPAI H5N1 viruses, such as memory T cell responses, in addition to HA-inhibition or neutralizing antibodies.

Morpho-phylogenetic evidence reveals novel species and new records of Nigrograna (Nigrogranaceae) associated with medicinal plants in Southwestern China

During a survey of saprobic fungal niches in Southwestern China, eighteen ascomycetous collections of Nigrograna (Nigrogranaceae, Pleosporales, Dothideomycetes) were found on dead branches of medicinal plants. These taxa were characterized and identified based on morphological and culture characteristics, and phylogenetic analyses of a combined the internal transcribed spacer region of rDNA (ITS), nuclear large subunit rDNA (28S, LSU), RNA polymerase second-largest subunit (rpb2), nuclear small subunit rDNA (18S, SSU), and translation elongation factor 1-alpha (tef1-α) sequence dataset also confirmed their placement. As a result, four novel species, namely Nigrogranacamelliae, N.guttulata, N.longiorostiolata and N.neriicola were described. Additionally, four new host records of N.acericola, N.magnoliae, N.oleae and N.thymi were introduced. Furthermore, this study addresses the taxonomic status of N.trachycarpi, proposing its synonymy under N.oleae. Detailed illustrations, descriptions and informative notes for each newly identified taxon and novel host record are provided in this study.

The complete mitochondrial genome of the shining leaf chafer Mimela junii (Duftschmidt, 1805) (Coleoptera: Scarabaeidae)

The complete mitochondrial genome of the shining leaf chafer Mimela junii was sequenced and is herein described. The mitogenome consists of a circular molecule of 16,805 bp, with an overall AT content of 75.7%. It encodes for 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and contains a non-coding Control Region (CR) characterized by the presence of tandem repeats. The gene order corresponds to the ancestral Pancrustacea model and mitogenome characteristics are congruous with those of hexapods. In the phylogenetic analysis, M. junii is nested within a paraphyletic Anomala with high support, and is herein associated with Anomala corpulenta with medium/low support.

Whole Genome Analysis Reveals Evolutionary History and Introgression Events in Bale Monkeys

Background/Objective: The Bale monkey (Chlorocebus djamdjamensis) is a threatened primate species endemic to Ethiopia and, in contrast to other members of the genus Chlorocebus, lives at high altitudes and feeds mainly on bamboo. Two populations of the species are present, one in continuous bamboo forest (CF) in the eastern part of the species' range, and the other in fragmented forest (FF) in the western part. Based on mitochondrial DNA and phenotypic characteristics, previous studies have suggested introgression by parapatric congeners into the FF population but not into the CF population. The objective of this study was to gain insights into the evolutionary history of Bale monkeys and their potential genetic adaptations to high altitudes and for bamboo consumption. Methods: We sequenced the whole genomes of individuals from both populations and compared their genomes with those of the other five Chlorocebus species. We applied phylogenetic methods and conducted population demographic simulations to elucidate their evolutionary history. A genome-wide analysis was conducted to assess gene flow and identify mutations potentially associated with adaptations to high altitudes and for bamboo metabolism. Results: Our analyses revealed Bale monkeys as the sister clade to Chlorocebus aethiops and showed that gene flow occurred between C. aethiops and FF but not between C. aethiops and CF. In addition, we detected non-synonymous mutations in genes potentially associated with the adaptation to high altitudes (EPAS1) in both populations and with the adaptation for bamboo metabolism (TAS2R16, MPST, and TST) mainly in the CF population. Conclusions: Our study provides insights into the evolutionary history of a threatened primate species and reveals the genetic basis for its adaptions to unique environments and for diet specialization.

Exploring Dengue Infection in a Vaccinated Individual: Preliminary Molecular Diagnosis and Sequencing Insights

This study examines a case involving a 7-year-old child who developed dengue symptoms following Qdenga vaccination. Despite initial negative diagnostic results, molecular analysis confirmed an infection with DENV4. Next-generation sequencing detected viral RNA from both DENV2 and DENV4 serotypes, which were identified as vaccine-derived strains using specific primers. Phylogenetic analysis further confirmed that these sequences belonged to the Qdenga vaccine rather than circulating wild-type viruses. This case underscores the critical need for precise diagnostic interpretation in vaccinated individuals to avoid misdiagnosis and to strengthen public health surveillance. A comprehensive understanding of vaccine-induced viremia is essential for refining dengue surveillance, improving diagnostic accuracy, and informing public health strategies in endemic regions.

New Helminthosporium (Massarinaceae, Dothideomycetes) and Nigrospora (Incertae sedis, Sordariomycetes) species associated with walnut (Juglansregia L.) in China

Six collections of ascomycetes were obtained from samples collected from dead branches and leaves of Juglansregia in Guizhou and Yunnan provinces, China. By incorporating multigene phylogenetic analysis (ITS, LSU, rpb2, SSU, tef1-α, tub2) supplemented by morphological data, we establish two novel species, namely Helminthosporiumguizhouense and Nigrosporayunnanensis. In morphology, H.guizhouense can be distinguished from H.caespitosum by its narrower conidia (13-16 µm vs. 27.3-35.5 µm), and N.yunnanensis is characterized by black, globose conidia (16.2 × 14.4 µm). The phylogenetic results further substantiated them as novel taxa. The present study contributes to our comprehension of the range of fungi found in Juglansregia, thereby expanding our knowledge of the diversity of fungi within this host.

Characterization of hAT DNA transposon superfamily in the genome of Neotropical fish Apareiodon sp

DNA transposons are diverse in fish genomes and have been described to generate genomic evolutionary novelties. hAT transposable element data are scarce in Teleostei genomes, making it challenging to conduct comparative genomic studies to understand their neutrality or function. This study aimed to perform a genomic and molecular characterization of hAT copies to assess the diversity of these elements and associate changes in these sequences to genomic and karyotypic novelties in Apareiodon sp. The data revealed that hAT TEs are highly abundant in the Apareiodon sp. genome, with few possibly autonomous copies. Highly conserved sequences with likely functional transposases were observed in nine hAT elements. A great diversity of hAT subgroups was observed, especially from Ac, Charlie, Blackjack, Tip100, hAT6, and hAT5, and a similar wave of hAT genomic invasion was identified in the genome for these six groups of hAT sequences. The data also revealed a distinct number of microsatellites within degenerated hAT copies. hAT sites were demonstrated to be dispersed in the Apareiodon sp. chromosomes and not involved in W chromosome-specific region differentiation. In conclusion, the genomic analysis revealed a great diversity of hAT elements, possible autonomous copies, and differentiation of degenerated transposable elements into tandem sequences.

Coevolutionary Analysis of the Pfs47-P47Rec Complex: A Bioinformatics Approach

Background

The ability to predict and comprehend molecular interactions offers significant insights into the biological functions of proteins. The interaction between surface protein 47 of Plasmodium falciparum (Pfs47) and receptor of the protein 47 (P47Rec) has attracted increased attention due to their role in parasite evasion of the mosquito immune system and the concept of geographical coevolution between species. The aims of this study were as follows: to apply a bioinformatics approach to investigate the interaction between Pfs47 and P47Rec proteins and to identify the potential binding sites, protein orientations and receptor specificity sites concerning the geographical origins of the vectors and the parasite.

Methods

Public sequences of the pfs47 and p47rec genes were downloaded and subsequently filtered to predict functional and structural annotations of the Pfs47-P47Rec complex. Phylogenetic analyses of both proteins were carried out. In addition, the p47Rec gene was subjected to sequencing and subsequent analysis in 2 distinct Anopheles species collected in Honduras.

Results

The examination of motifs reveals a significant degree of conservation in pfs47, suggesting that Pfs47 might have undergone recent evolutionary development and adaptation. Structural models and docking analyses supported the theory of selectivity of Plasmodium falciparum strains towards their vectors in diverse geographical regions. A detailed description of the putative interaction between the Pfs47-P47Rec complex is shown.

Conclusions

The study identifies coevolutionary patterns between P47Rec and Pfs47 related to the speciation and geographic dispersion of Anopheles species and Plasmodium falciparum, with Pfs47 evolving more recently than P47Rec. This suggests a link between the parasite's adaptability and existing anopheline species across different regions. P47Rec likely has a cytoplasmic localization due to its lack of membrane attachment elements. However, these findings are based on simulations and require validation through methods like cryo-electron microscopy. A significant limitation is the scarcity of sequences in global databases, which restricts precise interaction modelling. Further research with diverse parasite isolates and anopheline species is recommended to enhance understanding of these proteins' structure and interaction.

Two new species of Pholiota (Agaricales, Strophariaceae) from the southwest of China

Two new mushroom species from Southwest China, Pholiotacylindrospora and P.subterrestris, are described in this study. Pholiotacylindrospora is characterized by its dry pileus with slightly recurved and triangular scales, cylindrical basidiospores, and two types of pleurocystidia-leptocystidia and chrysocystidia-as well as its growth on soil. Pholiotasubterrestris is identified by a brownish-orange pileus with numerous brown fibrillose scales; pale brown lamellae with even edges; a stipe covered with recurved fibrillose scales; elliptical spores with a distinct but small germ pore; and pleurocystidia containing typical amorphous refractive inclusions of chrysocystidia. Both species are described and illustrated, and a phylogenetic analysis of a multigene dataset (ITS + 28S) is presented. Morphological and phylogenetic analyses confirm that P.cylindrospora and P.subterrestris are distinct from the other Pholiota species, and both belong to the subgenus Pholiota. A key to the species of subgenus Pholiota from China is provided.

Local patterns of spread of influenza A H3N2 virus in coastal Kenya over a 1-year period revealed through virus sequence data

The patterns of spread of influenza A viruses in local populations in tropical and sub-tropical regions are unclear due to sparsity of representative spatiotemporal sequence data. We sequenced and analyzed 58 influenza A(H3N2) virus genomes sampled between December 2015 and December 2016 from nine health facilities within the Kilifi Health and Demographic Surveillance System (KHDSS), a predominantly rural region, covering approximately 891 km2 along the Kenyan coastline. The genomes were compared with 1571 contemporaneous global sequences from 75 countries. We observed at least five independent introductions of A(H3N2) viruses into the region during the one-year period, with the importations originating from Africa, Europe, and North America. We also inferred 23 virus location transition events between the nine facilities included in the study. International virus imports into the study area were captured at the facilities of Chasimba, Matsangoni, Mtondia, and Mavueni, while all four exports from the region were captured from the Chasimba facility, all occurring to Africa destinations. A strong spatial clustering of virus strains at all locations was observed associated with local evolution. Our study shows that influenza A(H3N2) virus epidemics in local populations appear to be characterized by limited introductions followed by significant local spread and evolution. Knowledge of the viral lineages that circulate within specific populations in understudied tropical and subtropical regions is required to understand the full diversity and global ecology of influenza viruses and to inform vaccination strategies within these populations.

Leveraging transcriptome sequence read archives for virus detection in wild and colony populations of triatomines (Hemiptera: Reduviidae: Triatominae)

Triatomines are infamous as vectors of the parasite Trypanosoma cruzi, the causative agent of Chagas disease. However, climate-driven range expansion and urbanization adaptation of triatomine populations, coupled with their highly diverse feeding strategies (vertebrate haematophagy, kleptohaematophagy, and coprophagy), and has elevated interest in triatomines as potential arboviral vectors. Information on the triatomine virome is scant, with prior records including only eight insect-specific viruses: Triatoma virus (TrV) and Rhodnius prolixus viruses 1-7. Here, we leverage publicly available transcriptome datasets to assess viral diversity in 122 wild and colony kissing bugs representing eight species from six countries. In total, six viruses were detected (including Rhodnius prolixus viruses 4-6), and TrV was detected in almost half of all screened triatomines. This is the first report of TrV in Triatoma brasiliensis and in members of the genus Mepraia (M. gajardoi, M. spinolai, and M. parapatrica), and this effort has vastly expanded the publicly available genomic resources of TrV, adding 39 genome sequences to the single genome sequence currently available in the GenBank database. Furthermore, two additional viruses-Meccus longipennis virus 1 and Drosophila melanogaster Nora virus-are herein reported for the first time from kissing bugs. Meccus longipennis virus 1 was detected in Triatoma infestans from Argentina, Brazil, Chile, and Peru, and Drosophila melanogaster Nora virus was found in T. infestans from Argentina. Our results illustrate the advantage and utility of low-cost transcriptome data mining for the discovery of known and novel arboviruses in triatomines and other potential insect vectors.

Tracing the Evolutionary History of the Temperature-Sensing Prion-like Domain in EARLY FLOWERING 3 Highlights the Uniqueness of AtELF3

Plants have evolved mechanisms to anticipate and adjust their growth and development in response to environmental changes. Understanding the key regulators of plant performance is crucial to mitigate the negative influence of global climate change on crop production. EARLY FLOWERING 3 (ELF3) is one such regulator playing a critical role in the circadian clock and thermomorphogenesis. In Arabidopsis thaliana, ELF3 contains a prion-like domain (PrLD) that acts as a thermosensor, facilitating liquid-liquid phase separation at high ambient temperatures. To assess the conservation of this function across the plant kingdom, we traced the evolutionary emergence of ELF3, with a focus on the presence of PrLDs. We found that the PrLD, primarily influenced by the length of polyglutamine (polyQ) repeats, is most prominent in Brassicales. Analyzing 319 natural A. thaliana accessions, we confirmed the previously described wide range of polyQ length variation in AtELF3, but found it to be only weakly associated with geographic origin, climate conditions, and classic temperature-responsive phenotypes. Interestingly, similar polyQ length variation was not observed in several other investigated Bassicaceae species. Based on these findings, available prediction tools and limited experimental evidence, we conclude that the emergence of PrLD, and particularly polyQ length variation, is unlikely to be a key driver of environmental adaptation. Instead, it likely adds an additional layer to ELF3's role in thermomorphogenesis in A. thaliana, with its relevance in other species yet to be confirmed.

Spatio-temporal distribution and international context of bovine viral diarrhoea virus genetic diversity in France

Bovine viral diarrhoea (BVD) is one of the most economically damaging livestock enzootic diseases in the world. BVD aetiological agents are three pestiviruses (BVDV-1, -2 and HoBi-like pestivirus), which exhibit high genetic diversity and complex transmission cycles. This considerably hampers the management of the disease, which is why eradication plans have been implemented in several countries. In France, a national plan has been in place since 2019. Our understanding of its impact on the distribution of BVDV genotypes is limited by the availability of French genetic data. Here, we conducted a molecular epidemiology study to refine our knowledge of BVDV genetic diversity in France, characterise its international relationships, and analyse national spatio-temporal genotypic distribution. We collated 1037 BVDV-positive samples throughout France between 2011 and 2023, with a greater sampling effort in two major cattle production areas. We developed a high-throughput sequencing protocol which we used to complete the 5'UTR genotyping of this collection. We show that two main BVDV-1 genotypes, 1e and 1b, account for 88% of genotyped sequences. We also identified seven other BVDV-1 genotypes occurring at low frequencies and three BVDV-2 samples (genotype 2c). Phylogenetic analyses indicate different worldwide distribution patterns between the two main BVDV-1 genotypes. Their relative frequencies present no major changes in France since the 1990s and few variations at the national scale. We also found some degree of local spatial structuring in western France. Overall, our results demonstrate the potential of large-scale sequence-based surveillance to monitor changes in the epidemiological situation of enzootic diseases.

Phylogeographic analysis of Begomovirus coat and replication-associated proteins

Begomoviruses are globally distributed plant pathogens that significantly limit crop production. These viruses are traditionally described according to phylogeographic distribution and categorized into two groups: begomoviruses from the Africa, Asia, Europe and Oceania (AAEO) region and begomoviruses from the Americas. Monopartite begomoviruses are more common in the AAEO region, while bipartite viruses predominate in the Americas, where the begomoviruses lack the V2/AV2 gene involved in inter-cellular movement and RNA silencing suppression found in AAEO begomoviruses. While these features are generally accepted as lineage-defining, the number of known species has doubled due to sequence-based discovery since 2010. To re-evaluate the geographic groupings after the rapid expansion of the genus, we conducted phylogenetic analyses for begomovirus species representatives of the two longest and most conserved begomovirus proteins: the coat and replication-associated proteins. Both proteins still largely support the broad AAEO and Americas begomovirus groupings, except for sweet potato-infecting begomoviruses that form an independent, well-supported clade for their coat protein regardless of the region they were isolated from. Our analyses do not support more fine-scaled phylogeographic groupings. Monopartite and bipartite genome organizations are broadly interchanged throughout the phylogenies, and the absence of the V2/AV2 gene is highly reflective of the split between Americas and AAEO begomoviruses. We observe significant evidence of recombination within the Americas and within the AAEO region but rarely between the regions. We speculate that increased globalization of agricultural trade, the invasion of polyphagous whitefly vector biotypes and recombination will blur begomovirus phylogeographic delineations in the future.

Mitogenomics clarifies the position of the Nearctic magpies (Pica hudsonia and Pica nuttalli) within the Holarctic magpie radiation

Partial separation of a peripheral population may lead to its divergence and, potentially, speciation due to genetic drift followed by selection and geographic isolation. This process may cause taxonomic uncertainty because reproductive isolation in allopatry cannot be verified directly. The two Nearctic allopatric species of magpies (Aves, Corvidae: Pica) serve as a good example of these problems. The Black-billed magpie Pica hudsonia is widely distributed in North America, whereas the Yellow-billed Magpie Pica nuttalli is endemic to a restricted range in California. Their relationships with Palearctic species have been little studied. We obtained complete mitochondrial genomes of both Nearctic magpie species, along with the Eurasian Magpie (Pica pica) and the Oriental Magpie (Pica serica), 20 mitogenomes in total. Phylogenetic analysis reveals a basal position of P. serica, and P. pica as a sister clade to the two Nearctic species. P. hudsonia and P. nuttalli form reciprocal monophyletic subclades, showing recent divergence between and within them. Our data show that the Nearctic magpie lineage diverged from the common ancestor with P. pica, with a single migration wave via the Beringia. Within the Nearctic, we hypothesize a peripatric mode of speciation among Pica taxa due to the divergence and separation of the small marginal population in California below the Sierra-Nevada mountains. Diversifying amino acid substitutions in ND4-ND5-ND6 genes along the branch leading to the New World clade may indicate selection for heat-tolerance. Considering the clear phenotypic differences between P. hudsonia and P. nuttalli, our data, showing their reciprocal monophylies and genetic distinctness, is consistent with the two-species taxonomy.

Surface protein distribution in Group B Streptococcus isolates from South Africa and identifying vaccine targets through in silico analysis

Group B Streptococcus (GBS) is a major cause of pneumonia, sepsis, and meningitis in infants younger than 3 months of age. Furthermore, GBS infection in pregnant women is associated with stillbirths and pre-term delivery. It also causes disease in immunocompromised adults and the elderly, but the highest incidence of the disease occurs in neonates and young infants. At this time, there are no licensed vaccines against GBS. Complete GBS genome sequencing has helped identify genetically conserved and immunogenic proteins, which could serve as vaccine immunogens. In this study, in silico reverse vaccinology method were used to evaluate the prevalence and conservation of GBS proteins in invasive and colonizing isolates from South African infants and women, respectively. Furthermore, this study aimed to predict potential GBS vaccine targets by evaluating metrics such as antigenicity, physico-chemical properties, subcellular localization, secondary and tertiary structures, and epitope prediction and conservation. A total of 648 invasive and 603 colonizing GBS isolate sequences were screened against a panel of 89 candidate GBS proteins. Ten of the 89 proteins were highly genetically conserved in invasive and colonizing GBS isolates, nine of which were computationally inferred proteins (gbs2106, SAN_1577, SAN_0356, SAN_1808, SAN_1685, SAN_0413, SAN_0990, SAN_1040, SAN_0226) and one was the surface Immunogenic Protein (SIP). Additionally, the nine proteins were predicted to be more antigenic than the SIP protein (antigenicity score of > 0.6498), highlighting their potential as GBS vaccine antigen targets.

Complex genetic variation in nearly complete human genomes

Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here, we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (130 Mbp median continuity), closing 92% of all previous assembly gaps1,2 and reaching telomere-to-telomere (T2T) status for 39% of the chromosomes. We highlight complete sequence continuity of complex loci, including the major histocompatibility complex (MHC), SMN1/SMN2, NBPF8, and AMY1/AMY2, and fully resolve 1,852 complex structural variants (SVs). In addition, we completely assemble and validate 1,246 human centromeres. We find up to 30-fold variation in α-satellite high-order repeat (HOR) array length and characterize the pattern of mobile element insertions into α-satellite HOR arrays. While most centromeres predict a single site of kinetochore attachment, epigenetic analysis suggests the presence of two hypomethylated regions for 7% of centromeres. Combining our data with the draft pangenome reference1 significantly enhances genotyping accuracy from short-read data, enabling whole-genome inference3 to a median quality value (QV) of 45. Using this approach, 26,115 SVs per sample are detected, substantially increasing the number of SVs now amenable to downstream disease association studies.

Morphological and molecular identification of two new Marasmiellus species (Omphalotaceae, Agaricales) from Thailand

Marasmiellus (Omphalotaceae, Agaricales) specimens collected in Thailand were investigated based on morphological characteristics and molecular phylogenetic analyses. In the present study, two species are introduced as new to science, namely Marasmiellusthailandicus and M.minutisporus. Phylogenetic analyses were carried out based on the internal transcribed spacer (nrITS) and nuclear ribosomal RNA large subunit (nrLSU) regions, and the results revealed that the two new taxa are distinct species within Marasmiellus. Another specimen was identified as M.scandens and is reported for the first time with morphology and molecular data from Thailand. Descriptions, illustrations, and phylogenetic results are provided. In addition, M.diaphanus and M.colocasiae are proposed as new combinations of Collybiopsisdiaphana and Paramarasmiuscolocasiae, respectively, based on the phylogenetic evidence.

Species limits and hybridization in Andean leaf-eared mice (Phyllotis)

Leaf-eared mice (genus Phyllotis) are among the most widespread and abundant small mammals in the Andean Altiplano, but species boundaries and distributional limits are often poorly delineated due to sparse survey data from remote mountains and high-elevation deserts. Here we report a combined analysis of mitochondrial DNA variation and whole-genome sequence (WGS) variation in Phyllotis mice to delimit species boundaries, to assess the timescale of diversification of the group, and to examine evidence for interspecific hybridization. Estimates of divergence dates suggest that most diversification of Phyllotis occurred during the past 3 million years. Consistent with the Pleistocene Aridification hypothesis, our results suggest that diversification of Phyllotis largely coincided with climatically induced environmental changes in the mid- to late Pleistocene. Contrary to the Montane Uplift hypothesis, most diversification in the group occurred well after the major phase of uplift of the Central Andean Plateau. Species delimitation analyses revealed surprising patterns of cryptic diversity within several nominal forms, suggesting the presence of much undescribed alpha diversity in the genus. Results of genomic analyses revealed evidence of ongoing hybridization between the sister species Phyllotis limatus and P. vaccarum and suggest that the contemporary zone of range overlap between the two species represents an active hybrid zone.

The first complete chloroplast genome for the species-rich genus Anthemis (Asteraceae)

Anthemis L. 1753 is a species-rich genus of Asteraceae. It includes species of economic value as ornamental, edible and medicinal plants. We report here the complete chloroplast genome of Anthemis cretica subsp. calabrica (Arcang.) R. Fern. 1975, the first chloroplast genome of any Anthemis species. For the scope, we have used long reads obtained with Oxford Nanopore technology. The assembled plastome is 149,509 bp long and is subdivided in a large single-copy region (LSC, 82,317 bp), a small single-copy region (SSC, 18,212 bp) and two inverted repeat regions (IR: 24,490 bp). It comprehends 136 predicted genes, of which 92 protein-coding genes, 35 tRNAs, and 8 rRNAs. The overall GC content is 37.54%. The position of A. cretica subsp. calabrica in the phylogenetic tree is congruent with those of previous analyses based on a few chloroplast or nuclear regions.

The diversity and taxonomy of Tomentella (Thelephoraceae, Thelephorales) with descriptions of four new species from Southwestern China

Taxonomy plays a central role in understanding the diversity of life, translating the products of biological exploration and discovery specimens and observations into systems of names that settle a "classification home" to taxa. Up to this point, studies on the taxonomy and phylogeny of the basidiomycetous genus Tomentella stemmed mainly from the temperate to boreal zones of the North Hemisphere, but were scarce in tropical Asia. In this study, four new species, viz. Tomentellaolivaceobasidiosa, T.velutina, T.wumenshanensis and T.yunnanensis from China, are described and illustrated based on the morphological characteristics and molecular phylogenetic analyses, in which the sequences of ITS+nLSU+mtSSU+RPB2 genes were used for the phylogenetic analyses using Maximum Likelihood, Maximum Parsimony and Bayesian Inference methods. All the new species can be well recognised by their macroscopical and anatomical characteristics. The four new species, closely related taxa in the phylogenetic tree and morphologically similar species are discussed.

Genome Mining Leads to the Identification of a Stable and Promiscuous Baeyer-Villiger Monooxygenase from a Thermophilic Microorganism

Baeyer-Villiger monooxygenases (BVMOs) are NAD(P)H-dependent flavoproteins that convert ketones to esters and lactones. While these enzymes offer an appealing alternative to traditional Baeyer-Villiger oxidations, these proteins tend to be either too unstable or exhibit too narrow of a substrate scope for implementation as industrial biocatalysts. Here, sequence similarity networks were used to search for novel BVMOs that are both stable and promiscuous. Our genome mining led to the identification of an enzyme from Chloroflexota bacterium (strain G233) dubbed ssnBVMO that exhibits i) the highest melting temperature of any naturally sourced BVMO (62.5 °C), ii) a remarkable kinetic stability across a wide range of conditions, similar to those of PAMO and PockeMO, iii) optimal catalysis at 50 °C, and iv) a broad substrate scope that includes linear aliphatic, aromatic, and sterically bulky ketones. Subsequent quantitative assays using propiophenone demonstrated >95 % conversion. Several fusions were also constructed that linked ssnBVMO to a thermostable phosphite dehydrogenase. These fusions can recycle NADPH and catalyze oxidations with sub-stoichiometric quantities of this expensive cofactor. Characterization of these fusions permitted identification of PTDH-L1-ssnBVMO as the most promising protein that could have utility as a seed sequence for enzyme engineering campaigns aiming to develop biocatalysts for Baeyer-Villiger oxidations.

Insights from multigene analysis: first report of a Southeast Asian Mosquito, Aedes (Mucidus) laniger (Diptera: Culicidae) on Jeju Island from Korea

BACKGROUND

Certain mosquitoes are known as dominant vectors worldwide, and transmit infectious diseases. The expansion of mosquito habitats due to climate change and increased human activities poses a significant health threat by facilitating the spread of various non-native infectious diseases. This study focused on the detection of the Southeast Asian mosquito species, Aedes (Mucidus) laniger (Wiedemann, 1820) on Jeju Island, the southernmost region of the Republic of Korea (ROK), highlighting the potential risks associated with the spread of vector-borne diseases, particularly emphasizing the elevated likelihood of invasion by Southeast Asian mosquitoes.

METHODS

Field surveys were conducted in August 2023 on Jeju Island. Adult mosquitoes were collected using BG-sentinel traps and identified to the species level using taxonomic keys. Morphological and molecular analyses were employed to confirm species designations. Molecular data, including mitochondrial and nuclear genes, were used for phylogenetic analysis, which was performed to compare and identify among recorded subgenera in ROK. Species distribution modeling for Ae. laniger was performed to predict potential habitats using R package 'BIOMOD2'.

RESULTS

The two specimens of Ae. laniger were collected for the first time on Jeju Island. Morphological and molecular analyses confirmed the identity of this species within the subgenus Mucidus and validated the first record of this species in the ROK. We employed a simple multigene phylogenetic analysis to confirm a new mosquito record at the genus and subgenus levels, finally validating the consistency between morphological identification and molecular phylogenetic outcomes. Furthermore, we have updated the taxonomic keys for the genus Aedes in the ROK, and revised mosquito lists for Jeju Island, incorporating the inclusion of Ae. laniger. On the basis of species distribution modeling, the area of suitable habitat for Ae. laniger is expected to expand due to climate change, but this change did not appear to be meaningful in East Asia.

CONCLUSIONS

This case offers the first report of the Southeast Asian mosquito, Ae. laniger, in the ROK. The detection of this species on Jeju Island suggests the potential establishment of a breeding population their habitat and raises concerns about further expansion into the Korean Peninsula. Considering the annual occurrence of mosquito-borne disease cases in the Southeast Asia, it is essential to conduct monitoring not only in Jeju Island, where Ae. laniger has been identified, but also across the entire Korean Peninsula.

Comparative plastome assembly of the yellow ironweed (Verbesina alternifolia) using Nanopore and Illumina reads

Chloroplast genomes (plastomes) represent a very important source of valuable information for phylogenetic and biogeographic reconstructions. The use of short reads (as those produced from Illumina sequencing), along with de novo read assembly, has been considered the "gold standard" for plastome reconstruction. However, short reads often cannot reconstruct long repetitive regions in chloroplast genomes. Long Nanopore (ONT) reads can help bridging long repetitive regions but are by far more error-prone than those produced by Illumina sequencing. Verbesina is the largest genus of tribe Heliantheae (Asteraceae) and includes species of economic importance as ornamental or as invasive weeds. However, no complete chloroplast genomes have been published yet for the genus. We utilized Illumina and Nanopore sequencing data and different assembly strategies to reconstruct the plastome of Verbesina alternifolia and evaluated the usefulness of the Nanopore assemblies. The two plastome sequence assemblages, one obtained with the Nanopore sequencing and the other inferred with Illumina reads, were identical, except for missing bases in homonucleotide regions. The best-assembled plastome of V. alternifolia was 152,050 bp in length and contained 80, 29, and four unique protein-coding genes, tRNAs, and rRNAs, respectively. When used as reference for mapping Illumina reads, all plastomes performed similarly. In a phylogenetic analysis including 28 other plastomes from closely related taxa (from the Heliantheae alliance), the two Verbesina chloroplast genomes grouped together and were nested among the other members of the tribe Heliantheae s.str. Our study highlights the usefulness of the Nanopore technology for assembling rapidly and cost-effectively chloroplast genomes, especially in taxonomic groups with paucity of publicly available plastomes.

Mapping Transmission Dynamics and Drug Resistance Surveillance in the Cyprus HIV-1 Epidemic (2017-2021)

The human immunodeficiency virus type 1 (HIV-1) epidemic has been a major public health threat on a global scale since the early 1980s. Despite the introduction of combination antiretroviral therapy (cART), the incidence of new HIV-1 infections continues to rise in some regions around the world. Thus, with the continuous transmission of HIV-1 and the lack of a cure, it is imperative for molecular epidemiological studies to be performed, to monitor the infection and ultimately be able to control the spread of this virus. This work provides a comprehensive molecular epidemiological analysis of the HIV-1 infection in Cyprus, through examining 305 HIV-1 sequences collected between 9 March 2017 and 14 October 2021. Employing advanced statistical and bioinformatic techniques, the research delved deeply into understanding the transmission dynamics of the HIV-1 epidemic in Cyprus, as well as the monitoring of HIV-1's genetic diversity and the surveillance of transmitted drug resistance. The characterization of Cyprus's HIV-1 epidemic revealed a diverse landscape, comprising 21 HIV-1 group M pure subtypes and circulating recombinant forms (CRFs), alongside numerous uncharacterized recombinant strains. Subtypes A1 and B emerged as the most prevalent strains, followed by CRF02_AG. The findings of this study also revealed high levels of transmitted drug resistance (TDR) patterns, raising concerns for the efficacy of cART. The demographic profiles of individuals involved in HIV-1 transmission underscored the disproportionate burden borne by young to middle-aged Cypriot males, particularly those in the MSM community, who reported contracting the virus in Cyprus. An assessment of the spatiotemporal evolutionary dynamics illustrated the global interconnectedness of HIV-1 transmission networks, implicating five continents in the dissemination of strains within Cyprus: Europe, Africa, Asia, North America, and Oceania. Overall, this study advances the comprehension of the HIV-1 epidemic in Cyprus and highlights the importance of understanding HIV-1's transmission dynamics through continuous surveillance efforts. Furthermore, this work emphasizes the critical role of state-of-the-art bioinformatics analyses in addressing the challenges posed by HIV-1 transmission globally, laying the groundwork for public health interventions aimed at curbing its spread and improving patient outcomes.

Two +ssRNA mycoviruses cohabiting the fungal cultivar of leafcutter ants

Leafcutter ants are dominant herbivores in the Neotropics and rely on a fungus (Leucoagaricus gongylophorus) to transform freshly gathered leaves into a source of nourishment rather than consuming the vegetation directly. Here we report two virus-like particles that were isolated from L. gongylophorus and observed using transmission electron microscopy. RNA sequencing identified two +ssRNA mycovirus strains, Leucoagaricus gongylophorus tymo-like virus 1 (LgTlV1) and Leucoagaricus gongylophorus magoulivirus 1 (LgMV1). Genome annotation of LgTlV1 (7401 nt) showed conserved domains for methyltransferase, endopeptidase, viral RNA helicase, and RNA-dependent RNA polymerase (RdRp). The smaller genome of LgMV1 (2636 nt) contains one open reading frame encoding an RdRp. While we hypothesize these mycoviruses function as symbionts in leafcutter farming systems, further study will be needed to test whether they are mutualists, commensals, or parasites.

Detection and spread of high pathogenicity avian influenza virus H5N1 in the Antarctic Region

Until recent events, the Antarctic was the only major geographical region in which high pathogenicity avian influenza virus (HPAIV) had never previously been detected. Here we report on the detection of clade 2.3.4.4b H5N1 HPAIV in the Antarctic and sub-Antarctic regions of South Georgia and the Falkland Islands, respectively. We initially detected H5N1 HPAIV in samples collected from brown skuas at Bird Island, South Georgia on 8th October 2023. Since this detection, mortalities were observed in several avian and mammalian species at multiple sites across South Georgia. Subsequent testing confirmed H5N1 HPAIV across several sampling locations in multiple avian species and two seal species. Simultaneously, we also confirmed H5N1 HPAIV in southern fulmar and black-browed albatross in the Falkland Islands. Genetic assessment of the virus indicates spread from South America, likely through movement of migratory birds. Critically, genetic assessment of sequences from mammalian species demonstrates no increased risk to human populations above that observed in other instances of mammalian infections globally. Here we describe the detection, species impact and genetic composition of the virus and propose both introductory routes and potential long-term impact on avian and mammalian species across the Antarctic region. We also speculate on the threat to specific populations following recent reports in the area.

A New Model and Dating for the Evolution of Complex Plastids of Red Alga Origin

Complex plastids, characterized by more than two bounding membranes, still present an evolutionary puzzle for the traditional endosymbiotic theory. Unlike primary plastids that directly evolved from cyanobacteria, complex plastids originated from green or red algae. The Chromalveolata hypothesis proposes a single red alga endosymbiosis that involved the ancestor of all the Chromalveolata lineages: cryptophytes, haptophytes, stramenopiles, and alveolates. As extensive phylogenetic analyses contradict the monophyly of Chromalveolata, serial plastid endosymbiosis models were proposed, suggesting a single secondary red alga endosymbiosis within Cryptophyta, followed by subsequent plastid transfers to other chromalveolates. Our findings based on 97 plastid-encoded markers, 112 species, and robust phylogenetic methods challenge all the existing models. They reveal two independent secondary endosymbioses, one within Cryptophyta and one within stramenopiles, precisely the phylum Ochrophyta, with two different groups of red algae. Consequently, we propose a new model for the emergence of red alga plastid-containing lineages and, through molecular clock analyses, estimate their ages.

Wolbachia strain diversity in a complex group of sympatric cryptic parasitoid wasp species

BACKGROUND

Maternally-inherited symbionts can induce pre-mating and/or post-mating reproductive isolation between sympatric host lineages, and speciation, by modifying host reproductive phenotypes. The large parasitoid wasp genus Cotesia (Braconidae) includes a diversity of cryptic species, each specialized in parasitizing one to few related Lepidoptera host species. Here, we characterized the infection status of an assemblage of 21 Cotesia species from 15 countries by several microbial symbionts, as a first step toward investigating whether symbionts may provide a barrier to gene flow between these parasitoid host lineages.

RESULTS

The symbiotic microbes Arsenophonus, Cardinium, Microsporidium and Spiroplasma were not detected in the Cotesia wasps. However, the endosymbiotic bacterium Wolbachia was present in at least eight Cotesia species, and hence we concentrated on it upon screening additional DNA extracts and SRAs from NCBI. Some of the closely related Cotesia species carry similar Wolbachia strains, but most Wolbachia strains showed patterns of horizontal transfer between phylogenetically distant host lineages.

CONCLUSIONS

The lack of co-phylogenetic signal between Wolbachia and Cotesia suggests that the symbiont and hosts have not coevolved to an extent that would drive species divergence between the Cotesia host lineages. However, as the most common facultative symbiont of Cotesia species, Wolbachia may still function as a key-player in the biology of the parasitoid wasps. Its precise role in the evolution of this complex clade of cryptic species remains to be experimentally investigated.

Phylogenetic evidence of extensive spatial mixing of diverse HIV-1 group M lineages within Cameroon but not between its neighbours

From the perspective of developing relevant interventions for treating HIV and controlling its spread, it is particularly important to comprehensively understand the underlying diversity of the virus, especially in countries where the virus has been present and evolving since the cross-species transmission event that triggered the global pandemic. Here, we generate and phylogenetically analyse sequences derived from the gag-protease (2010 bp; n = 115), partial integrase (345 bp; n = 36), and nef (719 bp; n = 321) genes of HIV-1 group M (HIV-1M) isolates sampled between 2000 and 2022 from two cosmopolitan cities and 40 remote villages of Cameroon. While 52.4% of all sequenced viruses belonged to circulating recombinant form (CRF) 02_AG (CRF02_AG), the remainder were highly diverse, collectively representing seven subtypes and sub-subtypes, eight CRFs, and 36 highly divergent lineages that fall outside the established HIV-1M classification. Additionally, in 77 samples for which at least two genes were typed, 31% of the studied viruses apparently had fragments from viruses belonging to different clades. Furthermore, we found that the distribution of HIV-1M populations is similar between different regions of Cameroon. In contrast, HIV-1M demographics in Cameroon differ significantly from those in its neighbouring countries in the Congo Basin (CB). In phylogenetic trees, viral sequences cluster according to the countries where they were sampled, suggesting that while there are minimal geographical or social barriers to viral dissemination throughout Cameroon, there is strongly impeded dispersal of HIV-1M lineages between Cameroon and other locations of the CB. This suggests that the apparent stability of highly diverse Cameroonian HIV-1M populations may be attributable to the extensive mixing of human populations within the country and the concomitant trans-national movements of major lineages with very similar degrees of fitness; coupled with the relatively infrequent inter-national transmission of these lineages from neighbouring countries in the CB.

Phylogeography of horseshoe bat sarbecoviruses in Vietnam and neighbouring countries. Implications for the origins of SARS-CoV and SARS-CoV-2

Previous studies on horseshoe bats (Rhinolophus spp.) have described many coronaviruses related to SARS-CoV (SARSCoVr) in China and only a few coronaviruses related to SARS-CoV-2 (SARSCoV2r) in Yunnan (southern China), Cambodia, Laos and Thailand. Here, we report the results of several field missions carried out in 2017, 2021 and 2022 across Vietnam during which 1218 horseshoe bats were sampled from 19 locations. Sarbecoviruses were detected in 11% of faecal RNA extracts, with much more positives among Rhinolophus thomasi (46%). We assembled 38 Sarbecovirus genomes, including 32 SARSCoVr, four SARSCoV2r, and two recombinants of SARSCoVr and SARSCoV2r (RecSar), one showing a Spike protein very similar to SARS-CoV-2. We detected a bat co-infected with four coronaviruses, including two sarbecoviruses. Our analyses revealed that Sarbecovirus genomes evolve in Vietnam under strong geographical and host constraints. First, we found evidence for a deep separation between viruses from northern Vietnam and those from central and southern Vietnam. Second, we detected only SARSCoVr in Rhinolophus thomasi, both SARSCoVr and SARSCoV2r in Rhinolophus affinis, and only RecSar in Rhinolophus pusillus captured close to the border with China. Third, the bias in favour of Uracil in synonymous third codon positions of SARSCoVr extracted from R. thomasi showed a negative correlation with latitudes. Our results also provided support for an emergence of SARS-CoV in horseshoe bats from northern Yunnan and emergence of SARS-CoV-2 in horseshoe bats from northern Indochina subtropical forests (southern Yunnan, northern Laos and north-western Vietnam).

Phylogenetic systematics of Vigna sensu stricto in the context of Physostigma and allies

PREMISE

Vigna includes economically vital crops and wild species. Molecular systematic studies of Vigna species resulted in generic segregates of many New World (NW) species. However, limited Old World (OW) sampling left questions regarding inter- and intraspecific relationships in Vigna s.s.

METHODS

African species, including the putative sister genus Physostigma, were comprehensively sampled within the context of NW relatives. Maximum likelihood and Bayesian inference analyses of the chloroplast matK-trnK and nuclear ribosomal ITS/5.8 S (ITS) DNA regions were undertaken to resolve OW Vigna taxonomic questions. Divergence dates were estimated using BEAST to date key nodes in the phylogeny.

RESULTS

Analyses of matK and ITS data supported five clades of Vigna s.s.: subg. Lasiospron, a reduced subg. Vigna, subg. Haydonia, subg. Ceratotropis, an enlarged subg. Plectrotropis, and a clade including V. kirkii and V. stenophylla. Genome size estimates of 601 Mb for V. kirkii are near the overall mean of the genus, whereas V. stenophylla had a larger genome (810 Mb), similar to some Vigna subg. Ceratotropis or Plectrotropis species.

CONCLUSIONS

Former subg. Vigna is reduced to yellow- and blue-flowered species and subg. Plectrotropis is enlarged to mostly all white-, pink-, and purple-flowered species. The age of the split between NW and OW Vigna lineages is ~6-7 Myr. Genome size estimates cannot rule out a polyploid or hybrid origin for V. stenophylla, potentially involving extinct lineage ancestors of Vigna subg. Ceratotropis or Plectrotropis, as indicated by network and phylogenetic analyses. Taxonomic revisions are suggested based on these results.