ModelFinder: fast model selection for accurate phylogenetic estimates

Proteorhodopsin insights into the molecular mechanism of vectorial proton transport

Bacterial proton pumps, proteorhodopsins (PRs), are a major group of light-driven membrane proteins found in marine bacteria. They are functionally and structurally distinct from archaeal and eukaryotic proton pumps. To elucidate the proton transfer mechanism by PRs and understand the differences to nonbacterial pumps on a molecular level, high-resolution structures of PRs' functional states are needed. In this work, we have determined atomic-resolution structures of MAR, a PR from marine actinobacteria, in various functional states, notably the challenging late O intermediate state. These data and information from recent atomic-resolution structures on an archaeal outward proton pump bacteriorhodopsin and bacterial inward proton pump xenorhodopsin allow for deducing key universal elements for light-driven proton pumping. First, long hydrogen-bonded chains characterize proton pathways. Second, short hydrogen bonds allow proton storage and inhibit their backflow. Last, the retinal Schiff base is the active proton donor and acceptor to and from hydrogen-bonded chains.

Bacterial pathogen deploys the iminosugar glycosyrin to manipulate plant glycobiology

The extracellular space (apoplast) in plants is a key battleground during microbial infections. To avoid recognition, the bacterial model phytopathogen Pseudomonas syringae pv. tomato DC3000 produces glycosyrin. Glycosyrin inhibits the plant-secreted β-galactosidase BGAL1, which would otherwise initiate the release of immunogenic peptides from bacterial flagellin. Here, we report the structure, biosynthesis, and multifunctional roles of glycosyrin. High-resolution cryo-electron microscopy and chemical synthesis revealed that glycosyrin is an iminosugar with a five-membered pyrrolidine ring and a hydrated aldehyde that mimics monosaccharides. Glycosyrin biosynthesis was controlled by virulence regulators, and its production is common in bacteria and prevents flagellin recognition and alters the extracellular glycoproteome and metabolome of infected plants. These findings highlight a potentially wider role for glycobiology manipulation by plant pathogens across the plant kingdom.

Reporting complete chloroplast genome of endangered red mulberry, useful for understanding hybridization and phylogenetic relationships

Introgressive hybridization of the North American native red mulberry (Morus rubra) with its invasive congener white mulberry (Morus alba) has severely threatened the genetic integrity of M. rubra, which is primarily found in pristine riparian forests. The major objectives of the present study were (1) to sequence, assemble, and annotate the complete chloroplast genome of M. rubra, and (2) to perform phylogenomic analyses of Morus species to assess their evolutionary history and hybridization events within the genus. We sampled 45 mulberry trees representing populations from eight US states for chloroplast genome sequencing. We found that the chloroplast genome of M. rubra ranged from 159,396 to 159,423 basepair (bp) and contained 128 genes coding for eight rRNAs, 37 tRNAs, and 83 proteins. The chloroplast genome of M. rubra was at least 103 bp larger than that of M. alba. The chloroplast DNA sequence polymorphism analysis of M. rubra showed the presence of 12 haplotypes. The chloroplast genome analysis across 12 Morus species identified trnK-UUU-rps16, psbI-trnG-UCC, psbC-psbZ, psbZ-trnM-CAU, rps4-trnT-UGU, trnT-UGU-trnL-UAA, ndhC-trnV-UAC, psbE-petL, clpP1, ndhF-rpl32, rpl32-trnL-UAG, and ccsA-ndhD as having higher DNA polymorphism (Pi > 0.01). Phylogenomic analysis of the 12 Morus species revealed distinct clades for Asian, North American, South American, and African Morus, supporting the monophyly of the genus. Divergence time analysis showed the most recent common ancestor of the genus Morus diverged 38.67 million years ago (MYA), separating the African clade of M. mesozygia and M. insignis from the others, while the American and Asian clades diverged 28.63 MYA. The results from this study provide insights into the chloroplast genome structure of M. rubra, offering a foundational data that bridges the knowledge gaps for addressing complex taxonomic complexities within the genus and for developing molecular markers to study population genetics, including introgressive hybridization.

Isolation and genomic characterization of Psychrobacillus isolate L3 and bacteriophage Spoks: a new phage-host pair from Antarctic soil

BACKGROUND

Most habitats on Earth house unfathomable microbial diversity, yet much of it remains uncultured. The same applies to temperate phages, most of which documented to date are predicted purely in silico from the prophage-like genomic regions of the bacteria, lacking any experimental evidence of their functional integrity (e.g., the ability to undergo lytic replication). Hard-to-access parts of our planet with unique environments serve as especially promising places to collect samples for the isolation of novel microbes highly divergent from those isolated thus far. Antarctica, a continent mostly covered by a thick ice sheet, is one such area of our planet rife with novel microbiological entities. In this study, we aimed to isolate and characterize a novel culturable phage-host pair from Antarctic soils.

RESULTS

Psychrobacillus phage Spoks was retrieved alongside its host bacterial strain designated as "L3" from an ice-free soil sample collected at Waddington Bay, Graham Coast, Antarctica. Whole-genome sequencing of both the phage and the host revealed that they are divergent from, respectively, viruses and bacteria cultured and characterized thus far, and the intergenomic differences suggest that both might represent novel taxa. The genome of siphophage Spoks is a 36,472 bp long linear double-stranded DNA molecule with 11 base long 3' cohesive overhangs. Spoks can integrate into the chromosome of its isolation host strain in a site-specific fashion. Integration takes place in the genomic region of the host chromosome between the ORFs predicted to encode a DNA topoisomerase III and a BlaI/MecI/CopY family transcriptional regulator via recombination between attP and attB, which share a 19 bp "core" overlap sequence. L3 lysogens containing Spoks are not stable, with regular spontaneous induction occurring. Although the attachment site overlap sequence was found in the publicly available genomic sequences of several other Psychrobacillus spp. strains isolated from different habitats, none were found to contain a Spoks-like prophage.

CONCLUSIONS

The isolation and characterization of Psychrobacillus temperate phage Spoks and its host strain L3 from Antarctica highlight the potential for discovering novel biological entities divergent from their closest cultured relatives with relative ease, given access to such difficult-to-access undersampled environments, and are expected to encourage similar studies.

Studies of Vietnamese Pteridophyte Flora 3

This is the third paper in a series dedicated to updating the knowledge of the Vietnamese pteridophyte flora. Based on recent collections, we first reported three new national records of ferns: Haplopterisyakushimensis, Lindsaeakohkongensis, and Pterispseudowulaiensis. Secondly, we conducted phylogenetic analyses to investigate the placements of Lindsaeakohkongensis and Leptochiluspoilanei, each based on three plastid DNA markers. Our results revealed that Lindsaeakohkongensis is sister to L.ensifolia, while Leptochiluspoilanei is embedded within L.cantoniensis. We discussed these results in the context of systematics. Lastly, we reported chromosome numbers for 20 fern species in Vietnam. For seven of these species, including Gymnosphaerasalletii, Lepisorusspicatus, Leptochiluspoilanei, Pteridryscostularis, Pterislatipinna, Pyrrosiaeberhardtii, and Tectariasetulosa, these counts were recorded for the first time. Additionally, three new cytotypes were identified for Diplaziumdoederleinii, Pterisesquirolii, and Tectariaharlandii. This study underscores the need for more diverse data, including DNA sequences, chromosome numbers, and reproductive modes, to be collected and integrated into systematic studies and taxonomic treatments to enhance our understanding of Vietnam's pteridophyte flora.

Phylogenetic and epidemiological insights into centenarians' resilience to COVID-19: exploring the role of past coronavirus pandemics

In the 20th and 21st centuries, humanity has faced several global crises, including world wars, the 1918 Spanish flu, and the recent COVID-19 pandemic. Notably, the COVID-19 pandemic caused significant mortality, particularly among older adults, while younger ages were less affected. Strikingly, according to the Italian National Institute of Statistics (Istat), centenarians (aged 100 and above) in Italy experienced no significant increase in mortality in 2020. This retrospective study hypothesizes that elderly people may have developed an immune response that offered protection against COVID-19, potentially linked to their exposure to a specific past infectious event. We examined historical mortality data from 1872 to 2021 and performed phylogenetics analysis on sequencing data to explore the possibility that centenarians may have encountered another Coronavirus (misidentified as Russian Flu), which could have contributed to their resilience. This research provides insights into the adaptive responses of the most vulnerable populations, symbolically comparing them to the "left-standing trees" following catastrophic events.

Transcriptome remodeling drives acclimation to iron availability in the marine N2-fixing cyanobacterium Trichodesmium erythraeum IMS101

While enhanced phytoplankton growth as a result of iron (Fe) fertilization has been extensively characterized, our understanding of the underlying mechanisms remains incomplete. Here, we show in a laboratory setup mimicking Fe fertilization in the field that transcriptome remodeling is a primary driver of acclimation to Fe availability in the marine diazotrophic cyanobacterium Trichodesmium erythraeum IMS101. Fe supplementation promoted cell growth, photosynthesis and N2 fixation, and concomitant expression of the photosynthesis and N2 fixation genes. The expression of genes encoding major Fe-binding metalloproteins is tightly linked to cellular carbon and nitrogen metabolism and appears to be controlled by the ferric uptake regulator FurA, which is involved in regulating Fe uptake and homeostasis. This feedback loop is reinforced by substitutive expression of functionally equivalent or competitive genes depending on Fe availability, as well as co-expression of multiple Fe stress inducible isiA genes, an adaptive strategy evolved to elicit the Fe-responsive cascade. The study provides a genome-wide perspective on the acclimation of a prominent marine diazotroph to Fe availability, reveals an upgraded portfolio of indicator genes that can be used to better assess Fe status in the environment, and predicts scenarios of how marine diazotrophs may be affected in the future ocean.IMPORTANCEThe scarcity of trace metal iron (Fe) in global oceans has a great impact on phytoplankton growth. While enhanced primary productivity as a result of Fe fertilization has been extensively characterized, the underlying molecular mechanisms remain poorly understood. By subjecting the model marine diazotroph Trichodesmium erythraeum IMS101 to increasing concentrations of supplemented Fe, we demonstrate in it a comprehensively remodeled transcriptome that drives the mobilization of cellular Fe for coordinated carbon and nitrogen metabolism and reallocation of energy and resources. Our data provide broad genomic insight into marine diazotrophs acclimation to Fe availability, enabling the versatility and flexibility in choice of indicator genes for monitoring Fe status in the environment and having implications on how marine diazotrophs persist into the future ocean.

Genome-Wide Identification and Expression Profiling of Glycosidases, Lipases, and Proteases from Invasive Asian Palm Weevil, Rhynchophorus ferrugineus

The red palm weevil, Rhynchophorus ferrugineus, is a destructive, invasive pest to a diverse range of palm plantations globally. Commonly used broad-range chemical insecticides for insect control pose high risks to non-target organisms, humans, and the environment. A bio-rational approach of screening natural small-molecule inhibitors that specifically target R. ferrugineus proteins critical to its life processes can pave the way for developing novel bioinsecticides. Digestive enzymes (DEs), which impair feeding on plants (herbivory), are promising targets. We generated de novo transcriptomes, annotated DE-related genes from the R. ferrugineus gut and abdomen, manually annotated the DE gene family from the recently available genome and our transcriptome data, and reported 34 glycosidases, 85 lipases, and 201 proteases. We identified several tandem duplicates and allelic variants from the lipase and protease families, notably, 10 RferLip and 21 RferPro alleles, which emerged primarily through indels and single-site substitution. These alleles may confer enhanced digestive lipolysis and proteolysis. Phylogenetic analyses identified and classified different subfamilies of DEs and revealed close evolutionary relationships with other coleopterans. We assessed select candidate DEs' activity and the potential for inhibition in silico to better understand the herbivory arsenal. In silico analysis revealed that the selected enzymes exhibited similar ligand-binding affinity to their corresponding substrate, except for protease aminopeptidase N, RferPro40, which exhibited poorer affinity to the inhibitor bestatin. Overall, our study serves as a foundation for further functional analysis and offers a novel target for the development of a novel bio-rational insecticide for R. ferrugineus.

Phylogenomics of the superfamily Lygaeoidea with proposals on taxonomic system (Hemiptera: Heteroptera)

Lygaeoidea, one of the largest superfamilies of the true bugs (Hemiptera: Heteroptera), currently comprises 16 families and exhibits abundant diversification in habitats, body plans, and feeding habits. The relationships within this superfamily are complex, and comprehensive molecular phylogenetic studies, particularly those focusing on subfamilies and tribes within Rhyparochromidae, have been lacking. In the present study, we sampled 125 lygaeoid species representing all 16 families of Lygaeoidea, with a focus on two subfamilies and 12 tribes within Rhyparochromidae. A phylogenetic dataset with 102 genes was assembled, including two nuclear rRNA genes (18S rDNA, 28S rDNA), two mitochondrial rRNA genes (12S rDNA, 16S rDNA), 13 mitochondrial protein-coding genes (PCGs) and 85 nuclear PCGs generated from the low-coverage genomes. Our inferences indicate that Rhyparochromidae is not monophyletic, with one subfamily, one tribe, and one genus deserving elevation to the rank of family. Additionally, this phylogenetic result is also supported by corresponding morphological evidence. Besides, the transfer of the Heissothignus from Heterogastridae to Meschiidae is supported by molecular evidence in this study.

Discovery and characterisation of terpenoid biosynthesis enzymes from Daphniphyllum macropodum

Terpene synthase (TPS) enzymes are known to be pivotal in the biosynthesis of terpenoids in plants and microbes. These enzymes catalyse the transformation of ubiquitous acyclic prenyl diphosphate substrates into diverse hydrocarbon skeletons. Mining TPS genes from the genomes and transcriptomes of diverse taxa of plants and microbes is a powerful tool for the discovery of new enzymes and new chemistries. In this work, we used a combination of long-read and short-read RNA sequencing technologies to develop a high-quality transcriptomic data set for Daphniphyllum macropodum, a poorly studied plant rich in unique terpene derived metabolites. Through mining the transcriptome, we identified different terpene-related enzymes, including prenyl transferases (PTs), triterpene cyclases (TTCs), and terpene synthases (TPSs). These were expressed in a Nicotiana benthamiana system together with rate-limiting enzymes HMGR or DXS to boost the metabolic flux. The products were then analysed using GC-MS. We have identified four monoterpene synthases producing diverse linear, monocyclic and bicyclic monoterpenes including linalool, limonene, geraniol, and pinene. We also identified four sesquiterpene synthases, one producing caryophyllene, one α-guaiene, and two producing a blend of sesquiterpenes. In addition, we demonstrated the activity of two triterpene cyclases both forming cycloartenol, as well as a geranylgeranyl diphosphate synthase (GGPP synthase). Together, these findings expand the known chemical space of D. macropodum terpenoid metabolism and enable further investigations of terpenoids in this under-explored plant species.

Three novel species of Alternaria (Pleosporales, Pleosporaceae) from cereal crops (Poaceae) in China

The genus Alternaria (Pleosporales, Pleosporaceae) comprises saprophytes and pathogens that are widespread around the world. Currently, more than 400 species are recognized within this genus and are classified into 29 sections. In this study, Alternaria strains were isolated from diseased leaves of two cereal crops, rice (Oryzasativa) and maize (Zeamays) in China. These Alternaria spp. were characterized by morphological characterization and phylogenetic analysis using maximum likelihood and Bayesian inference with multiple loci (ITS, GAPDH, RPB2, TEF1, Alt a 1, EndoPG, and OPA10-2). Based on the above analyses, three novel species of AlternariasectionAlternaria were introduced, namely A.oryzicola sp. nov., A.poae sp. nov., and A.zeae sp. nov. This study expands the species diversity of Alternaria associated with Poaceae plants in China.

Development of a culture-independent whole-genome sequencing of Nipah virus using the MinION Oxford Nanopore platform

Nipah virus (NiV) is a deadly zoonotic pathogen in Southeast Asia causing severe respiratory and encephalitis symptoms with a high fatality rate. Whole-genome sequencing (WGS) is crucial for tracking transmission, conducting epidemiological analyses, and understanding NiV's adaptive evolution. WGS is essential for analyzing genomes, particularly in understanding pathogen nature, and pathogenesis and aiding in the development of therapeutics. However, sequencing this highly contagious virus directly from samples is challenging in low- and middle-income countries lacking BSL-4 facilities. This study developed and optimized a culture-independent, high-throughput multiplex PCR-based third-generation sequencing protocol for NiV using the Oxford Nanopore Technology platform and a proposed bioinformatics pipeline to generate consensus genome sequences directly from environmental and clinical specimens. We amplified 12 NiV RT-PCR-positive specimens (11 clinical, one environmental) to produce 60 amplicons, each approximately 400 bp, covering the entire ~18.2 kb genome. Using a two-step reverse transcriptase PCR approach, libraries were prepared with a ligation sequencing kit. Raw sequence data were then analyzed using bioinformatics tools. A minimum of 10,000 total reads per sample provided a nearly complete coverage (>95%) of the NiV genome, even with low virus concentrations (Ct ≤ 32), with an average quality score of 10.2. The WGS of 12 NiV-positive samples achieved coverage between 95.71% (Ct 29.54) and 99.3% (Ct 22.34). The entire process, from RNA extraction to finished sequences, took only 24 h. We developed a portable, culture-independent, high-throughput sequencing workflow suitable for resource-limited settings, aiding in real-time monitoring, outbreak investigation, and detection of new NiV strains and genetic evolution.

IMPORTANCE

The development of a culture-independent, high-throughput whole-genome sequencing (WGS) protocol for Nipah virus (NiV) using the Oxford Nanopore MinION technology marks a significant advancement in outbreak response, surveillance, and genomic analysis of NiV. NiV is an RG4 category C pathogen; working with the NiV virus is a deep concern of biosafety and biosecurity. It demands the development of biologically safe procedures to get genetic information. This protocol utilizes biologically safe samples that were collected into recommended lysis solution, multiplex PCR, and third-generation sequencing, effectively addressing challenges in sequencing NiV. This optimized workflow achieved over 95% genome coverage without the need for virus culture. It is a cost-effective, rapid, and efficient approach to the WGS of NiV, making it suitable for resource-limited settings like Bangladesh. The method enhances the capacity for outbreak investigations, epidemiological analyses, and monitoring virus, aiding in detecting emerging strains. This work contributes significantly to global pandemic preparedness and response efforts.

Structure of the ATP-driven methyl-coenzyme M reductase activation complex

Methyl-coenzyme M reductase (MCR) is the enzyme responsible for nearly all biologically generated methane1. Its active site comprises coenzyme F430, a porphyrin-based cofactor with a central nickel ion that is active exclusively in the Ni(I) state2,3. How methanogenic archaea perform the reductive activation of F430 represents a major gap in our understanding of one of the most ancient bioenergetic systems in nature. Here we purified and characterized the MCR activation complex from Methanococcus maripaludis. McrC, a small subunit encoded in the mcr operon, co-purifies with the methanogenic marker proteins Mmp7, Mmp17, Mmp3 and the A2 component. We demonstrated that this complex can activate MCR in vitro in a strictly ATP-dependent manner, enabling the formation of methane. In addition, we determined the cryo-electron microscopy structure of the MCR activation complex exhibiting different functional states with local resolutions reaching 1.8-2.1 Å. Our data revealed three complex iron-sulfur clusters that formed an electron transfer pathway towards F430. Topology and electron paramagnetic resonance spectroscopy analyses indicate that these clusters are similar to the [8Fe-9S-C] cluster, a maturation intermediate of the catalytic cofactor in nitrogenase. Altogether, our findings offer insights into the activation mechanism of MCR and prospects on the early evolution of nitrogenase.

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

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

Molecular analysis of multiple HIV-1 BC recombinant strains circulating worldwide shows predominance of the C genotype in the viral genomic structure

The Human Immunodeficiency Virus 1 (HIV-1) is characterized by high rates of genetic diversity, being classified into groups, subtypes and recombinant forms. To date, 15 Circulating Recombinant Forms (CRFs) of subtypes B and C have been identified, three of them in 2021: CRF108_BC in Spain, CRF110_BC and CRF118_BC in China and one in 2024: CRF146_BC in Brazil. This study investigated the genetic diversity among circulating BC recombinant viruses. Near-Full Length Genomes (NFLG) of 229 BC strains were retrieved from the Los Alamos database. Recombination and phylogenetic analysis were conducted using bioinformatics tools. Sequences were obtained from 17 countries between 1992 and 2022. Fifteen CRFs and 81 distinct Unique Recombinant Forms (URFs) recombination patterns were identified. Preferential recombination points were found in pol (66.7%) and env (62.5%) genes, while subtype C is the predominant genetic form in gag, vif, vpr, tat, rev, tat2, rev2, nef and 3'-LTR genomic regions. Specific positions in pol and env genes maintain the B subtype, which may be related to the acquisition of adaptive advantage over subtype C.

A conserved terpene cyclase gene in Sanghuangporus for abscisic acid-related sesquiterpenoid biosynthesis

BACKGROUND

The medicinal mushroom Sanghuangporus is renowned in East Asia for its potent therapeutic properties, attributed in part to its bioactive sesquiterpenoids. However, despite their recognized medicinal potential, the biosynthetic pathways and specific enzymes responsible for sesquiterpenoid production in Sanghuangporus remain unexplored, limiting opportunities to optimize their medicinal applications.

RESULTS

Sesquiterpenoids from four Sanghuangporus species were extracted through targeted isolation using mass spectrometry (MS)-based metabolomics, resulting in the discovery of six known abscisic acid-related compounds and one new compound, whose structure was determined through spectroscopic and computational analysis. We employed a natural product genome mining approach to identify a putative biosynthetic gene cluster (BGC) containing a sesquiterpene synthase gene, ancA, associated with the detected compounds. Biosynthetic pathways for these compounds were proposed based on an integrative approach combining BGC analysis and MS2 fragment-based dereplication. Further analyses revealed that the gene content and synteny of the ancA BGC are relatively well-conserved across Sanghuangporus species but less so outside the genus.

CONCLUSIONS

A sesquiterpene synthase gene, its associated BGC, and the biosynthetic pathway for a group of detected abscisic acid-related sesquiterpenoids in Sanghuangporus were predicted through genomic and metabolic data analyses. This study addresses a critical gap in understanding the genetic basis of sesquiterpenoid production in Sanghuangporus and offers insights for future research on engineering metabolic pathways to enhance sesquiterpenoid production for medicinal use.

Halzoun syndrome in Lebanon: Clinical and genetic insights into Dicrocoelium dendriticum

Halzoun syndrome is a rare parasitic infection associated with the consumption of raw liver, predominantly reported in the Eastern Mediterranean. The condition presents significant diagnostic challenges due to its symptom overlap with other parasitic and allergic disorders. We identified four cases of Halzoun syndrome in a family from the North Bekaa region of Lebanon. A detailed examination of the goat liver was conducted, followed by molecular characterisation using the ITS-2 region and phylogenetic analysis to establish the relationship of the local isolates with other Dicrocoelium species. Gross examination of the infected goat liver revealed small, pale nodules indicative of inflammation caused by flukes or their eggs. Molecular analysis confirmed D. dendriticum as the causative agent, with phylogenetic analysis placing the local isolates within the D. dendriticum clade, showing notable genetic divergence. Clinically, the patients experienced severe pharyngitis, nasal congestion, and allergic-like reactions typical of Halzoun syndrome, with one case requiring intensive treatment with corticosteroids and oxygen therapy. This study confirms D. dendriticum as the etiological agent of Halzoun syndrome in these cases, highlighting the potential presence of a distinct genetic lineage in Lebanon. The findings underscore the importance of accurate diagnosis and tailored treatment strategies in regions where raw liver consumption is common.

Simultaneous Cocirculation of 2 Genotypes of Dengue Virus Serotype 3 Causing a Large Outbreak in Sri Lanka in 2023

BACKGROUND

We observed a discrepancy between dengue NS1 antigen test and molecular diagnostics, with the emergence of dengue virus (DENV) serotype 3 in Sri Lanka, and sought to understand the cause for the rise in cases and high failure rates of molecular diagnostics.

METHODS

Whole-genome sequencing was carried out in 22 DENV-3 samples. Phylogenetic and molecular clock analyses were done for genotype assignment and to understand the rate of evolution. Mutation analysis was done to understand the reasons for polymerase chain reaction (PCR) nondetection.

RESULTS

We identified 2 DENV-3 genotypes (I and III) cocirculating. DENV-3 genotype III strains shared a common ancestor with a sequence from India collected in 2022, while DENV-3 genotype I, was found to share a common ancestor with DENV-3 sequences from China. DENV-3 genotype III was detected by the modified Centers for Disease Control and Prevention DENV-3 primers, whereas genotype I evaded detection due to key mutations at forward and reverse primer binding sites. We identified point mutations C744T and A756G in the forward primer binding sites and G795A in the reverse primer binding sites, which were not identified in DENV-3 genotype III. Furthermore, our Sri Lankan DENV-3 strains demonstrated a high root to tip ratio compared to the previous DENV-3 sequences, indicating a high mutation rate during the time of sampling (2017 to 2023).

CONCLUSIONS

The cocirculation of multiple genotypes associated with an increase in cases highlights the importance of continuous surveillance of DENVs to identify mutations resulting in nondetection by diagnostics and differences in virulence.

Creating an effective DNA identification system for discriminating cherries (Prunus subgenus Cerasus)

BACKGROUND

Cherries, a subgenus of Cerasus within Rosaceae, as fruit trees with high economic value and elegant garden plants, have broad prospects for development and utilization. However, traditional morphology and molecular data have struggled to accurately identify cherry species due to their extensive overlap in the distribution, frequent hybridization, both open and closed flowers, hysteranthy and limited species coverage, hindering the advancement of the cherry industry. In this study, 61 well-documented cherry species were collected and whole chloroplast genome data was used to develop an effective DNA identification system for precise species identification.

RESULTS

36 new cherry chloroplast genomes were added to the public database, resulting in the most comprehensive phylogenetic relationship of cherry species to date. While whole chloroplast genome data achieved an 85.26% species identification success rate, it did not fully resolve all species identification. Relying solely on whole chloroplast genome data is resource-intensive. Therefore, we explored using highly variable regions, species-specific SNPs, and structural variations for accurate species identification. This study revealed that 14 newly developed DNA barcodes could identify 71.88% of cherry samples, while 106 SNPs and Indels allowed for precise identification of 59 out of 61 cherry species.

CONCLUSIONS

This study not only clarified the phylogenetic relationships of major cherry species but also developed a precise identification system, providing a robust tool for accurate species identification and laying a solid foundation for breeding and the broader promotion of cherry species.

CLINICAL TRIAL NUMBER

Not applicable.

High diversity of nitrifying bacteria and archaea in biofilms from a subsea tunnel

Microbial biofilm formation can contribute to the accelerated deterioration of steel-reinforced concrete structures and significantly impact their service life, making it critical to understand the diversity of the biofilm community and prevailing processes in these habitats. Here, we analyzed 16S rRNA gene amplicon and metagenomics sequencing data to study the abundance and diversity of nitrifiers within biofilms on the concrete surface of the Oslofjord subsea road tunnel in Norway. We showed that the abundance of nitrifiers varied greatly in time and space, with a mean abundance of 24.7 ± 15% but a wide range between 1.2% and 61.4%. We hypothesize that niche differentiation allows the coexistence of several nitrifier groups and that their high diversity increases the resilience to fluctuating environmental conditions. Strong correlations were observed between the nitrifying families Nitrosomonadaceae and Nitrospinaceae, and the iron-oxidizing family Mariprofundaceae. Metagenome-assembled genome analyses suggested that early Mariprofundaceae colonizers may provide a protected environment for nitrifiers in exchange for nitrogen compounds and vitamin B12, but further studies are needed to elucidate the spatial organization of the biofilms and the cooperative and competitive interactions in this environment. Together, this research provides novel insights into the diverse communities of nitrifiers living within biofilms on concrete surfaces and establishes a foundation for future experimental studies of concrete biofilms.

Far from home: Morphological, ultrastructural, and molecular characterization of Thometrema patagonicum (Szidat, 1956) (Hemiuroidea: Derogenidae) from an unexpected host and locality, with taxonomic implications

While most higher taxa in the Hemiuroidea exhibit remarkable diversity and thrive worldwide in marine ecosystems, a few groups have successfully radiated into freshwater environments. Among them, species of Thometrema are well known from freshwater and brackish fishes in the New World. In this study, specimens of Thometrema from a single specimen of the endangered pimelodid catfish Steindachneridion scriptum in the Upper Paraná River basin, State of São Paulo, Brazil, were subjected to morphological, ultrastructural (first scanning electron microscopy data for the genus) and molecular analyses. Newly obtained sequences of the partial large subunit nuclear ribosomal RNA (28S rDNA) and partial mitochondrial cytochrome c oxidase subunit I (COI mtDNA) provided strong evidence supporting the identification of the specimens as T. patagonicum, a trematode previously known only from endemic percichthyid fishes (Percichthyidae) in the Argentinian Patagonia. This unexpected finding, along with critical morphological evaluation of new and deposited material, led us to propose T. overstreeti and T. bonariense as junior synonyms of T. patagonicum. Moreover, we reassessed certain morphological features, revealed new potential distinguishing characters (papillae) and raised doubts about the taxonomic value of commonly used features for species differentiation (e.g., vitellarium masses). To overcome taxonomic problems in Thometrema due to the paucity of morphological features to clearly set species boundaries, new descriptions could leverage integrative approaches, as employed here, to establish robust species hypotheses and ultimately unravel the actual species composition in the Americas.

Sinocrassulaobliquifolia (Crassulaceae), a new species from China

Based on a comprehensive morphological and molecular data analysis, we have confirmed and described a new species within the genus Sinocrassula, which is distributed in Sichuan Province, China. Morphologically, the new species resembles Sinocrassuladiversifolia and S.indica, but it is distinctly different from them in its asymmetrical leaves, leaf apex with glands, triangular petals that are white at the base and adorned with dense purple-red stripes and spots on the surfaces upward, and rectangular nectar scales. A phylogenetic analysis utilizing four plastid markers and one nuclear marker supports the conclusion that the new species is sister to S.ganluoensis.

Five new species of Cortinarius (Cortinariaceae) from Yunnan, China, based on molecular and morphological evidence

Cortinarius is a globally distributed, exceptionally species-rich genus of Cortinariaceae, serving as important ectomycorrhizal fungi. Yunnan province, located in southwestern China, boasts a vast array of environmental conditions and fungal resources, with numerous new Cortinarius species yet to be discovered. Based on morphological evidence and phylogenetic inference using a two-locus dataset, five novel species have been identified within the genus, namely C.brunneoverrucosus, C.coriaceus, C.fuscocandidus, C.neodisjungendus, and C.sinoconfirmatus. Notably, two of these species (C.brunneoverrucosus and C.neodisjungendus) occur in subtropical areas, while the other three species (C.coriaceus, C.fuscocandidus, and C.sinoconfirmatus) inhabit subalpine temperate areas. Taxonomic descriptions for these five species are provided.

Study of coronavirus diversity in wildlife in Northern Cambodia suggests continuous circulation of SARS-CoV-2-related viruses in bats

Since SARS-CoV-2's emergence, studies in Southeast Asia, including Cambodia, have identified related coronaviruses (CoVs) in rhinolophid bats. This pilot study investigates the prevalence and diversity of CoVs in wildlife from two Cambodian provinces known for wildlife trade and environmental changes, factors favoring zoonotic spillover risk. Samples were collected from 2020 to 2022 using active (capture and swabbing of bats and rodents) and non-invasive (collection of feces from bat caves and wildlife habitats) methods. RNA was screened for CoVs using conventional pan-CoVs and real-time Sarbecovirus-specific PCR systems. Positive samples were sequenced and phylogenetic analysis was performed on the partial RdRp gene. A total of 2608 samples were collected: 867 rectal swabs from bats, 159 from rodents, 41 from other wild animals, and 1541 fecal samples. The overall prevalence of CoVs was 2.0%, with a 3.3% positive rate in bats, 2.5% in rodents, and no CoVs detected in other wildlife species. Alpha-CoVs were exclusive to bats, while Beta-CoVs were found in both bats and rodents. Seven SARS-CoV-2-related viruses were identified in Rhinolophus shameli bats sampled in August 2020, March 2021, and December 2021. Our results highlight diverse CoVs in Cambodian bats and rodents and emphasize bats as significant reservoirs. They also suggest continuous circulation of bat SARS-CoV-2-related viruses may occur in a region where ecological and human factors could favor virus emergence. Continuous surveillance and integrated approaches are crucial to managing and mitigating emerging zoonotic diseases.

Complete Mitochondrial Genome of Two Amathusiini Species (Lepidoideae: Nymphalidae: Satyrinae): Characterization, Comparative Analyses, and Phylogenetic Implications

Background: The Satyrinae subfamily represents a taxonomically critical group within Nymphalidae, characterized by its remarkable species diversity. Despite its evolutionary significance, the phylogenetic relationships among tribal and subtribal lineages remain poorly resolved. Although mitochondrial genomes have become crucial molecular markers in Lepidoptera phylogenetics, their potential remains underutilized in the systematics of Satyrinae. Notably, Amathusiini exhibits a particular paucity, with only two congeneric representatives having been comprehensively sequenced to date. Methods: We employed high-throughput sequencing to assemble the complete mitochondrial genomes of two Amathusiini species, Discophora sondaica and Aemona amathusia. Our study revealed novel evolutionary insights through comparative genomics, which encompassed all available Satyrinae mitochondrial genomes. Additionally, we conducted phylogenetic reconstruction using maximum likelihood and Bayesian inference approaches, utilizing the most extensive dataset to date. Results: The closed, circular mitochondrial genomes measure 15,333 bp for D. sondaica and 15,423 bp for A. amathusia, maintaining the ancestral lepidopteran architecture: 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and an AT-rich control region. Comparative analyses of 71 mitochondrial genomes revealed strong evolutionary conservation across multiple parameters: nucleotide composition (AT content range: 77.9-81.8%), codon usage bias (ENC = 30.83-37.55), tRNA secondary structures, and control region organization. All PCGs showed purifying selection signals (Ka/Ks < 1.0), with atp8 exhibiting the highest evolutionary rate (Ka/Ks = 0.277). Phylogenetic reconstructions yielded congruent tribal-level topologies with strong nodal support: ((Satyrini + Melanitini) + (Amathusiini + Elymniini) + Zetherini), confirming a sister relationship between Amathusiini and Elymniini. Within Satyrini, five subtribes formed monophyletic groups: Ypthimina, Erebiina, Maniolina, Satyrina, and Melanargiina, arranged as ((Ypthimina + (Erebiina + Maniolina)) + (Satyrina + Melanargiina)). Mycalesina, Lethina, and Parargina comprised a well-supported clade (BS = 100%; PP = 1.0), though internal relationships required further resolution due to Lethina's polyphyly. Conclusions: This study provides novel insights into mitochondrial genomic evolution within the Satyrinae subfamily while elucidating the efficacy of mitogenomic data for resolving deep phylogenetic relationships within this ecologically significant subfamily. Our findings establish critical genome baselines for further systematic research and underscore essential pathways for refining subtribal-level taxonomy through integrative molecular approaches.

Histone H3 cysteine 110 enhances iron metabolism and modulates replicative life span in Saccharomyces cerevisiae

The discovery of histone H3 copper reductase activity provides a novel metabolic framework for understanding the functions of core histone residues, which, unlike N-terminal residues, have remained largely unexplored. We previously demonstrated that histone H3 cysteine 110 (H3C110) contributes to cupric (Cu2+) ion binding and its reduction to the cuprous (Cu1+) form. However, this residue is absent in Saccharomyces cerevisiae, raising questions about its evolutionary and functional significance. Here, we report that H3C110 has been lost in many fungal lineages despite near-universal conservation across eukaryotes. Introduction of H3C110 into S. cerevisiae increased intracellular Cu1+ levels and ameliorated the iron homeostasis defects caused by inactivation of the Cup1 metallothionein or glutathione depletion. Enhanced histone copper reductase activity also extended replicative life span under oxidative growth conditions but reduced it under fermentative conditions. Our findings suggest that a trade-off between histone copper reductase activity, iron metabolism, and life span may underlie the loss or retention of H3C110 across eukaryotes.

The vertical distribution and metabolic versatility of complete ammonia oxidizing communities in mangrove sediments

Recently discovered complete ammonia-oxidizing (comammox) microorganisms can completely oxidize ammonia to nitrate and play an important role in the nitrogen (N) cycle across various ecosystems. However, little is known about the vertical distribution and metabolic versatility of comammox communities in mangrove ecosystems. Here we profiled comammox communities from deep sediments (up to 5 m) in a mangrove wetland by combining metagenome sequencing and physicochemical properties analysis. Our results showed that the relative abundance of comammox bacteria (23.2 %) was higher than ammonia-oxidizing bacteria (AOB, 12.0 %), but lower than ammonia-oxidizing archaea (AOA, 64.8 %). The abundance of comammox communities significantly (p < 0.01) decreased with the sediment depth, and dissolved organic carbon and total sulfur appeared to be major environmental factors influencing the nitrifying microbial community structure. We also recovered a high-quality metagenome-assembled genome (MAG) of comammox bacteria (Nitrospira sp. bin2030) affiliated with comammox clade A. Nitrospira sp. bin2030 possessed diverse metabolic processes, not only the key genes for ammonia oxidation and urea utilization in the N cycle, but also key genes involved in carbon and energy metabolisms, sulfur metabolism, and environmental adaptation (e.g., oxidative stress, salinity, temperature, heavy metal tolerance). The findings advance our understanding of vertical distribution and metabolic versatility of comammox communities in mangrove sediments, having important implications for quantifying their contribution to nitrification processes in mangrove ecosystems.

Review of the genus Isca (Ephemeroptera, Leptophlebiidae) from China with a new species and a new species record

Previously, only one Isca species (Iscapurpurea Gillies, 1951) was recorded in China. In this review, three Isca species are presented and photographed. Among them, I.acutata sp. nov. is a new species with an acute male penal apex, a uniform brown abdomen of the imago, and a bilamellate gill VII of the nymph. Another species, I.fascia, previously reported from Vietnam, is found in China for the first time. The nymphs of I.fascia exhibit a banded body and a convex apex of the penes. The structure of the third species I.purpurea, shown graphically, has separated penes and a paler nymphal body than the other two species. The diverse morphology of the penes, wings, venation, and gills show that Isca has diverse species and evolutionary directions, suggesting that the previous subgeneric classification may not adequately represent some species. Biologically, their nymphs were observed living in tiny pits on substrate surfaces, where their ventral gills may facilitate respiration while they hide.

Intruders in beehives? New bee-associated Ellingsenius species (Pseudoscorpiones, Cheliferidae) from China based on morphological data and molecular analyses, with comments on pseudoscorpion-bee relationships

Ellingseniusrenae sp. nov., encountered in Guizhou, southern China and the eighth species of the genus, is described and illustrated. An analysis of the COI mitochondrial gene (LCO1490/HC02198) confirms the identity of the new species. An identification key to all Ellingsenius species is provided, and comments on the pseudoscorpion-bee relationships are included.

Ptolemeba bulliensis Watson et al. 2014 (Amoebozoa, Tubulinea) From Freshwater NGD-Affected Rainbow Trout (Oncorhynchus mykiss Walbaum, 1792) Gills Tolerates Brackish Water Conditions

The purpose of this study is to expand our knowledge of the diversity of lobose amoebae (Amoebozoa) that can be isolated from the gills of farmed rainbow trout (Oncorhynchus mykiss Walbaum, 1792) affected by nodular gill disease (NGD). A new strain of an amoebozoan, Ptolemeba bulliensis Watson et al. 2014 (Tubulinea) was isolated, studied and identified from the gills of farmed trout showing signs of NGD in the northwest of Russia. The strain was identified using morphological and molecular (small subunit [SSU] ribosomal RNA gene sequence data) characters. Actin and cytochrome c oxidase (Cox1) gene sequences were obtained for the representative of Ptolemeba for the first time. A peculiar feature of the Cox1 gene is the presence of group I intron that contains a 177 amino acids long open reading frame encoding a homing endonuclease. This is the first case of a group I intron in the Cox1 gene in Amoebozoa apart from Dictyostelium. In the experimental study, the studied amoebae demonstrate a broad range of salinity tolerance. They are capable of survival and reproduction in a range of salinities between freshwater Prescott and James medium and 18‰, but could not survive or reproduce in 25‰ and above. This indicates a possibility of this species' distribution through brackish water biotopes and shows that in case of pathogenicity for the farmed fish, the methods of treatment based on increasing salinity may be inefficient. In spite of the lack of direct evidence for pathogenicity, repeated observations of P. bulliensis isolated from the gills may suggest its association with the disease.

First detection of Amblyomma lepidum (Dönitz, 1909) in Zimbabwe

Herewith we present the first detection of Amblyomma lepidum (Dönitz, 1909) on cattle in Zimbabwe. Zimbabwe's smallholder farmers rely heavily on their livestock, mainly cattle and goats. Even though great importance is placed on cattle farming, no systematic surveillance of tick and tick-borne diseases is currently being conducted in the country. Forming part of the Amblyomma genus, A. lepidum is a brightly ornate tick with great vector potential, which could have harmful effects on cattle and cattle farming in Zimbabwe. This report documents the presence of both male and female A. lepidum ticks that were morphologically identified, and with the use of two ribosomal genes, were molecularly characterised as A. lepidum. Hypotheses can be made as to how this tick was introduced into Zimbabwe; however, its presence highlights the need for a systematic surveillance programme to track not only new introductions, such as the aforementioned, but the current distribution of this tick population in Zimbabwe.

Comparative pan-genomic analysis reveals pathogenic mechanisms and genomic plasticity in Vibrio parahaemolyticus clinical and environmental isolates

Introduction

Vibrio parahaemolyticus is a human pathogen capable of inducing bacterial gastroenteritis. Clinical strains of V. parahaemolyticus are considered pathogenic due to their possession of hemolysin and a type III secretion system (T3SS). Some environmental isolates are also acquiring corresponding virulence genes.

Methods

This study initially examines the infection characteristics of V. parahaemolyticus, and subsequently employs pan-genomic analysis to identify genes that exhibit significant differences in distribution between environmental and clinical isolates, thereby revealing their potential impact on virulence.

Results and discussion

The epidemiological analysis of clinical isolates suggests that infections of V. parahaemolyticus are more prevalent in warm seasons, with O4:KUT serotype presenting more severe symptoms. OrthoFinder analysis revealed that environmental isolates possess a higher number of core genes. PEPPAN and KEGG analysis revealed that the 10 genes exclusively found in clinical isolates were predominantly associated with virulence. Additionally, the functions of genes differentially distributed in the environment were significantly more diverse compared to those in clinical settings. Analysis of mobile genetic elements suggested that environmental isolates harbor more mobile genetic elements, implying a potential for an increased number of resistance genes. The pathogenic characteristics of the strains examined in this study, genomic diversity and variation in mobile genetic elements are highly significant for deepening our understanding of the pathogenic mechanisms of V. parahaemolyticus and for the development of strategies to prevent its infections.

Cryptic infection of a giant virus in a unicellular green alga

Latency is a common strategy in a wide range of viral lineages, but its prevalence in giant viruses remains unknown. Here we describe a 617 kbp integrated giant viral element in the model green alga Chlamydomonas reinhardtii. We resolve the integrated viral genome using long-read sequencing, identify a putative polinton-like integrase, and show that viral particles accumulate primarily during the stationary growth phase. A diverse array of viral-encoded selfish genetic elements is expressed during viral activity, including several Fanzor nuclease-encoding transposable elements. In addition, we show that field isolates of Chlamydomonas sp. harbor signatures of endogenous giant viruses related to the C. reinhardtii virus that exhibit similar infection dynamics, suggesting that giant virus latency is prevalent in natural host communities. Our work describes an unusually large temperate virus of a unicellular eukaryote, substantially expanding the scope of cryptic viral infections in the virosphere.

Roseateles cavernae sp. nov., a Bacterium Isolated from Freshwater of the Old Huanglong Cave in Yunnan Province, South-West China

A novel bacteria, designated as YIM B04394T, was isolated from a freshwater sample collected from the Old Huanglong Cave in Kunming, Yunnan province, South-west China. The cells of this strain were Gram negative and rod shaped. The strain was found to be aerobic, oxidase positive, and weakly catalase positive, grew at 10-40℃ (optimum, 28 °C), pH 6.0-8.0 (optimum, pH 7.0), and low NaCl concentrations (up to 5.0%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM B04394T clustered with Roseateles species. The DNA-DNA and ANI relatedness values of strain YIM B04394T with the related species R. toxinivorans DSM 16998 T and R. saccharophilus DSM 25082 T were 21.50-22.9%% and 76.47-76.93%, respectively. The predominant fatty acids included C16:1ω6c and/or C16:1 ω7c and C16:0. Ubiquinone- 8 was detected as the respiratory quinone, and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, and an unknown phospholipid. The DNA G + C content was 67.89%. Based on phylogenomic and phylogenetic analyses, combined with phenotypic and chemotaxonomic characterizations, this strain represents a novel Roseateles species for which the name Roseateles cavernae sp. nov. is proposed. The type strain is YIM B04394T (= NBRC 115775 T = KCTC 92438 T = CCTCC AB2021502T).

Aspergillus fumigatus secondary metabolite pyripyropene is important for the dual biofilm formation with Pseudomonas aeruginosa

The human pathogenic fungus Aspergillus fumigatus establishes dual biofilm interactions in the lungs with the pathogenic bacterium Pseudomonas aeruginosa. Screening of 21 A. fumigatus null mutants revealed seven mutants (two G protein-coupled receptors, three mitogen-activated protein kinase receptors, a Gα protein, and one histidine kinase receptor) with reduced biofilm formation, specifically in the presence of P. aeruginosa. Transcriptional profiling and metabolomics analysis of secondary metabolites produced by one of these mutants, ΔgpaB (gpaB encodes a Gα protein), showed GpaB controls the production of several important metabolites for the dual biofilm interaction, including pyripyropene A, a potent inhibitor of mammalian acyl-CoA cholesterol acyltransferase. Deletion of pyr2, encoding a non-reducing polyketide synthase essential for pyripyropene biosynthesis, showed reduced A. fumigatus Δpyr2-P. aeruginosa biofilm growth, altered macrophage responses, and attenuated mouse virulence in a chemotherapeutic murine model. We identified pyripyropene as a novel player in the ecology and pathogenic interactions of this important human fungal pathogen.IMPORTANCEAspergillus fumigatus and Pseudomonas aeruginosa are two important human pathogens. Both organisms establish biofilm interactions in patients affected with chronic lung pulmonary infections, such as cystic fibrosis (CF) and chronic obstructive pulmonary disease. Colonization with A. fumigatus is associated with an increased risk of P. aeruginosa colonization in CF patients, and disease prognosis is poor when both pathogens are present. Here, we identified A. fumigatus genetic determinants important for the establishment of in vitro dual A. fumigatus-P. aeruginosa biofilm interactions. Among them, an A. fumigatus Gα protein GpaB is important for this interaction controlling the production of the secondary metabolite pyripyropene. We demonstrate that the lack of pyripyropene production decreases the dual biofilm interaction between the two species as well as the virulence of A. fumigatus in a chemotherapeutic murine model of aspergillosis. These results reveal a complete novel role for this secondary metabolite in the ecology and pathogenic interactions of this important human fungal pathogen.

Lost in translation: conserved amino acid usage despite extreme codon bias in foraminifera

Analyses of codon usage in eukaryotes suggest that amino acid usage responds to GC pressure so AT-biased substitutions drive higher usage of amino acids with AT-ending codons. Here, we combine single-cell transcriptomics and phylogenomics to explore codon usage patterns in foraminifera, a diverse and ancient clade of predominantly uncultivable microeukaryotes. We curate data from 1,044 gene families in 49 individuals representing 28 genera, generating perhaps the largest existing dataset of data from a predominantly uncultivable clade of protists, to analyze compositional bias and codon usage. We find extreme variation in composition, with a median GC content at fourfold degenerate silent sites below 3% in some species and above 75% in others. The most AT-biased species are distributed among diverse non-monophyletic lineages. Surprisingly, despite the extreme variation in compositional bias, amino acid usage is highly conserved across all foraminifera. By analyzing nucleotide, codon, and amino acid composition within this diverse clade of amoeboid eukaryotes, we expand our knowledge of patterns of genome evolution across the eukaryotic tree of life.IMPORTANCEPatterns of molecular evolution in protein-coding genes reflect trade-offs between substitution biases and selection on both codon and amino acid usage. Most analyses of these factors in microbial eukaryotes focus on model species such as Acanthamoeba, Plasmodium, and yeast, where substitution bias is a primary contributor to patterns of amino acid usage. Foraminifera, an ancient clade of single-celled eukaryotes, present a conundrum, as we find highly conserved amino acid usage underlain by divergent nucleotide composition, including extreme AT-bias at silent sites among multiple non-sister lineages. We speculate that these paradoxical patterns are enabled by the dynamic genome structure of foraminifera, whose life cycles can include genome endoreplication and chromatin extrusion.

From insect endosymbiont to phloem colonizer: comparative genomics unveils the lifestyle transition of phytopathogenic Arsenophonus strains

Bacteria infecting the plant phloem represent a growing threat worldwide. While these organisms often resist in vitro culture, they multiply both in plant sieve elements and hemipteran vectors. Such cross-kingdom parasitic lifestyle has emerged in diverse taxa via distinct ecological routes. In the genus Arsenophonus, the phloem pathogens "Candidatus Arsenophonus phytopathogenicus" (Ap) and "Ca. Phlomobacter fragariae" (Pf) have evolved from insect endosymbionts, but the genetic mechanisms underlying this transition have not been explored. To fill this gap, we obtained the genomes of both strains from insect host metagenomes. The resulting assemblies are highly similar in size and functional repertoire, rich in viral sequences, and closely resemble the genomes of several facultative endosymbiotic Arsenophonus strains of sap-sucking hemipterans. However, a phylogenomic analysis demonstrated distinct origins, as Ap belongs to the "Triatominarum" clade, whereas Pf represents a distant species. We identified a set of orthologs encoded only by Ap and Pf in the genus, including hydrolytic enzymes likely targeting plant substrates. In particular, both bacteria encode putative plant cell wall-degrading enzymes and cysteine peptidases related to xylellain, a papain-like peptidase from Xylella fastidiosa, for which close homologs are found in diverse Pseudomonadota infecting the plant vasculature. In silico predictions and gene expression analyses further support a role during phloem colonization for several of the shared orthologs. We conclude that the double emergence of phytopathogenicity in Arsenophonus may have been mediated by a few horizontal gene transfer events, involving genes acquired from other Pseudomonadota, including phytopathogens.

IMPORTANCE

We investigate the genetic mechanisms of a transition in bacterial lifestyle. We focus on two phloem pathogens belonging to the genus Arsenophonus: "Candidatus Arsenophonus phytopathogenicus" and "Ca. Phlomobacter fragariae." Both bacteria cause economically significant pathologies, and they have likely emerged among facultative insect endosymbionts. Our genomic analyses show that both strains are highly similar to other strains of the genus associated with sap-sucking hemipterans, suggesting a recent lifestyle shift. Importantly, although the phytopathogenic Arsenophonus strains belong to distant clades, they share a small set of orthologs unique in the genus pangenome. We provide evidence that several of these genes produce hydrolytic enzymes that are secreted and may target plant substrates. The acquisition and exchange of these genes may thus have played a pivotal role in the lifestyle transition of the phytopathogenic Arsenophonus strains.

Effect of Spiroplasma infection on the mating behavior of Glossina fuscipes fuscipes

Tsetse flies are insects of significant public health and zoonotic importance as they are the main vectors of African trypanosomes. To date, an effective vaccine is unavailable and efforts to limit the spread of the disease primarily rely on controlling the tsetse populations. The discovery of Spiroplasma (class Mollicutes) in Glossina fuscipes fuscipes (Gff) (palpalis subgroup), offers promising insights into its potential use as a biological control agent to hinder trypanosomes infection in tsetse flies. Indeed, a negative correlation between Spiroplasma and trypanosome co-infection has been observed. Using a laboratory strain of Gff, we provide fundamental biological insights into the effects of Spiroplasma infection on the mating behavior of the fly. We found a sex-biased Spiroplasma infection, with males exhibiting a higher infection rate. Mass mating experiments revealed a higher mating propensity in Spiroplasma-infected flies. Additionally, the presence of Spiroplasma influenced premating isolation, leading to nonrandom mating patterns that favored the pairing of individuals with matching infection statuses. Moreover, we present evidence of Spiroplasma vertical paternal transmission. By analyzing female reproductive tissues at 2 and 24 h postmating, we confirmed that an infected male can transfer Spiroplasma to the female via the spermatophore, which can subsequently migrate to the spermathecae. This study provides foundational insights into the role of Spiroplasma in tsetse fly mating behavior and provides supporting evidence for vertical transmission from infected males.

An Overview of the Firefly Genus Pygoluciola Wittmer, a Phylogeny of the Luciolinae Using Mitochondrial Genomes, a Description of Six New Species, and an Assessment of a Copulation Clamp in This Genus (Coleoptera: Lampyridae: Luciolinae)

Pygoluciola Wittmer 1939 is overviewed, with an expanded generic redescription comprising 28 species, including 6 new species from China, described from features of males, associated females, and larvae. Their placement in the genus is confirmed by a phylogenetic analysis of their mitogenomes. They include Pygoluciola baise Fu & Ballantyne sp. nov. from Baise City, Guangxi Province; P. manmaia Fu & Ballantyne sp. nov. from Yunnan Province; P. quzhou Fu & Ballantyne sp. nov. from the City of Quzhou in Zhejiang Province; P. tunchangia Fu & Ballantyne sp. nov. from Tunchang county, Hainan Island; P. yingjiangia Fu & Ballantyne sp. nov. from Yingjiang county in Yunnan Province; and P. yupingia Fu & Ballantyne sp. nov. from Mt. Yuping, Hongya County in Sichuan Province. Specimens are assigned to Luciola davidis Olivier, which is transferred to Pygoluciola and redescribed. Species are assigned to one of five Groups we define in the genus, and this classification is challenged by molecular information. We reject the possibility of a copulation clamp in P. kinabalua Ballantyne by dissection of pinned type females and comparison with other species newly described here.

Candidate Phyla Radiation (CPR) bacteria from hyperalkaline ecosystems provide novel insight into their symbiotic lifestyle and ecological implications

BACKGROUND

Candidate Phyla Radiation (CPR) represents a unique superphylum characterized by ultra-small cell size and symbiotic lifestyle. Although CPR bacteria have been identified in varied environments, their broader distribution, associations with hosts, and ecological roles remain largely unexplored. To address these knowledge gaps, a serpentinite-like environment was selected as a simplified model system to investigate the CPR communities in hyperalkaline environments and their association with hosts in extreme conditions. Additionally, the enzymatic activity, global distribution, and evolution of the CPR-derived genes encoding essential metabolites (e.g., folate or vitamin B9) were analyzed and assessed.

RESULTS

In the highly alkaline serpentinite-like ecosystem (pH = 10.9-12.4), metagenomic analyses of the water and sediment samples revealed that CPR bacteria constituted 1.93-34.8% of the microbial communities. Metabolic reconstruction of 12 high-quality CPR metagenome-assembled genomes (MAGs) affiliated to the novel taxa from orders UBA6257, UBA9973, and Paceibacterales suggests that these bacteria lack the complete biosynthetic pathways for amino acids, lipids, and nucleotides. Notably, the CPR bacteria commonly harbored the genes associated with essential folate cofactor biosynthesis and metabolism, including dihydrofolate reductase (folA), serine hydroxymethyltransferase (glyA), and methylenetetrahydrofolate reductase (folD). Additionally, two presumed auxotrophic hosts, incapable of forming tetrahydrofolate (THF) due to the absence of folA, were identified as potential hosts for some CPR bacteria harboring folA genes. The functionality of these CPR-derived folA genes was experimentally verified by heterologous expression in the folA-deletion mutant Escherichia coli MG1655 ΔfolA. Further assessment of the available CPR genomes (n = 4,581) revealed that the genes encoding the proteins for the synthesis of bioactive folate derivatives (e.g., folA, glyA, and/or folD genes) were present in 90.8% of the genomes examined. It suggests potential widespread metabolic complementarity in folate biosynthesis between CPR and their hosts.

CONCLUSIONS

This finding deepens our understanding of the mechanisms of CPR-host symbiosis, providing novel insight into essential cofactor-dependent mutualistic CPR-host interactions. Our observations suggest that CPR bacteria may contribute to auxotrophic organisms and indirectly influence biogeochemical processes. Video Abstract.

Monoclonality and Low Genetic Diversity in Vanilla shenzhenica: Highlighting Urgent Need for Genetic Preservation of China's Only Endangered Vanilla

Long-term clonality has profound consequences for genetic structure despite offering an alternative means of reproductive assurance under unfavorable conditions for sexual reproduction. Vanilla shenzhenica Z. J. Liu & S. C. Chen (Orchidaceae), the only endangered Vanilla species in China, exhibits a clear tendency towards asexual propagation, as evidenced by its small, fragmented wild populations. To develop effective conservation strategies for this species, it is essential to assess the extent of clonality and evaluate genetic diversity both within and among populations. In this study, we sampled 43 individuals from cultivated and wild populations of V. shenzhenica and analyzed their phylogenetic relationships, genetic structure, and diversity based on single-nucleotide polymorphisms (SNPs). Our results indicate that all the studied wild populations are predominantly sustained by vegetative growth, each forming a monoclonal patch with a single genotype. The overall genetic diversity within V. shenzhenica is low likely due to a combination of factors, including clonality, reduced effective population size, and environmental disturbances. These findings underscore the urgent need for the conservation management of this species. Conservation plans should prioritize ex situ conservation efforts, focusing on promoting assisted sexual reproduction to produce viable seeds and offspring that combine diverse genotypes from different populations. This study provides valuable insights in relation to effective conservation planning for endangered clonal species.

Mortality associated with Angiostrongylus cantonensis in non-human primates in Europe

Between December 2020 and March 2022, three cases of fatal meningoencephalitis were documented in two red-fronted brown lemurs (Eulemur rufus) and a ring-tailed lemur (Lemur catta) at the Bioparc in Valencia, eastern Spain. Post-mortem analyses revealed moderate congestion in the meninges of the brain in all cases. Multifocal areas of hemorrhage were observed in one lemur, primarily in the cerebellum and brainstem. Histopathological examination showed mainly acute hemorrhagic and necrotic changes, together with moderate eosinophilic and/or histiocytic meningoencephalitis, with perivascular cuffing, and gliosis. Numerous nematode larvae were found in the meninges, brain, and spinal cord, with or without associated inflammation, hemorrhage, and necrosis. Considering the affected host species, nematode morphology, and its anatomical localization, Angiostrongylus cantonensis (Nematoda: Metastrongylidae) was suspected as the causative agent. Phylogenetic studies based on the internal transcriber spacer 1/cytochrome c oxidase subunit I (ITS1/COI) genes confirmed the initial suspicion of this zoonotic parasite and its relationship to sequences from the Balearic and Canary Islands. This is the first known detection of A. cantonensis in non-human primates in Europe and it represents one of the few occurrences reported in the Palearctic region to date. Further research on this zoonotic parasite is crucial to understanding its spread in Spain, assessing public health risks, and developing effective control measures to mitigate outbreaks and protect human and animal health.

Phylodynamic of Tomato Brown Rugose Fruit Virus and Tomato Chlorosis Virus, Two Emergent Viruses in Mixed Infections in Argentina

Tobamovirus fructirugosum (ToBRFV) and Crinivirus tomatichlorosis (ToCV) are emerging viral threats to tomato production worldwide, with expanding global distribution. Both viruses exhibit distinct biological characteristics and transmission mechanisms that influence their spread. This study aimed to reconstruct the complete genomes of ToBRFV and ToCV from infected tomato plants and wastewater samples in Argentina to explore their global evolutionary dynamics. Additionally, it compared the genetic diversity of ToBRFV in plant tissue and sewage samples. Using metagenomic analysis, the complete genome sequences of two ToBRFV isolates and two ToCV isolates from co-infected tomatoes, along with four ToBRFV isolates from sewage, were obtained. The analysis showed that ToBRFV exhibited higher genetic diversity in environmental samples than in plant samples. Phylodynamic analysis indicated that both viruses had a recent, single introduction in Argentina but predicted different times for ancestral diversification. The evolutionary analysis estimated that ToBRFV began its global diversification in June 2013 in Israel, with rapid diversification and exponential growth until 2020, after which the effective population size declined. Moreover, ToCV's global expansion was characterized by exponential growth from 1979 to 2010, with Turkey identified as the most probable location with the current data available. This study highlights how sequencing and monitoring plant viruses can enhance our understanding of their global spread and impact on agriculture.

Substantial structural variation and repetitive DNA content contribute to intraspecific plastid genome evolution

BACKGROUND

Plastids have highly conserved genomes in most land plants. However, in several families, plastid genomes exhibit high rates of nucleotide substitution and structural rearrangements among species. This elevated rate of evolution has been posited to lead to increased rates of plastid-nuclear incompatibilities (PNI), potentially acting as a driver of speciation. However, the extent to which plastid structural variation exists within a species is unknown. This study investigates whether plastid structural variation, observed at the interspecific level in Campanulaceae, also occurs within Campanula americana, a species with strong intraspecific PNI. We assembled multiple plastid genomes from three lineages of C. americana that exhibit varying levels of PNI when crossed. We then investigated the structural variation and repetitive DNA content among these lineages and compared the repetitive DNA content with that of other species within the family.

RESULTS

We found significant variation in plastid genome size among the lineages of C. americana (188,309-201,788 bp). This variation was due in part to multiple gene duplications in the inverted repeat region. Lineages also varied in their repetitive DNA content, with the Appalachian lineage displaying the highest proportion of tandem repeats (~ 10%) compared to the Eastern and Western lineages (~ 6%). In addition, genes involved in transcription and protein transport showed elevated sequence divergence between lineages, and a strong correlation was observed between genome size and repetitive DNA content. Campanula americana was found to have one of the most repetitive plastid genomes within Campanulaceae.

CONCLUSIONS

These findings challenge the conventional view of plastid genome conservation within a species and suggest that structural variation, differences in repetitive DNA content, and divergence of key genes involved in transcription and protein transport may play a role in PNI. This study highlights the need for further research into the genetic mechanisms underlying PNI, a key process in the early stages of speciation.

Marsupial cathelicidins: characterization, antimicrobial activity and evolution in this unique mammalian lineage

Introduction

Cathelicidins are a family of antimicrobial peptides well-known for their antimicrobial and immunomodulatory functions in eutherian mammals such as humans. However, cathelicidins in marsupials, the other major lineage of mammals, have received little attention despite lineage-specific gene expansions resulting in a large and diverse peptide repertoire.

Methods

We characterized cathelicidins across the marsupial family tree and investigated genomic organisation and evolutionary relationships amongst mammals. Ancestral sequence reconstruction was used to predict ancestral marsupial cathelicidins, which, alongside extant peptides, were synthesized and screened for antimicrobial activity.

Results

We identified 130 cathelicidin genes amongst 14 marsupial species representing 10 families, with gene expansions identified in all species. Cathelicidin genes were encoded in a highly syntenic region of the genome amongst all mammals, although the number of gene clusters differed amongst lineages (eutherians one, marsupials two, and monotremes three). 32 extant and ancestral marsupial cathelicidins displayed rapid, potent, and/or broad-spectrum antibacterial and antifungal activity. Phylogenetic analysis revealed that marsupial and monotreme cathelicidin repertoires may reflect both mammals and birds, as they encode non-classical cathelicidins found only in birds, as well as multiple copies of neutrophil granule protein and classic cathelicidins found only in eutherian mammals.

Conclusion

This study sheds light on the evolutionary history of mammalian cathelicidins and highlights the potential of wildlife for novel bioactive peptide discovery.

The mitogenome of Triatoma brasiliensis brasiliensis (Hemiptera: Reduviidae), the main Chagas disease vector in the semi-arid region of northeastern Brazil

BACKGROUND

Triatoma brasiliensis brasiliensis is the primary vector of Chagas disease in Brazil's semi-arid regions, exhibiting adaptability to various environments, including domestic and peridomestic. Despite its significance, comprehensive genomic data for this subspecies remain limited.

METHODS

We assembled the complete mitochondrial genome of T. b. brasiliensis using a combination of Illumina and Sanger sequencing technologies, the latter being necessary to obtain the control region with eight primers designed in this study. The mitogenome was annotated to identify gene content and organization. Phylogenetic relationships were inferred using conserved blocks of 13 protein-coding genes and 22 transfer RNA genes. For this analysis, 18 representative triatomines with near-complete mitogenomes were selected, and phylogenetic reconstruction was performed using the maximum ikelihood method.

RESULTS

The complete mitogenome spans 16,575 base pairs and includes 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes, consistent with the typical structure of insect mitochondrial genomes. The control region exhibited tandem and inverted repeats arranged in blocks, as observed for other Reduviidae. Given the limited availability of mitogenomes, our phylogenetic analysis provided statistical support for T. b. brasiliensis as a sister taxon to Triatoma infestans, forming a well-supported clade that is sister to Triatoma vitticeps.

CONCLUSIONS

The availability of this mitogenome provides insights into the systematics, biology, and genomics of triatomine species while also enhancing our understanding of their evolutionary relationships. However, the limited number of available mitogenomes, particularly for South American Triatoma species, underscores the need for further sequencing efforts to improve phylogenetic resolution and support comparative genomic studies.

Reconstructing the phylogeny and evolutionary history of freshwater fishes (Nemacheilidae) across Eurasia since early Eocene

Eurasia has undergone substantial tectonic, geological, and climatic changes throughout the Cenozoic, primarily associated with tectonic plate collisions and a global cooling trend. The evolution of present-day biodiversity unfolded in this dynamic environment, characterised by intricate interactions of abiotic factors. However, comprehensive, large-scale reconstructions illustrating the extent of these influences are lacking. We reconstructed the evolutionary history of the freshwater fish family Nemacheilidae across Eurasia and spanning most of the Cenozoic on the base of 471 specimens representing 279 species and 37 genera plus outgroup samples. Molecular phylogeny using six genes uncovered six major clades within the family, along with numerous unresolved taxonomic issues. Dating of cladogenetic events and ancestral range estimation traced the origin of Nemacheilidae to Indochina around 48 mya. Subsequently, one branch of Nemacheilidae colonised eastern, central, and northern Asia, as well as Europe, while another branch expanded into the Burmese region, the Indian subcontinent, the Near East, and northeast Africa. These expansions were facilitated by tectonic connections, favourable climatic conditions, and orogenic processes. Conversely, aridification emerged as the primary cause of extinction events. Our study marks the first comprehensive reconstruction of the evolution of Eurasian freshwater biodiversity on a continental scale and across deep geological time.

Metagenomic analysis reveals the diversity of the vaginal virome and its association with vaginitis

Introduction

The human vaginal virome is an essential yet understudied component of the vaginal microbiome. Its diversity and potential contributions to health and disease, particularly vaginitis, remain poorly understood.

Methods

We conducted metagenomic sequencing on 24 pooled vaginal swab libraries collected from 267 women, including both healthy individuals and those diagnosed with vaginitis. Viral community composition, diversity indices (Shannon, Richness, and Pielou), and phylogenetic characteristics were analyzed. Virus-host associations were also investigated.

Results

DNA viruses dominated the vaginal virome. Anelloviridae and Papillomaviridae were the most prevalent eukaryotic viruses, while Siphoviridae and Microviridae were the leading bacteriophages. Compared to healthy controls, the vaginitis group exhibited significantly reduced alpha diversity and greater beta diversity dispersion, indicating altered viral community structure. Anelloviruses, detected in both groups, showed extensive lineage diversity, frequent recombination, and pronounced phylogenetic divergence. HPV diversity and richness were significantly elevated in the vaginitis group, alongside an unbalanced distribution of viral lineages. Novel phage-bacterial associations were also identified, suggesting a potential role for bacteriophages in shaping the vaginal microbiome.

Discussion

These findings provide new insights into the composition and structure of the vaginal virome and its potential association with vaginal dysbiosis. The distinct virome characteristics observed in women with vaginitis highlight the relevance of viral communities in reproductive health. Future studies incorporating individual-level sequencing and metatranscriptomics are warranted to explore intra-host viral dynamics, assess viral activity, and clarify the functional roles of vaginal viruses in host-microbiome interactions.

Indicators for Increased Likelihood of Epidemic Kaposi Sarcoma Progression after Antiretroviral Therapy Initiation

Kaposi sarcoma (KS) is a common malignancy for people living with HIV (PLWH), despite antiretroviral therapy (ART). Curiously, even with improved CD4+ T-cell counts and low viral loads following ART, some PLWH with KS may still experience KS progression or even death and require adjuvant chemotherapy to manage their KS. The factors associated with persistent or unresponsive KS after ART initiation remain poorly characterized, and biomarkers to identify patients at risk of KS progression are needed, particularly in resource-limited areas where access to chemotherapy is limited. Here we analyzed baseline KS tumor biopsies from PLWH with KS who required chemotherapy due to unresolved KS after ART initiation and those who did not require chemotherapy after ART initiation. By examining participant metadata and viral copy number for Kaposi sarcoma-associated herpesvirus (KSHV), HIV, cytomegalovirus, and Epstein-Barr virus and KSHV gene expression in the tumor biopsies prior to ART initiation, we identified a model of factors associated with KS progression after ART initiation, including biological sex, age, and the log ratio of KSHV/HIV copy number in the tumor. We believe that the ratio of KSHV/HIV may be linked to the cell types that each virus infects, and future work exploring the relationship between tumor and immune cells in the baseline tumors is planned. Innovation would be necessary to reduce costs and simplify the viral quantification assays, enabling the translation of these findings into routine clinical care, particularly in resource-limited settings.

Acanthocephalans from freshwater fishes in northeast Thailand with the description of a new species of the subgenus Acanthosentis Verma & Dutta, 1929 (Acanthocephala, Quadrigyridae)

During an ichthyoparasitological survey in northeast Thailand in 2015, four species of acanthocephalans were found in four species of freshwater fishes. Adult stages of Pallisentisrexus Wongkham & Whitfield, 1999 and Raosentis sp. (Eoacanthocephala, Quadrigyridae) were collected from Channastriata (Anabantiformes, Channidae) and Mystusmysticetus (Siluriformes, Bagridae), respectively, and cystacanths of Arhythmorhynchus sp. (Palaeacanthocephala, Polymorphidae) were found on the visceral organs of M.albolineatus (Siluriformes, Bagridae). Adult acanthocephalans of the subgenus Acanthosentis Verma & Dutta, 1929 isolated from Barbonymusschwanenfeldii (Cypriniformes, Cyprinidae) were morphologically distinct from all described species of the subgenus in the arrangement of rings of tegumental spines in two fields with a more or less pronounced distance between them, and by the presence of a dome-shaped process with a ring of small spines at the base at the posterior end in females. Molecular data were generated for three species and phylogenetic analysis based on the 18S rDNA clearly supported the generic identification of Acanthogyrus (Acanthosentis) barbonymisp. nov. and P.rexus. While the phylogenetic position of the former species within the genus could not be clarified, the latter species formed a well-supported sister lineage in a clade with isolates of four congeneric species. Acanthogyrus (Acanthosentis) barbonymisp. nov. is formally described, the first genetic data for P.rexus are generated, a species of the genus Raosentis Datta, 1947 is reported for the first time outside the Indian subcontinent, and a key to the species of the latter genus is presented.