RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

Gut dysbiosis was inevitable, but tolerance was not: temporal responses of the murine microbiota that maintain its capacity for butyrate production correlate with sustained antinociception to chronic morphine

The therapeutic benefits of opioids are compromised by the development of analgesic tolerance, which necessitates higher dosing for pain management thereby increasing the liability for drug dependence and addiction. Rodent models indicate opposing roles of the gut microbiota in tolerance: morphine-induced gut dysbiosis exacerbates tolerance, whereas probiotics ameliorate tolerance. Not all individuals develop tolerance, which could be influenced by differences in microbiota, and yet no study design has capitalized upon this natural variation. We leveraged natural behavioral variation in a murine model of voluntary oral morphine self-administration to elucidate the mechanisms by which microbiota influences tolerance. Although all mice shared similar morphine-driven microbiota changes that largely masked informative associations with variability in tolerance, our high-resolution temporal analyses revealed a divergence in the progression of dysbiosis that best explained sustained antinociception. Mice that did not develop tolerance maintained a higher capacity for production of the short-chain fatty acid (SCFA) butyrate known to bolster intestinal barriers and promote neuronal homeostasis. Both fecal microbial transplantation (FMT) from donor mice that did not develop tolerance and dietary butyrate supplementation significantly reduced the development of tolerance independently of suppression of systemic inflammation. These findings could inform immediate therapies to extend the analgesic efficacy of opioids.

Isolation and Identification of Six Newly Recorded Wheat Fusarium Crown Rot-Associated Fusarium Species

Fusarium crown rot (FCR) has become one of the most serious diseases affecting wheat production worldwide. To date, many Fusarium species associated with wheat FCR disease have been reported. To gain a deeper understanding of Fusarium species diversity associated with wheat FCR, extensive research was conducted to identify different Fusarium species. A total of 194 diseased wheat samples were collected from Dezhou, Heze, Jining, Linyi, Qingdao, Rizhao, Weihai, and Zaozhuang cities of Shandong Province, China. A total of 1,512 Fusarium isolates were obtained from collected samples and identified using sequence analysis of the translation elongation factor-1α (TEF-1α), RNA polymerase II largest subunit (RPB1), and RNA polymerase II second largest subunit (RPB2) gene sequences. Of these Fusarium isolates, 1,082 were identified as Fusarium pseudograminearum, and the remaining isolates were identified as F. graminearum (n = 338), F. asiaticum (n = 41), F. proliferatum (n = 17), F. sinensis (n = 8), F. oxysporum (n = 7), F. acuminatum (n = 6), F. verticillioides (n = 5), F. nanum (n = 3), F. sulawesiense (n = 2), F. fujikuroi (n = 1), F. odoratissimum (n = 1), and F. reticulatum (n = 1). Among the 13 Fusarium species, F. verticillioides, F. nanum, F. sulawesiense, F. fujikuroi, F. odoratissimum, and F. reticulatum were obtained from wheat FCR samples for the first time and were considered six new record species. Pathogenicity tests of all the six newly recorded Fusarium species on the major wheat cultivar 'Jimai 22' revealed that all the tested isolates caused FCR disease. This is the first report of F. fujikuroi, F. nanum, F. odoratissimum, F. reticulatum, F. sulawesiense, and F. verticillioides causing wheat FCR worldwide.

The historical connection of the Arctic and Qinghai-Tibet Plateau floras and their asynchronous diversification in response to Cenozoic climate cooling

The Arctic and the Qinghai-Tibet Plateau (QTP) are two northern regions with the most extensive cold habitats on Earth and have undergone dramatic warming in recent decades. However, we know little about the historical connection between the Arctic and QTP biotas and their respective diversification processes. Here, we used Meconopsis and Oreomecon, an Arctic-QTP disjunct angiosperm genus pair with poor seed dispersal abilities, to shed light on the evolutionary connection of the Arctic and QTP floras and their respective diversification patterns. Our results show that the Meconopsis-Oreomecon clade colonized the Arctic from the QTP in the Late Eocene, suggesting the hitherto earliest known dispersal event between two regions. The Arctic Oreomecon split from the QTP Meconopsis at ~34 Ma, associated with their climatic niche differentiation and aridification of the Asian interior. Although both Oreomecon and Meconopsis preadapted to open and low-temperature environments and had similar diversification patterns, they diversified asynchronously in respondence to different Cenozoic climate cooling events. The Arctic is approaching its carrying capacity, whereas the QTP is still far from saturation. These findings improve knowledge of the evolutionary connection and difference between Arctic and QTP floras and have important conservation implications given enhanced warming in both regions.

Genomic insights into antibiotic-resistant non-typhoidal Salmonella isolates from outpatients in Minhang District in Shanghai

BACKGROUND

Salmonella enterica (S. enterica) causes tens of thousands of cases of diarrheal disease worldwide each year. However, our understanding of the genome and transmission dynamics of S. enterica in Minhang District in Shanghai, China is still insufficient. This study is aimed to better understand the population structure, antibiotic resistance patterns, and evolution dynamics of local strains.

METHODS

We sequenced 458 S. enterica strains from outpatients at Minhang District Central Hospital in Shanghai, China, from 2012 to 2021. Bioinformatics analyses on antibiotic resistance genes, virulence factors, mobile genetic elements, pathogenic islands, and phylogenetic relationships were performed.

RESULTS

Here we show that two dominant serovars are S. Enteritidis and S. Typhimurium isolated from outpatients in Minhang District in Shanghai, China. A total of 40 serovars and 53 sequence types (STs) are identified, two S. Montevideo strains isolated in 2013 belong to a newly identified ST10844, which is firstly identified in Minhang District in Shanghai, China. More than half of the isolates show resistance to fluoroquinolones and beta-lactams. Notably, 259 (56.6%) of the 458 isolates exhibit a multidrug-resistant pattern. Third-generation cephalosporin resistance gene blaCTX-M-55 is identified in 15 (3.3%) isolates, and fluoroquinolone resistance gene qnrS1 is identified in 42 (9.2%) isolates, both of which are strongly correlated with IS26. Mutations of T57S in ParC and D87Y in GyrA are observed in 149 (32.5%) and 133 (29.0%) isolates, respectively. In addition, phylogenetic analysis confirms the presence of outbreaks caused by S. Enteritidis and S. Typhimurium, respectively.

CONCLUSIONS

These results suggest local expansion and evolution in Salmonella occurred in Shanghai, China, and the underlying emergence of the undefined multidrug-resistant clone. Our findings enlarge the knowledge of local epidemics of Salmonella, especially S. Enteritidis and S. Typhimurium in Shanghai, and provide a piece of useful baseline information for future whole-genome sequencing surveillance.

Chloroplast whole genome assembly and phylogenetic analysis of Persicaria criopolitana reveals its new taxonomic status

Persicaria criopolitana (Polygonaceae), a dominant annual herb in wetland ecosystems, is ecologically and horticulturally significant. Despite its prevalence, genomic resources for clarifying its phylogenetic relationships and supporting conservation efforts remain limited. The complete chloroplast genome of P. criopolitana was sequenced, assembled, and annotated. Comparative genomic analyses with other Persicaria species were conducted to identify structural variations and evolutionary dynamics. Phylogenetic relationships were reconstructed using maximum-likelihood methods based on whole chloroplast genome sequences. The chloroplast genome (159,427 bp) exhibits a conserved quadripartite structure, encoding 131 genes, including 86 protein-coding, 37 tRNA, and 8 rRNA genes. Key features include: 208 simple sequence repeats (SSRs) were detected, predominantly mononucleotide motifs. A pronounced preference for A/U-ending codons, with leucine as the most frequent amino acid. A 62-bp extension of the ndhF gene into the inverted repeat (IRb) region within the small single-copy (SSC) region.Phylogenetic resolution: P. criopolitana clusters within Persicaria sect. Polygonum, demonstrating distant divergence from sect. Cephalophilon.This study provides the first complete chloroplast genome resource for P. criopolitana, resolving its taxonomic position and revealing adaptive genomic signatures. These findings advance molecular tools for species identification, inform conservation strategies, and elucidate evolutionary mechanisms in Persicaria.

Camarosporidiella, a challenge

The genus Camarosporidiella is here assessed with respect to its phylogenetic structure and species composition. More than 160 pure cultures from ascospores and conidia of more than 150 fresh collections, mostly from Fabaceae, were prepared as DNA sources. Molecular phylogenetic analyses of a multigene matrix of partial nuSSU-, complete ITS, partial LSU rDNA, and tef1 exon sequences of our isolates and those of previous workers revealed that these markers are insufficient to provide a complete species resolution. From this reduced data matrix, however, we propose synonyms and accept taxa for previously described species, which could not be included in the final phylogenetic tree due to lack of rpb2, tef1 intron and tub2 sequences. The final phylogenetic tree, which was inferred from a combined nuSSU-ITS-LSU-rpb2-tef1-tub2 sequence matrix resolved our isolates into 27 statistically supported phylogenetic species, of which 15 are new. Altogether 34 species are here accepted in Camarosporidiella. Using type studies we stabilise old names, lectotypify Cucurbitaria asparagi, Cucurbitaria caraganae, Cucurbitaria coluteae, Cucurbitaria euonymi, Dichomera elaeagni Hendersonia mori, Sphaeria elongata, Sphaeria laburni Sphaeria spartii and epitypify them as well as Cucurbitaria cytisi, Cucurbitaria retamae and Cucurbitaria steineri to place them in their correct phylogenetic positions and fix their taxonomic concepts. Morphology alone is not suitable to identify these species, and therefore no determinative key to species can be given. However, if hosts are reliably identified, many species can be determined without molecular data. Host images are included with the figures of each fungal species. Taxonomic novelties: New species: Camarosporidiella aceris Jaklitsch & Voglmayr, Camarosporidiella aetnensis Jaklitsch & Voglmayr, Camarosporidiella aragonensis Jaklitsch & Voglmayr, Camarosporidiella asparagicola Jaklitsch & Voglmayr, Camarosporidiella astragalicola Jaklitsch & Voglmayr, Camarosporidiella cretica Jaklitsch & Voglmayr, Camarosporidiella echinosparti Jaklitsch & Voglmayr, Camarosporidiella hesperolaburni Jaklitsch & Voglmayr, Camarosporidiella longipedis Jaklitsch & Voglmayr, Camarosporidiella maroccana Jaklitsch & Voglmayr, Camarosporidiella ononidis Jaklitsch & Voglmayr, Camarosporidiella radiatae Jaklitsch & Voglmayr, Camarosporidiella spartioidis Jaklitsch & Voglmayr, Camarosporidiella sphaerocarpae Jaklitsch & Voglmayr, Camarosporidiella tridentatae Jaklitsch & Voglmayr. New combinations: Camarosporidiella asparagi (Maire) Jaklitsch & Voglmayr, Camarosporidiella caraganae (P. Karst.) Jaklitsch & Voglmayr, Camarosporidiella coluteae (Rabenh.) Jaklitsch & Voglmayr, Camarosporidiella cytisi (Mirza) Jaklitsch & Voglmayr, Camarosporidiella elaeagni (P. Karst.) Jaklitsch & Voglmayr, Camarosporidiella euonymi (Cooke) Jaklitsch & Voglmayr, Camarosporidiella retamae (Pat.) Jaklitsch & Voglmayr, Camarosporidiella steineri (Petr.) Jaklitsch & Voglmayr. New names: Camarosporidiella neomori Jaklitsch & Voglmayr, Camarosporidiella neospartii Jaklitsch & Voglmayr. Citation: Jaklitsch WM, Blanco MN, Rejos FJ, Tello S, Voglmayr H (2025). Camarosporidiella, a challenge. Studies in Mycology 111: 19-100. doi: 10.3114/sim.2025.111.02.

A new species of Samsoniella (Cordycipitaceae: Hypocreales) on the herald moth, Scoliopteryx libatrix (Erebidae: Noctuoidea), from caves in the British Isles

Samsoniella scoliopterygis (Cordycipitaceae: Hypocreales), pathogenic on the herald moth Scoliopteryx libatrix (Erebidae: Noctuoidea), is described as a new species, based on morphological, ecological and molecular evidence. Infected specimens of this troglophilic moth were recorded from caves, as well as from a copper mine, in southern England (Devon, Norfolk), Northern Ireland (Fermanagh) and the Republic of Ireland (Sligo). The moths were found consistently on the cave floor or rock ledges, rather than on the ceiling amongst the over-wintering, healthy moth populations; producing multiple, white or non-pigmented clavae of the cordyceps-like sexual morph. Synnemata of the asexual morph occurred sporadically in situ but were produced consistently in vitro. The ecology and taxonomy are discussed in relation to previous records of entomopathogenic fungi on Scoliopteryx libatrix and other trogloxene moths. Citation: Evans HC, Fogg T, Buddie AG, Yeap YT, Araújo JPM (2025). A new species of Samsoniella (Cordycipitaceae: Hypocreales) on the herald moth, Scoliopteryx libatrix (Erebidae: Noctuoidea), from caves in the British Isles. Fungal Systematics and Evolution 15: 201-223. doi: 10.3114/fuse.2025.15.09.

Genomic and phenotypic insights into Serratia interaction with plants from an ecological perspective

We investigated the plant growth-promoting potential of two endophytic strains of Serratia marcescens, namely SmCNPMS2112 and SmUFMG85, which were isolated from the roots of the same maize (Zea mays) plant. The strains were evaluated in vitro for their ability to produce siderophores and indoleacetic acid, form biofilm, solubilize iron phosphate (Fe-P) and Araxá rock phosphate (RP), mineralize phytate, and for their ability to adhere and colonize host roots. Additionally, their plant growth-promoting potential was tested in vivo under greenhouse conditions using millet grown in soil under two fertilization schemes (triple superphosphate, TSP, or commercial rock phosphate, cRP). Both strains improved at least five physiological traits of millet or P content in soil. In order to elucidate the genetic basis of the plant growth-promoting ability of these strains, their genomes were compared. While both genomes exhibited a similar overall functional profile, each strain had unique features. SmCNPMS2112 contained genes related to arsenic and aromatic hydrocarbons degradation, whereas SmUFMG85 harbored genes related to rhamnolipid biosynthesis and chromium bioremediation. Also, we observe a unique repertoire of genes related to plant growth-promotion (PGP) in the SmUFMG85 genome, including oxalate decarboxylase (OxdC), associated with the catabolism of oxalic acid, and aerobactin siderophore (lucD) in the genome of SmCNPMS2112. The alkaline phosphatase was observed on two strains, but acid phosphatase was exclusive to SmUFMG85. Eighteen secondary metabolic gene clusters, such as those involved in the biosynthesis of macrolides and bacillomycin, among others, occur in both strains. Moreover, both genomes contained prophages, suggesting that viral-mediated horizontal gene transfer may be a key mechanism driving genomic variability in the endophytic environment. Indeed, the most genes unique and accessory of SmUFMG85 and SmCNPMS2112 were localized in genomic islands, highlighting genome plasticity and its underlying drivers. To investigate the ecological distribution of plant-interaction traits in the genus Serratia, the genomes of SmUFMG85 and SmCNPMS2112 strains were compared with those of other 19 Serratia strains of different species, which were isolated from different environments. We observe that many features for PGP are present in all genomes, regardless of niche, for instance: formation of flagella, fimbriae and pili, chemotaxis, biosynthesis of siderophores, indole-3-acetic acid (IAA) and volatile organic (VOC) and inorganic (VIC) compounds, such as acetoin and HCN. Also, all the analyzed genomes show an antimicrobial resistance repertoire of genes that confer resistance to several antibiotics belonging to the groups of aminoglycosides and quinolones, for instance. Also, from a niche partitioning perspective, secretion system preference and the ability to produce exopolysaccharides involved in biofilm formation are among the features that vary the most among strains, and most likely influence niche adaptation in Serratia spp., even though only the latter seems to be a feature specifically associated with virulence in the analyzed strains. Our results show that populations of bacteria sharing the same niche can present significant physiological and genomic differences, and reveal the intraspecific metabolic plasticity that underlie plant-bacteria interactions. Also, this study reveals the potential of two Serratia marcescens strains as bioinoculants in agriculture. Considering that Serratia spp. are regarded as low risk biological agents, despite the fact that they can be associated with human disease, we suggest that strain biosafety be evaluated using a combination of genome and phenotypic analyses, as presented herein.

Hygrophorus citrinofuscus: epitypification of a rare waxcap species from Central Europe and its transfer to the genus Neohygrocybe

Hygrophorus citrinofuscus is a striking and rarely reported grassland species originally described by J. Favre from the Swiss Alps. In absence of sequence data for the type specimen, a recent collection from Austria, which is well documented based on morphology and sequence data, is designated as the epitype of H. citrinofuscus to stabilise the species concept. Further collections from Austria and the Czech Republic are given. Morphologically similar species are discussed. Hygrophorus citrinofuscus is morphologically and phylogenetically well delimited and macroscopically characterised by yellow-brown pileus colours, a fibrillose pileus surface, pale lamellae and a yellow stipe, making it readily recognisable in the field. Morphology of the lamellar trama as well as phylogenetic analyses of a combined matrix of ITS, LSU, SSU and RPB2 sequence data clearly place this species in the genus Neohygrocybe, and a transfer is proposed. Citation: Friebes G, Fuljer F, Boertmann D, Voglmayr H, Kautmanová I (2025). Hygrophorus citrinofuscus: epitypification of a rare waxcap species from Central Europe and its transfer to the genus Neohygrocybe. Fungal Systematics and Evolution 15: 121-132. doi: 10.3114/fuse.2025.15.05.

High-resolution DNA metabarcoding of modern surface sediments uncovers a diverse assemblage of dinoflagellate cysts in the Pacific and Arctic Oceans

Resting cysts of dinoflagellates can persist in sediments, seeding harmful algal blooms (HABs). A DNA metabarcoding approach was employed, targeting the large subunit ribosomal (LSU D1-D2) and the internal transcribed spacer (ITS1) to investigate the diversity and biogeography of dinoflagellate cysts from the South China Sea to the Chukchi Sea. The LSU and ITS1 datasets identified 196 and 118 species, respectively, with only 59 dinoflagellate cyst species revealed by both approaches. Eleven cyst species of potentially toxic dinoflagellates and 82 species previously unknown as cyst producers were detected. Cysts of Heterocapsa cf. horiguchii, Heterocapsa minima, Heterocapsa iwatakii, Heterocapsa rotundata, and Heterocapsa steinii were documented through germination for the first time, with the latter three species also detected via metabarcoding. This study provides critical insights into the diversity and biogeography of dinoflagellate cysts by highlighting the complementary detection capabilities of LSU and ITS1 molecular markers and their trans-latitudinal distribution patterns. The identification of potentially toxic cysts and their ecological distributions offers crucial information on the ecology of harmful dinoflagellates. These findings underscore the importance of molecular techniques in monitoring dinoflagellate cysts.

Identification of the CYPome associated with acetamiprid resistance based on the chromosome-level genome of Megalurothrips usitatus (Bagnall) (Thysanoptera: Thripidae)

BACKGROUND

The bean flower thrips, Megalurothrips usitatus, poses a great threat to cowpea and other legume cultivars. Chemical insecticides have been applied to control M. usitatus, but have resulted in little profit because of the rapid evolution of insecticide resistance. To characterize the potential insecticide resistance mechanisms in M. usitatus, we sequenced and assembled a chromosome-level genome of M. usitatus by combining PacBio sequencing and Hi-C technology using a susceptible population.

RESULTS

The genome size was 248.60 Mb and contained 14 128 protein-coding genes. The expansion genes of M. usitatus were enriched in the functional categories of heme binding and monooxygenase activity. We further identified 103 cytochrome P450 genes from the M. usitatus genome, 33 of which belonged to the CYP6 family. Ten CYP6 genes were significantly overexpressed in an acetamiprid-resistant population of M. usitatus. An RNA interference bioassay showed that knockdown of CYP6FW1, CYP6GM5, CYP6GM6, and CYP6GM7 significantly reduced acetamiprid resistance in the resistant population. In addition, the expression of all four genes could be induced by acetamiprid exposure. AlphaFold2-based homology modeling and molecular docking analysis showed that the proteins with relevance to acetamiprid resistance had relatively lower binding free energy with the acetamiprid molecule.

CONCLUSION

This study provides a reference genome and gene resources for future studies on the evolution of M. usitatus and related pest species, and highlights the importance of cytochrome P450s in insecticide resistance in this pest insect. © 2025 Society of Chemical Industry.

A glimpse into Oomycota diversity in freshwater lakes and adjacent forests using a metabarcoding approach

Oomycota, a diverse group of fungus-like protists, play key ecological roles in aquatic and terrestrial ecosystems, yet their habitat-specific diversity and distribution remain poorly understood. This study investigates the diversity of two major Oomycota classes, Saprolegniomycetes and Peronosporomycetes, in two freshwater lakes and their adjacent forests in northeastern Germany. Using a combination of targeted metabarcoding and traditional isolation techniques, we analyzed samples from six habitats, including soil (forest), rotten leaves (forest and shoreline), sediments (shoreline), and surface waters (littoral and pelagic zones). Metabarcoding revealed 401 Oomycota OTUs, with Pythium, Globisporangium, and Saprolegnia as dominant genera. Culture-based methods identified 110 strains, predominantly from surface water and sediment, with Pythium sensu lato and Saprolegnia as the most frequent taxa. Alpha and beta diversity analyses highlighted distinct community structures influenced by lake and habitat type, with significant co-occurrence of Saprolegniomycetes and Peronosporomycetes across habitats. This study provides the first comprehensive metabarcoding-based exploration of Oomycota biodiversity in interconnected freshwater and terrestrial ecotones, uncovering previously unrecognized patterns of habitat-specific diversity.

Identification and therapeutic efficacy of Pleurotus djamor var fuscopruinosus

Pleurotus is an edible mushroom that is consumed and cultivated worldwide. Pleurotus djamor var. fuscopruinosus is newly reported in Thailand, confirmed through morphological and phylogenetic analyses. Cultivation trials showed optimal mycelial growth on PDA, with sorghum supporting the highest spawn production. Sawdust was a suitable substrate, with fruiting bodies forming at 25-28 °C and 70-80% humidity, maturing within 4-5 days. Nutritional analysis (per 100 g dry weight) revealed 25.00 ± 1.5% protein, 15.99 ± 0.2% carbohydrates, 19.10 ± 0.9% fiber, 7.59 ± 1.0% ash, 2.07 ± 0.5% fat, and 30.25 ± 0.5% moisture. The 50% ethyl acetate extract exhibited the strongest antioxidant activity (IC50: 694.47 ± 3.92 µg/mL for DPPH; 652.92 ± 2.53 µg/mL for ABTS). The extract showed selective cytotoxicity against lung (A549, IC50 = 245.73 ± 7.60 µg/mL) and colorectal (SW480, IC50 = 382.03 ± 4.55 µg/mL) cancer cells but was less potent than doxorubicin (IC50 = 14.96 ± 1.58 µg/mL). Moderate cytotoxicity was observed in RAW 264.7 macrophages (IC50 = 213.08 ± 4.08 µg/mL). Antidiabetic potential was demonstrated through α-glucosidase inhibition, with the hot water extract (IC50 = 582.91 ± 3.0 µg/mL) showing the highest activity, followed by ethyl acetate (IC50 = 473.87 ± 1.4 µg/mL) and methanol (IC50 = 357.63 ± 3.3 µg/mL), comparable to acarbose (IC50 = 635.70 ± 4.9 µg/mL). Glucose consumption in 3T3-L1 adipocytes was enhanced (IC50 = 582.91 ± 3.0 µg/mL) but lower than metformin (IC50 = 99.58 ± 0.59 µg/mL). These results highlight P. djamor var. fuscopruinosus as a promising functional food with strong antioxidant, anticancer effects, and antidiabetic properties. Further studies should optimize cultivation, isolate bioactive compounds, assess safety, and validate therapeutic properties through in vivo studies.

Conserved genome structure and phylogenetic insights for the heterogeneous subfamily of Convallarioideae (Asparagaceae) revealed from plastome data

BACKGROUND

Convallarioideae, a subfamily of Asparagaceae, encompasses a wide range of morphologically diverse lineages previously classified under different traditional families and holds significant economic value. Despite its importance, chloroplast genome data for Convallarioideae remain limited, hindering a comprehensive understanding of their genome structural evolution and phylogenetic relationships. This study aims to provide a detailed characterization of chloroplast genome features and to conduct robust phylogenetic analyses of this subfamily using an expanded dataset of chloroplast genomes.

RESULTS

The plastomes of the subfamily exhibit a typical circular quadripartite structure with conserved genomic organization and gene content. However, variations were observed in genome size, SSRs, and codon usage across the subfamily. Nine highly variable regions and positive selection genes were identified. Phylogenetic analyses based on complete plastid genomes resolved the non-monophyly of Polygonateae. Compared to Eriospermum mackenii, the chloroplast genomes of tribe Rusceae, tribe Dracaeneae, and the Polygonatum-Disporopsis lineage showed significant size reduction.

CONCLUSIONS

Chloroplast genomes across Convallarioideae exhibit remarkable structural conservation. The phylogenetic analyses revealed weakly resolved backbone relationships among core members of this subfamily. Indels in the LSC region and gene loss were identified as key drivers of structural divergence in plastome size. These results clarify the interplay between genomic architecture and phylogenetic discordance, advancing our understanding of genomic evolution within Convallarioideae.

Population genetic diversity and structure of the endangered species Tetracentron sinense Oliver (Tetracentraceae) with SNPs based on RAD sequencing

Tetracentron sinense Oliv. (T. sinense), as a tertiary living fossil, has experienced a significant decline in population numbers. Currently, genetic resources depletion and human activities have led to habitat fragmentation of relict and endangered plants, despite the abundant evidence of its medicinal, economic, and ecological value. Conservation strategies were clarified and evaluated based on the genetic structure characteristics and diversity patterns among 25 wild populations using Restriction site-associated DNA sequencing (RAD-seq) technology. Through SNP calling, filtering, genetic diversity analysis, discriminant analysis of principal components (DAPC), maximum-likelihood phylogenetic tree, and ADMIXTURE clustering, significant population structure and differentiation were identified. The results revealed a total of 2,169 single nucleotide polymorphisms (SNPs), indicating lower genetic variation but higher genetic differentiation (He: 0.10, I: 0.16, Fst: 0.33). Analysis of molecular variance (AMOVA) showed that genetic variation within populations accounted for 77% of the total variance. DAPC, maximum-likelihood phylogenetic tree, and ADMIXTURE clustering analysis grouped the 25 populations into five distinct clades influenced by isolation, restricted gene flow, and complex topography. To preserve the genetic integrity of T. sinense, it is recommended to establish conservation units corresponding to different geographic clades, with a focus on populations with low/high genetic diversity by implementing artificial reproduction and germplasm resource nurseries. Given the species' vulnerable conservation status, urgent implementation of the aforementioned conservation strategies is necessary to safeguard the remaining genetic resources.

Comprehensive genomic and evolutionary analysis of biofilm matrix clusters and proteins in the Vibrio genus

Vibrio cholerae pathogens cause cholera, an acute diarrheal disease resulting in significant morbidity and mortality worldwide. Biofilms in vibrios enhance their survival in natural ecosystems and facilitate transmission during cholera outbreaks. Critical components of the biofilm matrix include the Vibrio polysaccharides produced by the vps-1 and vps-2 gene clusters and the biofilm matrix proteins encoded in the rbm gene cluster, together comprising the biofilm matrix cluster. However, the biofilm matrix clusters and their evolutionary patterns in other Vibrio species remain underexplored. In this study, we systematically investigated the distribution, diversity, and evolution of biofilm matrix clusters and proteins across the Vibrio genus. Our findings reveal that these gene clusters are sporadically distributed throughout the genus, even appearing in species phylogenetically distant from Vibrio cholerae. Evolutionary analysis of the major biofilm matrix proteins RbmC and Bap1 shows that they are structurally and sequentially related, having undergone structural domain and modular alterations. Additionally, a novel loop-less Bap1 variant was identified, predominantly represented in two phylogenetically distant V. cholerae subspecies clades that share specific gene groups associated with the presence or absence of the protein. Furthermore, our analysis revealed that rbmB, a gene involved in biofilm dispersal, shares a recent common ancestor with Vibriophage tail proteins, suggesting that phages may mimic host functions to evade biofilm-associated defenses. Our study offers a foundational understanding of the diversity and evolution of biofilm matrix clusters in vibrios, laying the groundwork for future biofilm engineering through genetic modification.

IMPORTANCE

Biofilms help vibrios survive in nature and spread cholera. However, the genes that control biofilm formation in vibrios other than Vibrio cholerae are not well understood. In this study, we analyzed the biofilm matrix gene clusters and proteins across diverse Vibrio species to explore their patterns and evolution. We discovered that these genes are spread across different Vibrio species, including those not closely related to V. cholerae. We also found various forms of key biofilm proteins with different structures. Additionally, we identified genes involved in biofilm dispersal that are related to vibriophage genes, highlighting the role of phages in biofilm development. This study not only provides a foundational understanding of biofilm diversity and evolution in vibrios but also leads to new strategies for engineering biofilms through genetic modification, which is crucial for managing cholera outbreaks and improving the environmental resilience of these bacteria.

Three new species of Camporesiomyces (Tubeufiaceae, Tubeufiales, Dothideomycetes) associated with coffee in Yunnan, China

During our surveys of microfungi associated with coffee plants in Yunnan Province, China, three saprobic fungi were isolated from dead coffee branches. Multigene phylogenetic analyses (ITS, LSU, tef1-α, and rpb2) and morphological characteristics resulted in the identification of three novel species in Camporesiomyces, namely C.bhatii, C.coffeae, and C.puerensis. Detailed morphological descriptions, illustrations, and phylogenetic analyses of these three new species are provided, along with morphological comparisons to closely related taxa. These findings have global implications for understanding the diversity of microfungi associated with coffee trees.

Origin of Polyploidy, Phylogenetic Relationships, and Biogeography of Botiid Fishes (Teleostei: Cypriniformes)

Botiidae is a small family of freshwater fishes distributed across Southeast Asia, South Asia, and East Asia. It comprises two subfamilies: the diploid Leptobotiinae and the tetraploid Botiinae. Whether species in the Botiinae are autotetraploids or allotetraploids and how many polyploidization events occurred during the evolution of this subfamily remain open questions. The phylogenetic relationships and biogeography of the Botiidae also require further investigation. In the current study, we compared phylogenetic trees constructed using DNA sequences from the mitochondrial genome and five phased nuclear genes. We also performed whole genome sequencing for two tetraploid species: Chromobotia macracanthus and Yasuhikotakia modesta. Genome profiling of five botiine species suggests that they are likely of allotetraploid origin. Nuclear gene tree topologies indicate that the tetraploidization of the Botiinae occurred only once in the common ancestor of this subfamily. Although the possible maternal progenitor and paternal progenitor of the Botiinae cannot be determined, the subfamily Leptobotiinae can be excluded as a progenitor. The gene trees built in this study generally agree on the following sister group relationships: Leptobotiinae/Botiinae, Leptobotia/Parabotia, Chromobotia/Botia, Yasuhikotakia/Syncrossus, and Sinibotia/Ambastaia. Clades formed by the last two generic pairs are also sisters to each other. Timetree analyses and ancestral range reconstruction suggest that the family Botiidae might have originated in East Asia and Mainland Southeast Asia approximately 51 million years ago and later dispersed to South Asia and the islands of Southeast Asia.

Comparative Chloroplast Genomics of Actinidia deliciosa Cultivars: Insights into Positive Selection and Population Evolution

The chloroplast genome, as an important evolutionary marker, can provide a new breakthrough direction for the population evolution of plant species. Actinidia deliciosa represents one of the most economically significant and widely cultivated fruit species in the genus Actinidia. In this study, we sequenced and analyzed the complete chloroplast genomes of seven cultivars of Actinidia. deliciosa to detect the structural variation and population evolutionary characteristics. The total genome size ranged from 156,404 bp (A. deliciosa cv. Hayward) to 156,495 bp (A. deliciosa cv. Yate). A total of 321 simple sequence repeats (SSRs) and 1335 repetitive sequences were identified. Large-scale repeat sequences may facilitate indels and substitutions, molecular variations in A. deliciosa varieties' chloroplast genomes. Additionally, four polymorphic chloroplast DNA loci (atpF-atpH, atpH-atpI, atpB, and accD) were detected, which could potentially provide useful molecular genetic markers for further population genetics studies within A. deliciosa varieties. Site-specific selection analysis revealed that six genes (atpA, rps3, rps7, rpl22, rbcL, and ycf2) underwent protein sequence evolution. These genes may have played key roles in the adaptation of A. deliciosa to various environments. The population evolutionary analysis suggested that A. deliciosa cultivars were clustered into an individual evolutionary branch with moderate-to-high support values. These results provided a foundational genomic resource that will be a major contribution to future studies of population genetics, adaptive evolution, and genetic improvement in Actinidia.

Genome Sequencing of a Fusarium Endophytic Isolate from Hazelnut: Phylogenetic and Metabolomic Implications

This study reports on the whole genome sequencing of the hazelnut endophytic Fusarium isolate Hzn5 from Poland. It was identified as a member of the Fusarium citricola species complex based on a phylogenetic analysis which also pointed out that other hazelnut isolates, previously identified as F. lateritium and F. tricinctum, actually belong to this species complex. Genome annotation allowed the mapping of 4491 different protein sequences to the genome assembly. A further in silico search for their potential biosynthetic activity showed that predicted genes are involved in 1110 metabolic pathways. Moreover, the analysis of the genome sequence carried out in comparison to another isolate, previously identified as an agent of hazelnut gray necrosis in Italy, revealed a homology to several regions containing biosynthetic gene clusters for bioactive secondary metabolites. The resulting indications for the biosynthetic aptitude concerning some emerging mycotoxins, such as the enniatins and culmorin, should be taken into consideration with reference to the possible contamination of hazelnuts and derived products.

Chromosome-level genome assembly of the synanthropic fly Chrysomya megacephala: insights into oviposition location

The oriental latrine fly, Chrysomya megacephala (Diptera: Calliphoridae), is a medically important synanthropic blow fly species characterized by its necrophagy and coprophagy, often observed near carrion and animal feces. Notably, C. megacephala always arrives at carcass earlier than other species. To elucidate the underlying mechanisms behind the host choice in C. megacephala, we present the chromosome-scale genome assembly for this species. The genome size is 816.79 Mb, with a contig N50 of 1.60 Mb. The Hi-C data were anchored to six chromosomes, accounting for 99.93% of the draft assembled genome. Comparative genomic analysis revealed significant expansions in pathways of ligand-gated ion channel activity, passive transmembrane transporter activity, and protein methyltransferase activity, which may be closely associated with host localization and oviposition. After identifying 69 odor-binding proteins (OBPs) in the assembled genome, phylogenetic analysis showed that DmelOBP99b and CmegOBP99b exhibited high homology. Transcriptome analysis demonstrated that the relative expression of CmegOBP99b was consistently the highest during the metamorphosis, and RT-qPCR further confirmed the similar results. Additionally, CmegOBP99b exhibited a strong binding affinity to DMDS (dimethyl disulfide) as determined by molecular docking. To determine the protein expression level of CmegOBP99b in various body parts, we prepared recombinant CmegOBP99b protein and anti-CmegOBP99b polyclonal antibodies. Western blot analysis showed that CmegOBP99b was significantly expressed in the female's head compared to other parts, which is consistent with RT-qPCR results. Therefore, CmegOBP99b may be the primary odor-binding protein responsible for olfactory recognition and the behavioral coordination of C. megacephala. This study not only provides valuable insights into the molecular mechanisms of oviposition localization in C. megacephala but also facilitates further research into the genetic diversity and phylogeny of the Calliphoridae family.

Unraveling the genetic traits and functional diversity of the pan-genome in Pantoea dispersa

BACKGROUND

Medical devices are crucial in modern healthcare, but commonly used clinical tools such as cotton swabs can be easily contaminated by microorganisms (such as Pantoea), becoming vectors for pathogens and leading to patient infections or more severe outcomes. Despite the dual nature of the Pantoea that has garnered significant attention, research investigating Pantoea dispersa (P. dispersa) remains limited. This study conducted a pan-genome analysis of three isolates and 57 P. dispersa strains from NCBI to investigate their evolutionary relationships, population structure, and functional characteristics.

RESULTS

Whole-genome analysis revealed high genomic diversity among 60 strains of P. dispersa, identifying 6,791 orthologous gene clusters (OGs), with core genes accounting for 45.1% and accessory genes accounting for 54.9%. Additionally, 2,185 gene clusters were not annotated in the reference genome. Further analysis demonstrated that 782 gene clusters were annotated as 406 VFs that were unevenly distributed among different strains and primarily associated with nutritional or metabolic factors, motility, and immune modulation. This study also identified four VFs genes related to the type III secretion system (T3SS) and observed some VFs present only in specific genetic clusters. In the analysis of antibiotic resistance genes (ARGs), 12 ARGs were identified, with nine being highly conserved across all isolates, and resistance mechanisms primarily involved antibiotic efflux and antibiotic target alteration. Secondary metabolite analysis identified 289 gene clusters, with 23 matching known gene clusters, while the rest were new discoveries, including arylpolyene, NRPS, and terpene types. These results reveal the complex virulence factors (VFs) and secondary metabolite genes in P. dispersa, providing significant insights into its genetic diversity and biological significance.

CONCLUSION

This study provides the first pan-genome framework for P. dispersa, along with a map of its VFs, ARGs, and secondary metabolite gene clusters. This study provides a deep insight into the genetic diversity and potential biological significance of P. dispersa, offering valuable references for leveraging its unique strain characteristics and metabolic capabilities in industrial production and clinical therapy.

Development and application of a sex-linked marker for Herpetospermum pedunculosum based on whole-genome resequencing

Sex-specific DNA markers are effective tools for sex identification and sex-controlled breeding of dioecious organisms. The seeds of the dioecious Herpetospermum pedunculosum are utilized in traditional Chinese medicine, and the development of sex-linked markers for seedlings is crucial for enhancing the number of female plants. In this study, we screened sex-specific markers based on whole-genome resequencing of 20 male and 24 female H. pedunculosum individuals, and validated a male-specific DNA fragment of 505 bp among 80 individuals from four populations using simple PCR. The findings provide a reliable male-specific marker for the sex identification of H. pedunculosum seedlings.

The pet café is a neglected site for transmission of antimicrobial-resistant Escherichia coli in urban life

The process of urbanization has brought with it several novel lifestyles, but it remains to be seen whether such lifestyles are the potential driver behind the spread of antimicrobial resistance (AMR) in modern society. Hence, this study employs the pet café as a proof of concept to observe how one pathway of AMR transmission occurs within a megacity. A total of 111 samples were collected from consumers, workers, animals and the surrounding environment from three pet cafés in Guangzhou, and 163 bacterial strains were isolated, with Escherichia coli (n=60) being the most dominant species. The sequence type and genomic diversity of E. coli were observed in all three cafés. Notably, 19 highly related ST328 strains were isolated in a single pet café from both workers (skin and faeces) and animals (faeces), suggesting transmission between distinct hosts. The number of SNPs between ST328 E. coli isolated in this study and strains from other provinces in China was minimal, with the possibility of clonal transmission. In terms of AMR, 90% of the isolates exhibited resistance to at least three distinct classes of antimicrobials (multidrug resistance). Multiple antimicrobial resistance genes (ARGs) such as tet(X4) were detected in this study, and plasmid, especially hybrid plasmid, is the main transmission vector of these ARGs. Our findings highlight that the pet café is a neglected site for the transfer of ARGs among Enterobacteriaceae, with a propensity for continuous contamination through either clonal or horizontal transmission of ARGs.

Reversible excision of the wzy locus in Salmonella Typhimurium may aid recovery following phage predation

Bacteriophage (phage) are promising novel antimicrobials but a key challenge to their effective implementation is the rapid emergence of phage resistance. An improved understanding of phage-host interactions is therefore needed. The Anderson phage typing scheme differentiates closely related strains of Salmonella enterica serovar Typhimurium (S. Typhimurium) based on sensitivity to a panel of phage preparations. Switches in phage type are indicative of changes in phage sensitivity and inform on the dynamics of phage interaction with their host bacteria. We investigated the molecular basis of switches between the relatively phage sensitive S. Typhimurium DT8 and phage resistant DT30 strains that are present in the same phylogenetic clade. DT30 strains emerged from DT8 strains predominantly by deletion of a genomic region affecting the wzy locus encoding an O-antigen polymerase. The deletion site was flanked by two perfect direct repeats designated attL and attR. During broth culture in the presence of a typing phage that used O-antigen as primary receptor the Δwzy genotype increased in frequency compared with culture in the absence of phage and removal of attL prevented deletion of the wzy locus. Co-culture of S. Typhimurium DT8 with a strain lacking wzy resulted in reversion of the latter to wild type. We propose a model in which reversible deletion of the wzy locus enables recovery of S. Typhimurium DT8 following predation by phage that use O-antigen as their primary receptor. This was consistent with ancestral state reconstruction of DT8 and DT30 phylogeny that supported a model of reversible transition from DT8 to DT30 in natural populations.

Therapeutic Scrutiny of Lentinus polychrous with Attention to Its Antioxidant, Antimicrobial, and Anticancer Attributes

Mushrooms, being a source of therapeutically active compounds, are of great interest to researchers due to their historical usage in traditional therapies and the significant role that natural products have played in the development of contemporary medications. Lentinus polychrous is one underutilized mushroom species collected from the laterites of West Bengal, India. Our study aims toward its taxonomic validation, deciphering the secondary metabolic fingerprint, and testing its efficiency in countering many clinical issues, including oxidative stress, growing microbial drug resistance, and cancer. In vitro investigations have shown that the methanolic extract of the mushroom has a broad spectrum of antioxidant activities with effective concentration (EC50) ranging from 403.6 ± 3.8 to 841.2 ± 10.7 µg/mL depending on the type of free radicals and is effective in combating human pathogenic bacterial strains where MIC50 varies from as low as 302.2 ± 3.8 to 570.6 ± 1.8 µg/mL, mediated likely through inducing the breakdown of the outer coat and inducing increased porosity. The fraction was also shown to possess anticancer properties against A549 cells (LD50 120.9 ± 1.83 µg/mL) by triggering apoptosis. The modulation of Bcl-2 family gene expression was found to be the primary factor responsible for the induction of apoptosis in A549 cells during the experimental approaches. The findings revealed that the mushroom exhibits significant antioxidant, antibacterial, and particular cytotoxic effects on lung cancer cells, indicating its potential medical importance. These results provide essential insights into possibilities for the development of new therapeutic medicines derived from this mushroom.

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

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

Genome-Wide Identification and Evolution-Profiling Analysis of Heat Shock Protein Gene Family in Poaceae Barnhart

Heat shock proteins (HSPs) function as molecular chaperones to maintain protein homeostasis and repair denatured proteins, counteracting abiotic stresses. Despite their functional importance, a systematic bioinformatics analysis of the HSP gene family was lacking in Poaceae. In this study, we revealed that HSPs are widely distributed from algae to eudicots, with varying numbers in Poaceae including Oryza, Triticum, and Panicum. Gene duplication events, particularly dispersed duplication (DSD), tandem duplication (TD), and genome polyploidization, have probably driven the increased number of HSP genes and the expansion of HSP family proteins. Gene Ontology (GO) annotation analyses suggested their conserved functions. Promoter cis-acting element analyses indicated that their expression levels were tightly regulated by abiotic stresses. We validated that many collinear HSP genes are indeed regulated by the cold stress by analyzing the published RNA-seq data in rice, maize, and wheat, and performing RT-qPCR in rice. Our findings shed light on the role of HSPs in the abiotic stress response, laying the groundwork for further exploration of HSP functions in Poaceae.

Geography is a stronger predictor of diversification of monogenean parasites (Platyhelminthes) than host relatedness in characin fishes of Middle America

Host-parasite associations have historically been considered compelling examples of coevolution and useful in examining cospeciation. However, modern molecular methods have revealed more complex dynamics than previously assumed, with host-switching events appearing commonly across taxa and challenging traditional views of strict coevolution in host-parasite relationships. Monogenean parasites are considered highly host-specific and have long served as models for probing evolution of host-parasite associations, particularly in differentiating geographic and phylogenetic patterns of parasite diversification. We investigated the phylogeographic patterns of monogenean ectoparasites associated with four species of characin fishes across Panama, Nicaragua, and Mexico. We hypothesize that parasite diversity and community structure are more strongly correlated with host species (suggesting cospeciation) than with geographic location (indicative of allopatric speciation). We found high genetic differentiation among parasites and their hosts across different locations. However, while geography explained the genetic structure of both host fishes and parasites, the observed patterns were neither congruent nor parallel. Parasite community structure and genetic similarity were consistently better explained by geographic location than by host species identity, although both factors played a significant role. Contrary to our predictions, we found no evidence of cospeciation. Instead, the diversification of these monogenean parasites appears to be primarily driven by their ability to switch hosts. At this taxonomical scale, host-switching is mediated by the geographical proximity of potential hosts, underscoring the importance of spatial factors in parasite evolution.

Complete mitochondrial genome of Medicago sativa ssp. falcata (Papilionoideae, Fabaceae): characterization and phylogenetic analysis

MAIN CONCLUSION

The first mitogenome of Medicago sativa ssp. falcata complete assembly and a comparative analysis of the four Medicago species base on mitogenome reveal taxonomic insights. Medicago sativa ssp. falcata is primarily distributed in the northern part of the geographical range where alfalfa grows and is a subspecies of the Medicago sativa complex (also called Mediacago falacta). However, compared to M. sativa, M. falcata has better performance in cold resistance and drought tolerance, making it a high-quality gene source for the breeding improvement of Medicago species. We sequenced and assembled the mitochondrial genome of M. falcata with a length of 307,026 bp and successfully annotated 50 genes, of which nad2 exhibited high nucleotide polymorphism in four Medicago species. A total of 197 RNA-editing sites were predicted across 24 protein-coding genes, with alterations at these editing sites resulting in a substantial number of leucine-coding sites, which is consistent with the results of codon usage bias. In addition, we conducted a horizontal comparison of four types of Medicago, including Medicago truncatula, and found that repetitive sequences in their mitogenomes exhibited consistent distribution characteristics. Phylogenetic trees generated through two methods indicated the independent genetic status of M. falcata within the Medicago genus and its partial kinship relationships within the Fabaceae family. The analysis of non-synonymous and synonymous substitution rates of shared protein-coding genes in different plants, along with gene transfer results, suggests that the mitogenome of M. falcata evolved smoothly without showing phases of intense change. This study provides useful information for further understanding the genetic background of M. falcata, with the expectation of contributing to the genomic mining and utilization of germplasm resources in the Medicago genus.

Unveiling β-Tubulin Isotype-1 Polymorphisms in Haemonchus contortus from Pakistani Livestock: New Insights into Benzimidazole Resistance and Protein Structure Analysis

BACKGROUND

Haemonchus contortus, a gastrointestinal hematophagous parasitic nematode, causes substantial economic losses to the livestock sector across the globe. The widespread use of benzimidazoles in livestock has contributed greatly to the evolution of resistance in H. contortus. To effectively tackle this expanding threat, regular and diligent monitoring is required to identify and manage resistance, ensuring that treatment techniques continue to be effective.

OBJECTIVES

This study aimed to investigate the genetic and structural variations in β-tubulin isotype-1 of Haemonchus contortus isolated from goats and cattle in Pakistan, with a focus on understanding the mechanisms underlying resistance to benzimidazole.

METHODS

A total of 150 goats and 100 cattle from four abattoirs in Rawalpindi were tested for Haemonchus contortus. Faecal samples were cultured for L3 larvae, DNA was isolated, and whole genome sequencing was performed. β-tubulin isotype 1 gene sequence was extracted. Phylogenetic tree with reference genome from GenBank, and protein models were generated via ExPaSy and I-TASSER and validated with SAVESv.6.0.

RESULTS

Six genotypes of Haemonchus contortus isotype1 β-tubulin gene, each with a length of 385 base pairs were identified. The E198A SNP was the most prevalent mutation among the larvae of Haemonchus contortus collected from cattle (62.5%) and goats (50%), followed by the F200Y which was detected in 6 (37.5%) larvae collected from cattle and 9 (37.5%) larvae from goats. SNP F167Y was not identified in any of the samples. The phylogenetic analysis showed that the isolates were closely related to H. contortus from China (KX258930) and H. contortus × H. placei hybrids from Pakistan. Six genotypes of β-tubulin isotype 1 gene were translated into three haplotypes based on protein sequences: wild type/susceptible, E198A-resistant/mutant, and F200Y-resistant/mutant. Structural analysis revealed high model quality and confidence, with the E198A and F200Y resistant/mutants exhibiting different characteristics, with refined quality factors exceeding 91%.

CONCLUSION

The study demonstrated alterations in tubulin structure and function are crucial for understanding anthelmintic resistance patterns. These findings help for improving therapeutic approaches, comprehending resistance mechanisms, and promoting sustainable parasite control.

Two new species of Penicillium and a new genus in Xylariomycetidae from the forest dump-sites in Chiang Mai, Thailand

Waste accumulation in forest regions can have a severe impact on the soil mycobiome. However, research on soil fungi inhabiting forest disposal sites remains limited. Therefore, this study focused on the taxonomy and phylogeny of ascomycetes isolated from soil in forest dump-sites in Chiang Mai, Thailand. The fungal strains were identified using morphological characterisations and multigene phylogenetic reconstruction. A new genus, Pseudoleptodontidium, typified by Ps.chiangmaiense sp. nov. (Amphisphaeriales genera incertae sedis, Xylariomycetidae), along with two new species, Penicilliumchiangmaiense (series Janthinella, section Lanata-Divaricata) and P.terrae (series Erubescentia, section Exilicaulis) (Aspergillaceae, Eurotiales), are described in detail and compared with closely-related species. Our discovery offers valuable insights into the soil ascomycetes associated with forest disturbances.

Characterisation of the Gillenia S-locus provides insight into evolution of the nonself-recognition self-incompatibility system in apple

Self-incompatibility (SI) in plants has evolved independently multiple times and S-RNase-based gametophytic self-incompatibility (GSI) is most common. The Rosaceae family possesses both self-recognition (Prunus) and nonself-recognition (Malus) GSI systems, and the latter is widespread in flowering plants. Gillenia trifoliata is a Rosaceae species related to Prunus and Malus, providing utility for understanding SI evolution. Gillenia is sister taxon to Malus, but unlike Malus, has not undergone polyploidisation. In addition, the common ancestor of Gillenia and Prunus is close to the origin of the subfamily. Using a highly contiguous Gillenia genome, orthologous regions to both Malus and Prunus S-loci were identified. Only the Prunus-like S-locus was highly polymorphic and had signatures of a functional S-locus including positive selection of the S-RNase. This suggests a self-recognition system controls SI in Gillenia, and the common ancestors of Gillenia and Prunus, and Gillenia and the apple tribe, likely had a self-recognition SI system. Comparative genomics between Gillenia and Malus suggest apple lost the self-recognition mechanism, and a nonself-recognition mechanism evolved independently from a rudimentary locus with at least one male S-determinant. Repetitive sequences in the Malus-like S-locus in Gillenia may facilitate illegitimate recombination, suggesting putative mechanisms of evolution of nonself-recognition S-loci.

Exploring Diversity of Conopeptides and Revealing Novel Conoinsulins from Conus betulinus by Proteomic Analyses

The venom of cone snails, a potent weapon for predation and defense, contains diverse bioactive peptides (known as conopeptides, or conotoxins) that target various ion channels and receptors, offering potential as pharmacological tools or therapeutics. While transcriptomic studies have expanded conopeptide databases, proteomic validation remains limited. Here, we integrated two high-resolution mass spectrometry platforms to explore conopeptide diversity in Conus betulinus. A total of 283 conopeptides were identified, with 268 classifiable into known gene superfamilies or homology classes, while 15 unclassified conopeptides represent novel superfamilies. There were 46 newly discovered sequences and five new cysteine frameworks. Notably, we report the first proteomic identification of two novel conoinsulins in C. betulinus, Con-ins Be1 and Con-ins Be2. Both of them were predicted to retain insulin's canonical A/B-chain architecture. Structure modeling using the AlphaFold2 multimer suggested that Con-ins Be1 has a four-disulfide-bond arrangement, differing from the three disulfide bonds found in vertebrate insulin. In contrast, Con-ins Be2 was predicted to have three disulfide bonds, consistent with the structure of the vertebrate insulin. In summary, our study not only expanded the conopeptide repository but also provided two novel conoinsulins that may serve as pharmacological tools for insulin system research and merit further investigation.

Spegazzinia menglaensis, A Novel Species of Didymosphaeriaceae from Air in China

A novel fungal species, viz. Spegazzinia menglaensis belonging to Didymosphaeriaceae (Pleosporales, Dothideomycetes), was isolated from air samples in China. Spegazzinia menglaensis is characterized by basauxic conidiophores, with a light brown conidiophore mother cell, and 4-celled, stellate α conidia and disc-shaped β conidia. To further confirm its taxonomic placement, in-depth molecular analyses were conducted, utilizing multiple loci including internal transcribed spacers (ITS), large subunit of nuclear ribosomal RNA gene (LSU), translation elongation factor 1-α (tef1-α). The molecular analyses revealed that S. menglaensis formed distinct clade within Spegazzinia, which is close to S. jinghaensis. To provide a comprehensive understanding of the new fungal species, detailed descriptions, accompanied by illustrative images, as well as a phylogenetic tree showcasing the position of S. menglaensis within the taxonomic framework, have been included.

Biotrophic and saprophytic fungi from the Rhodocybe-Clitopilus clade (Entolomataceae): two new species and one new record in subtropical China

This study proposes two new species and a new record in the Rhodocybe-Clitopilus clade, based on comprehensive morphological and molecular analyses. The nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS), the large subunit ribosomal RNA gene (LSU), the RNA polymerase II second largest subunit (RPB2) and the translation elongation factor 1-alpha gene (TEF1), were employed to elucidate the relationships of Clitopilus and Rhodocybe. The first species, Clitopilusparasiticus, is capable of infecting the leaves of host plants in the genera Dryopteris and Oplismenus, exhibiting typical biotrophic behaviour while also demonstrating saprophytic growth on soil. Intraspecific comparisons were conducted, examining environmental factors as well as macro- and microscopic characteristics amongst individuals found on different plant hosts. Furthermore, this study reports the new saprophytic species, Rhodocybezijinshanensis and provides a detailed description of Clitopilusbaronii, a newly-recorded species in China.

Insights into the genetic diversity and species distribution of Oswaldocruzia nematodes (Trichostrongylida: Molineidae) in Europe: apparent absence of geographic and population structuring in amphibians

The genus Oswaldocruzia represents a taxonomically diverse group of nematodes with global distribution. Although Oswaldocruzia species are widespread and exhibit a remarkably wide host range in some species, their genetic diversity and biogeographic patterns remain poorly understood. This study investigated the genetic variability and distribution of Oswaldocruzia spp. in nine anuran species from the genera Bufo, Bufotes, Pelophylax, and Rana across Central Europe and the Balkans. Two species were identified: Oswaldocruzia filiformis and O. ukrainae, each exhibiting a different range of host associations. Phylogenetic analyses based on mitochondrial COI sequences revealed significant haplotype diversity in the generalist O. filiformis, with low geographic and host-associated genetic structuring. In contrast, O. ukrainae, which is closely associated with Bufotes viridis, exhibited only one genetic variant across all samples, highlighting its restricted genetic diversity. The findings emphasize contrasting genetic diversities among nematode parasites exhibiting different levels of host-specificity and expand the known distribution of O. filiformis into new regions of the Balkans. In addition, they highlight the need for additional studies on the ecological and evolutionary factors that influence the genetic diversity of parasites in amphibians.

Additions to the family Junewangiaceae (Sordariomycetes): novel species and new records from freshwater habitats in Southwestern China

Junewangiaceae (Sordariomycetes) is a family with a relatively recent taxonomic history and a small number of described species. However, a major challenge within this family is the inability to distinguish between various genera based solely on the phylogenetic analysis. In this study, we introduced two new species, Junewangia guangxiensis and J. synnematica, which formed independent clades in phylogenetic analysis and displayed characteristics that were easily distinguishable from other species within this family. Additionally, three previously known species, viz., Dictyosporella aquatica, D. thailandensis, and J. thailandensis, are reported from China for the first time. Furthermore, D. bambusicola is documented from a freshwater habitat. The results enhance our understanding of Junewangiaceae and provide some suggestions for addressing the taxonomic problems of this family in the future.

Fungal Pathogens of Peach Palm Leaf Spot in Thailand and Their Fungicide Sensitivity

Peach palm (Bactris gasipaes Kunth) is a long-lived tropical palm valued for its edible, nutritious fruits. The cultivation area of peach palm, which was introduced to Thailand for fruit production, has been steadily expanding. Small brown spots that expanded into irregular lesions with dark margins were first observed on B. gasipaes seedlings in commercial nurseries in Phetchaburi Province, southern Thailand. To identify the causal pathogens, ten fungal isolates were obtained from symptomatic leaves and subjected to pathogenicity tests, confirming their ability to cause the disease. Morphological and molecular analyses identified five isolates as Colletotrichum fructicola (BGC02.2, BGC03) and C. theobromicola (BGC01, BGC02.1, BGC04) and five isolates as Fusarium pernambucanum (BGF01, BGF02, BGF03, BGF04.1, BGF04.2). Phylogenetic analysis was based on act, cal, gapdh, ITS, and tub2 regions for Colletotrichum spp. and cal, rpb2, and tef1-α for Fusarium spp. In vitro fungicide assays revealed that C. fructicola and C. theobromicola were the most sensitive to carbendazim, mancozeb, and prochloraz, while F. pernambucanum was effectively inhibited by mancozeb and prochloraz. This study represents the first report of C. fructicola, C. theobromicola, and F. pernambucanum causing leaf spot disease on B. gasipaes in Thailand, providing essential insights for disease management strategies in the region.

Resolving floral development dynamics using genome and single-cell temporal transcriptome of Dendrobium devonianum

Dendrobium devonianum, a species of the Orchidaceae family, is notable for its unique floral characteristics, which include two yellow spots and purple tips on its labellum, as well as fringed edges. However, the molecular mechanisms underlying flower pattern formation in D. devonianum remain poorly understood, hindering advancements in its breeding process. Here, a chromosome-scale genome of D. devonianum was presented for the first time, revealing two significant polyploidization events. Additionally, a high-resolution single-cell transcriptomic atlas was constructed, capturing 11 distinct cell clusters. Expression patterns of MADS-box genes were identified through temporal and spatial bulk RNA-Seq, revealing alignment with the ABCDE model of flower formation. Meanwhile, mass spectrometry imaging and scRNA analyses showed that the yellow spots were primarily associated with carotenoid biosynthesis gene expression, while the purple colour is predominantly linked to anthocyanin biosynthesis gene expression. These genes were mainly expressed in the epidermis and vascular cells. Developmental trajectory analyses of epidermal cells further uncovered a gene regulatory network and several transcription factors likely responsible for fringes formation along the labellum margin. This study provides valuable insights into the molecular mechanisms driving floral colour differentiation and structural traits in D. devonianum, contributing to a deeper understanding of orchid evolution, diversification and breeding.

Temperature-related growth limits and wood decay capacity of the warmth-loving fungus Biscogniauxia nummularia in vitro

Temperature-related growth characteristics and wood decay capacities of Biscogniauxia nummularia strains were analysed in vitro, revealing variability between strains. To model the growth characteristics fitted dose-response curves were generated using the four-parameter Brain-Cousens hormesis model. The different strains showed distinct optimum growth temperatures, with some achieving maximum growth at 25°C, while others peaked at 28°C, depending on the tested culture media. Strains tested also exhibited variation in their temperature ranges for measurable growth, with some tolerating a broader range than others. The results of the study lead to the consideration that temperature tolerance as well as the optimal growth temperature might be influenced by the strains' geographic origin, with those from southern Germany possibly adapted to higher temperatures. In terms of wood decay, mass loss caused by the various strains differed clearly in many cases, suggesting potential strain-dependent differences in pathogenicity. Additionally, genetic analysis of the beta-tubulin DNA region of B. nummularia specimens examined revealed considerable variations between the strains.

Draft genome sequences of five glacial fungi from Styx Glacier, Antarctica

We generated four high-quality draft genomes of fungi isolated from Styx Glacier, Antarctica. The genome announcement of these fungal strains offers insights into their evolution and adaptation to extreme glacial environments, as well as their potential biotechnological applications.

Four new species of Beltraniella (Amphisphaeriales, Beltraniaceae) revealed by morphology and phylogenetic analyses from China

Beltraniella is a widely-distributed genus on Earth, although its abundance is relatively limited in relation to other dematiaceous hyphomycetes. In the present study, diseased leaves of Myristicafragrans and decaying leaves were collected from Hainan and Sichuan Province. Fungal DNA was amplified and sequenced using two barcodes, the internal transcribed spacer (ITS) and large subunit of ribosomal RNA (LSU), and phylogenetic analyses were conducted through maximum likelihood (ML) and Bayesian inference (BI) algorithms. Four new species of Beltraniella, B.dujiangyanensis, B.jianfengensis, B.myristicae, and B.xinglongensis are identified through phylogenetic analyses and morphological comparison during a survey of fungal diversity in Hainan and Sichuan Provinces, China. Detailed descriptions of the morphological characteristics of these four new species are provided and illustrated with figures.

Genomic and functional analysis of rmp locus variants in Klebsiella pneumoniae

BACKGROUND

Klebsiella pneumoniae is an opportunistic pathogen and a leading cause of healthcare-associated infections in hospitals, which are frequently antimicrobial resistant (AMR). Exacerbating the public health threat posed by K. pneumoniae, some strains also harbour additional hypervirulence determinants typically acquired via mobile genetic elements such as the well-characterised large virulence plasmid KpVP-1. The rmpADC locus is considered a key virulence feature of K. pneumoniae and is associated with upregulated capsule expression and the hypermucoid phenotype, which can enhance virulence by contributing to serum resistance. Typically such strains have been susceptible to all antimicrobials besides ampicillin; however, the recent emergence of AMR hypermucoid strains is concerning.

METHODS

Here, we investigate the genetic diversity, evolution, mobilisation and prevalence of rmpADC, in a dataset of 14,000 genomes from isolates of the Klebsiella pneumoniae species complex, and describe the RmST virulence typing scheme for tracking rmpADC variants for the purposes of genomic surveillance. Additionally, we examine the functionality of representatives for variants of rmpADC introduced into a mutant strain lacking its native rmpADC locus.

RESULTS

The rmpADC locus was detected in 7% of the dataset, mostly from genomes of K. pneumoniae and a very small number of K. variicola and K. quasipneumoniae. Sequence variants of rmpADC grouped into five distinct lineages (rmp1, rmp2, rmp2A, rmp3 and rmp4) that corresponded to unique mobile elements, and were differentially distributed across different populations (i.e. clonal groups) of K. pneumoniae. All variants were demonstrated to produce enhanced capsule production and hypermucoviscosity.

CONCLUSIONS

These results provide an overview of the diversity and evolution of a prominent K. pneumoniae virulence factor and support the idea that screening for rmpADC in K. pneumoniae isolates and genomes is valuable to monitor the emergence and spread of hypermucoid K. pneumoniae, including AMR strains.

Dated Phylogeny of Banisteriopsis (Malpighiaceae) Suggests an Ancient Colonization of the Cerrado and No Evidence of Human Manipulation in the Origin of B. caapi

Banisteriopsis is a genus in the Malpighiaceae family with 61 species, notable for including ritualistic taxa such as B. caapi (Spruce ex Griseb.) C.V. Morton, one of the main components of Ayahuasca tea. We analyzed 38 Banisteriopsis species, representing more than 60% of the genus, to investigate its geographical origin, diversification period, and colonization routes in the Neotropics. Plastid genes (matK, ndhF, and rbcL) and nuclear regions (ETS, ITS, and PHYC) were used in our analyses. Divergence time analyses were performed using Bayesian inference with a relaxed molecular clock and ancestral area reconstruction. Our results show that Banisteriopsis originated in the Miocene approximately 22 million years ago, and its diversification coincides with the expansion of dry areas in South America. Banisteriopsis began colonizing the Cerrado earlier than most other plants, and the history of the genus reveals that the biome served as a source of species for Neotropical rainforests. Our results also indicate a probable ancient origin for B. caapi, with no evidence of human manipulation in its diversification, and they reinforce archaeological evidence of a millennia-old exchange of uses among Amazonian peoples.

Plasmid-driven strategies for clone success in Escherichia coli

Escherichia coli is the most widely studied microbe in history, but the population structure and evolutionary trends of its extrachromosomal elements known as plasmids remain poorly delineated. Here we used long-read technology to high-resolution sequence the entire plasmidome and the corresponding host chromosomes from an unbiased longitudinal survey covering two decades and over 2000 E. coli isolates. We find that some plasmids have persisted in lineages even for centuries, demonstrating strong plasmid-lineage associations. Our analysis provides a detailed map of recent vertical and horizontal evolutionary events involving plasmids with key antibiotic resistance, competition and virulence determinants. We present genomic evidence of both chromosomal and plasmid-driven success strategies adopted by distant lineages by independently inheriting the same genomic elements. Further, we use in vitro experiments to verify the importance of key bacteriocin-producing plasmids for clone success. Our study has general implications for understanding plasmid biology and bacterial evolutionary strategies.

Complete mitogenome and phylogenetic analysis of Brassica oleracea L. var. italica Plenck

In this study, we assembled and annotated the mitochondrial genome (mitogenome) of B. oleracea L. var. italica Plenck. This mitogenome was found to span 219 964 bp, with a GC content of 45.25%. It comprised 61 genes, including 35 protein-coding, 23 transfer RNA, and three ribosomal RNA genes. Among these, only 11 genes contained introns. Codon preference analysis revealed a bias toward codons ending in A/U bases. A phylogenetic analysis demonstrated a close relationship between B. oleracea L. var. italica Plenck, B. oleracea L. botrytis, and B. oleracea var. capitata. This reference mitogenome provides a basis for research on genetic conservation, phylogenetic relationships, and molecular breeding strategies among members of the Brassica genus.

Diversification of an emerging bacterial plant pathogen; insights into the global spread of Xanthomonas euvesicatoria pv. perforans

Emerging and re-emerging plant diseases continue to present multifarious threats to global food security. Considerable recent efforts are therefore being channeled towards understanding the nature of pathogen emergence, their spread and evolution. Xanthomonas euvesicatoria pv. perforans (Xep), one of the causal agents of bacterial spot of tomato, rapidly emerged and displaced other bacterial spot xanthomonads in many tomato production regions around the world. In less than three decades, it has become a dominant xanthomonad pathogen in tomato production systems across the world and presents a compelling example for understanding diversification of recently emerged bacterial plant pathogens. Although Xep has been continuously monitored in Florida since its discovery, the global population structure and evolution at the genome-scale is yet to be fully explored. The objectives of this work were to determine genetic diversity globally to ascertain if different tomato production regions contain genetically distinct Xep populations, to examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, and to evaluate variation in type III secretion effectors, which are critical pathogenicity and virulence factors, in relationship to population structure. We used genome data from 270 strains from 13 countries for phylogenetic analysis and characterization of type III effector gene diversity among strains. Our results showed notable genetic diversity in the pathogen. We found genetically similar strains in distant tomato production regions, including seed production regions, and diversification over the past 100 years, which is consistent with intercontinental dissemination of the pathogen in hybrid tomato production chains. Evolution of the Xep pangenome, including the acquisition and loss of type III secreted effectors, is apparent within and among phylogenetic lineages. The apparent long-distance movement of the pathogen, together with variants that may not yet be widely distributed, poses risks of emergence of new variants in tomato production.

Not Ancient But Neotenic: Neotenactis amateras gen. et sp. nov., the First Record of a Gonactiniid Anemone from the North Pacific (Cnidaria: Anthozoa: Enthemonae)

The metridioid enthemonaean sea-anemone family Gonactiniidae Carlgren, 1893 is characterized by having one of the simplest morphologies among the Actiniaria. It currently includes two monotypic genera, each consisting of a species described in the 19th century from the Atlantic, although additional specimens have also been reported from the Mediterranean and South Pacific. In this study, we discovered a new species of gonactiniid anemone from Kumano-Nada, off the Pacific coast of Japan. This is the first record of this family from the North Pacific. According to our phylogenetic analyses, this anemone is the sister group to the other two genera of Gonactiniidae, Gonactinia Sars, 1851 and Protanthea Carlgren, 1891. Accordingly, we establish a new genus for this new species. Additionally, we discuss the simplification of body form in this lineage of sea anemones based on the discovery of this new species, which exhibits an intermediate morphology between the other gonactiniids and non-gonactiniid actiniarians.

The virome of the panglobal, wide host-range plant pathogen Phytophthora cinnamomi: phylogeography and evolutionary insights

Phytophthora cinnamomi stands out as one of the most devastating plant pathogens worldwide, rapidly expanding its range and impacting a wide range of host species. In this study, we investigated the virome of P. cinnamomi across 222 isolates from Africa, Asia, Europe, Oceania, and the Americas using stranded total RNA sequencing, reverse transcription polymerase chain reaction screening, and Sanger sequencing of selected isolates. Our analysis revealed that virus infections were prevalent across all sampled populations, including RNA viruses associated with the orders Ghabrivirales, Martellivirales, and Tolivirales, and the classes Amabiliviricetes, Bunyaviricetes, and the recently proposed Orpoviricetes. Viruses were mainly found in East and Southeast Asian populations, within the geographic origin of P. cinnamomi but have also spread to new regions where the pathogen has emerged as a clonal destructive pathogen. Among the identified viruses, eight species, including two bunya-like viruses, one narna-like virus, and five ormycoviruses, exhibit a global distribution with some genetic divergence between continents. The interaction between P. cinnamomi and its virome indicates a dynamic coevolution across diverse geographic regions. Indonesia is indicated to be the viral epicentre of P. cinnamomi, with the highest intra- and interspecies diversity of viruses. Viral diversity is significantly enhanced in regions where sexual recombination of P. cinnamomi occurs, while regions with predominantly asexual reproduction harbour fewer viral species. Interestingly, only the partially self-fertile mating type (MAT) A2, associated with the global pandemic, facilitates the spread of viruses across different biogeographic regions, whereas viruses are absent in the self-sterile MAT A1 in its areas of introduction like Australia and South Africa. Intriguingly, the presence of a plant tombusvirus suggests a potential cross-kingdom infection among Chilean isolates and a plant host. This study sheds further light on the geographical origin of P. cinnamomi from a novel virome perspective.