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

Complete genome sequence of Vibrio fischeri strain H905, a planktonic isolate among squid symbiotic congeners

Here we describe the genome sequence of Vibrio (Aliivibrio) fischeri H905, a non-symbiotic isolate from Kaneohe Bay, Hawaii. Despite its close phylogenetic relationship to squid symbiont strains, H905 is not adept at colonization. Its genome serves as a valuable comparator, illustrating the complex evolutionary dynamics within V. fischeri clades.

Complete chloroplast genome and phylogenetic analysis of Lonicera microphylla Willd. ex Roem. & Schult. 1819 Caprifoliaceae

Lonicera microphylla Willd. ex Roem. & Schult. 1819 is a medicinal plant species, especially for treating chronic fever and dysentery. This study aimed to characterize the chloroplast genome of L. microphylla and reconstruct the phylogenetic relationships among Lonicera Linn. 1753. The circular complete chloroplast genome is 154,945 bp in length, with two inverted repeat regions (IRs; 23,841 bp), separated by a small single-copy region (SSC; 18,789 bp) and a large single-copy region (LSC; 88,474 bp). The overall GC content of L. microphylla plastome was 38.36%. The chloroplast genome encoded a total of 131 genes, including 84 protein-coding genes, 39 tRNA genes, and eight rRNA genes. Phylogenetic analysis reveals that L. microphylla was more closely related to Lonicera tangutica Maxim. 1878. Our result can provide reference for the phylogenetic relationship, resource development, and utilization of Lonicera.

Comparative analysis of chloroplast genome of Lonicera japonica cv. Damaohua

Lonicera japonica is a well-known medicinal plant, and the Damaohua cultivar is one of the oldest known honeysuckle cultivars in China. The 155,151 bp chloroplast genome of this cultivar was obtained through Illumina sequencing. The genome includes a pair of inverted repeats (IRa and IRb; 23,789 bp each), a large single-copy region (88,924 bp), and a small single-copy (SSC) region (18,649 bp). In total, 127 unique genes were identified: 80 protein-coding, 39 tRNA, and 8 rRNA genes. Only ycf3 contained two introns. Eighty-nine large repetitive sequences and 54 simple sequence repeats were detected. Fifty potential RNA editing sites were predicted. Adaptive evolution analysis revealed that infA, matK, petB, petD, rbcL, rpl16, rpl2, rps3, ycf1, and ycf2 were positively selected, possibly reflecting the specific environmental adaptations of this cultivar. Sequence alignment and analysis revealed several candidate fragments for Lonicera species identification, such as the intergenic regions rpoB-petN, rbcL-accD, and psaA-ycf3. The IR region boundary and phylogenetic analysis revealed that the L. japonica cv. Damaohua chloroplast genome was most closely related to the L. japonica genome, but there were five distinct differences between the two. There are four sites with high variability between L. japonica and L. japonica cv. Damaohua with nucleotide variability (Pi) greater than 0.002, including rps2-rpoC2, atpB-rbcL, ycf1, and ycf1-trnN GUU. The differences between L. japonica and L. japonica cv. Damaohua were further confirmed by the single nucleotide polymorphism sites between these two species. Therefore, this study revealed that the chloroplast genome can serve as a universal super barcode for plant identification, which can identify differences and help distinguish Lonicera japonica from related species. An understanding of Lonicera japonica cv. Damaohua chloroplast genomics and a comparative analysis of Lonicera species will provide a scientific basis for breeding, species identification, systematic evolution analysis, and chloroplast genetic engineering research on medicinal honeysuckle plants.

Characterization of Pseudomonas aeruginosa from subjects with diffuse panbronchiolitis

Diffuse panbronchiolitis (DPB) is a rare, idiopathic inflammatory disease primarily diagnosed in East Asian populations. DPB is characterized by diffuse pulmonary lesions, inflammation of the respiratory bronchioles, and bacterial infections of the airway. Historically, sputum cultures reveal Pseudomonas aeruginosa in 22% of DPB patients, increasing to 60% after 4 years from disease onset. Although DPB patients have a known susceptibility to respiratory P. aeruginosa infections, as is observed in other chronic lung diseases such as cystic fibrosis (CF), the characterization of DPB P. aeruginosa strains is limited. In this study, we characterized 24 strains obtained from a cohort of DPB patients for traits previously associated with virulence, including growth, motility, antibiotic susceptibility, lipopolysaccharide structure, and genomic diversity. Our cohort of DPB P. aeruginosa strains exhibits considerable genomic variability when compared with isolates from people with cystic fibrosis chronically colonized with P. aeruginosa and acute P. aeruginosa infection isolates. Similar to CF, DPB P. aeruginosa strains produce a diverse array of modified lipid A structures. Antibiotic susceptibility testing revealed increased resistance to erythromycin, a representative agent of the macrolide antibiotics used to manage DPB patients. Differences in the O-antigen type among P. aeruginosa strains collected from these different backgrounds were also observed. Ultimately, the characterization of DPB P. aeruginosa strains highlights several unique qualities of P. aeruginosa strains collected from chronically diseased airways, underscoring the challenges in treating DPB, CF, and other obstructive respiratory disease patients with P. aeruginosa infections.

IMPORTANCE

Diffuse panbronchiolitis (DPB), a chronic lung disease characterized by persistent P. aeruginosa infection, serves as an informative comparator to more common chronic lung diseases, such as cystic fibrosis (CF). This study aimed to better address the interplay between P. aeruginosa and chronically compromised airway environments through the examination of DPB P. aeruginosa strains, as existing literature regarding DPB is limited to case reports, case series, and clinical treatment guidelines. The evaluation of these features in the context of DPB, in tandem with prevailing knowledge of P. aeruginosa strains collected from more common chronic lung diseases (e.g., CF), can aid in the development of more effective strategies to combat respiratory P. aeruginosa infections in patients with chronic lung diseases.

A new genus and species of Microphalloidea (Digenea), parasite of Peropteryx spp. (Chiroptera: Emballonuridae) from the Neotropical region of Mexico revealed by morphological and phylogenetic analyses

The present study aims to describe a new genus and species of microphalloid digenean parasite of two species of bats of the genus Peropteryx from the Mexican Neotropics (in the states of Chiapas and Yucatán). Morphological and molecular data (28s rDNA ribosomal gene sequences) were used to study Digeneans. Sagittatrema zutzi gen. nov. sp., nov., is diagnosed morphologically by having a sagittiform body, a genital pore in the midline of the body, posterior to the ventral sucker, and a cirrus sac running through much of the diameter of the ventral sucker. The nine sequences generated from the 28S rDNA gene were used to examine the phylogenetic affinities of this new taxon within the superfamily Microphalloidea Ward, 1901, using Maximum Likelihood and Bayesian Inference analyses. Both analyses resulted in trees with similar topologies and formed a well-supported clade (Bt = 100; pp = 1) with the Sagittatrema sequences. Because of the new genus's phylogenetic position and that some sister families to the proposed taxa, like Pleurogenidae and Prosthogonimidae, are polyphyletic, we prefer to consider Sagittatrema as a genus incertae sedis within Microphalloidea. A full systematic review of microphalloids is needed to confirm their phylogenetic position.

Diversity of the Obligate Gut Bacteria Indicates Host-Symbiont Coevolution at the Population Level in the Plataspid Stinkbug Megacopta cribraria

Ishikawaella is an obligate gut bacterium in stinkbugs that belong to Plataspidae family (Hemiptera: Heteroptera). It is vertically transmitted to newborn nymphs through capsules laid on eggs by maternal stinkbugs. Previous research has established a pattern of strict cospeciation between Plataspidae stinkbugs and Ishikawaella. However, the possibility of host-symbiont coevolution at the population level within Plataspidae stinkbugs has not been thoroughly explored. This study analyzed the samples of Megacopta cribraria from three phylogenetic clades to investigate host-symbiont coevolution in this insect species. We compared data from third-generation sequencing (PacBio), next-generation sequencing (Illumina), and first-generation sequencing (Sanger), and the results indicated that Illumina sequencing most accurately represents the composition of gut bacterial communities. All stinkbug individuals shared a dominant amplicon sequence variant (ASV), which accounted for an average of 65.99% of Ishikawaella sequences (ranging from 58.68% to 87.01%). The top five ASVs (ASV0-ASV4) represented 99.82% of all Ishikawaella sequences. Among these, the number of base substitutions between any two ASVs ranged from 1 to 3, significantly lower than the number of substitutions between the main and minor ASVs. This finding suggests that closely related strains are likely to coexist in the same host. Beta diversity analyses revealed significant differences in Ishikawaella composition among the three phylogenetic clades, providing evidence for host-symbiont coevolution at the population level in Plataspidae stinkbugs.

Spatiotemporal transcriptome atlas reveals gene regulatory patterns during the organogenesis of the rapid growing bamboo shoots

Bamboo with its remarkable growth rate and economic significance, offers an ideal system to investigate the molecular basis of organogenesis in rapidly growing plants, particular in monocots, where gene regulatory networks governing the maintenance and differentiation of shoot apical and intercalary meristems remain a subject of controversy. We employed both spatial and single-nucleus transcriptome sequencing on 10× platform to precisely dissect the gene functions in various tissues and early developmental stages of bamboo shoots. Our comprehensive analysis reveals distinct cell trajectories during shoot development, uncovering critical genes and pathways involved in procambium differentiation, intercalary meristem formation, and vascular tissue development. Spatial and temporal expression patterns of key regulatory genes, particularly those related to hormone signaling and lipid metabolism, strongly support the hypothesis that intercalary meristem origin from surrounded parenchyma cells. Specific gene expressions in intercalary meristem exhibit regular and dispersed distribution pattern, offering clues for understanding the intricate molecular mechanisms that drive the rapid growth of bamboo shoots. The single-nucleus and spatial transcriptome analysis reveal a comprehensive landscape of gene activity, enhancing the understanding of the molecular architecture of organogenesis and providing valuable resources for future genomic and genetic studies relying on identities of specific cell types.

First Reported Sexual Recombination Between Pyrenophora teres Isolates from Barley and Barley Grass

Barley grass (Hordeum leporinum), which often occurs in proximity to commercial barley (H. vulgare) cultivars, is an alternative host to Pyrenophora teres, an economically important pathogen causing net blotch in barley. This study is the first to report the sexual recombination of P. teres isolates collected from barley with those collected from barley grass. The sexual recombination between P. teres isolates from barley and barley grass was confirmed using a neighbor-net network and haploblock plots based on whole-genome sequencing of seven progeny isolates. Pathogenicity assays revealed that P. teres isolates from barley grass were not host specific and could infect both barley and barley grass, and the progeny isolates were virulent on commercially grown barley cultivars. Our results contradict previous population and pathogenicity studies of P. teres isolates obtained from barley and barley grass that have reported that the two populations are genetically distinct and host specific, suggesting that isolates collected from barley or barley grass could be two different entities. Despite the genetic divergence of P. teres isolates from barley and barley grass revealed through our phylogenomic analysis, there seems to be no complete host or reproductive separation between these populations. Therefore, there is a potential for generation of novel pathotypes through sexual recombination between P. teres isolates associated with barley and barley grass, with a risk of increased impacts on commercial barley cultivars that do not carry resistance to these pathotypes.

Laetiporus (Laetiporaceae, Basidiomycota) in tropical Africa is represented by a single Afromontane lineage and four species, including Laetiporus discolor, Laetiporus oboensis, sp. nov., Laetiporus tenuiculus, sp. nov., and Laetiporus sp. 1

The tropical African Laetiporus species are revised, based on morphological, ecological, distribution, and phylogenetic data. Laetiporus discolor, originally described from insular Mauritius, is accepted for the species spanning over the African eastern mountain ranges. Laetiporus oboensis and Laetiporus tenuiculus are described as new from the African equatorial insular São Tomé, based on phylogenetic, morphological, and distribution data. Laetiporus oboensis is characterized by compound basidiomes, with densely imbricated pilei in pale orange tint, a lobed margin, 3-4 pores/mm, and basidiospores averaging 4.8 × 3.7 μm. Laetiporus tenuiculus has mostly solitary, small, thin basidiomes, with pale flesh to pale orange pileus, an incised margin, 4-5 pores/mm, and basidiospores averaging 5.4 × 4.2 µm. A fourth species, known from two isolates from Ethiopian highlands, but for which voucher specimens were not available for description, is uncertain. These four species form an African endemic lineage, whose distribution is Afromountainous.

Morphology, behavior, and phylogenomics of Oxytoxum lohmannii, Dinoflagellata

Dinoflagellates are an abundant and diverse group of protists representing a wealth of unique biology and ecology. While many dinoflagellates are photosynthetic or mixotrophic, many taxa are heterotrophs, often with complex feeding strategies. Compared to their photosynthetic counterparts, heterotrophic dinoflagellates remain understudied, as they are difficult to culture. One exception, a long-cultured isolate originally classified as Amphidinium but recently reclassified as Oxytoxum, has been the subject of a number of feeding, growth, and chemosensory studies. This lineage was recently determined to be closely related to Prorocentrum using phylogenetics of ribosomal RNA gene sequences, but the exact nature of this relationship remains unresolved. Using transcriptomes sequenced from culture and three single cells from the environment, we produce a robust phylogeny of 242 genes, revealing Oxytoxum is likely sister to the Prorocentrum clade, rather than nested within it. Molecular investigations uncover evidence of a reduced, nonphotosynthetic plastid and proteorhodopsin, a photoactive proton pump acquired horizontally from bacteria. We describe the ultrastructure of O. lohmannii, including densely packed trichocysts, and a new type of mucocyst. We observe that O. lohmannii feeds preferentially on cryptophytes using myzocytosis, but can also feed on various phytoflagellates using conventional phagocytosis. O. lohmannii is amenable to culture, providing an opportunity to better study heterotrophic dinoflagellate biology and feeding ecology.

Characterization of volatile profiles and markers prediction of eleven popular edible boletes using SDE-GC-MS and FT-NIR combined with chemometric analysis

Wild edible boletes mushrooms are regarded as a delicacy in many countries and regions due to their rich nutritional contents and strong aromatic compounds. This study aimed to identify 445 samples of 11 boletes species collected from Yunnan and Sichuan provinces through molecular analysis. Using simultaneous distillation-extraction (SDE) combined with gas chromatography-mass spectrometry (GC-MS), 97 volatile compounds were identified. Chemometric methods were then applied to analyze the heterogeneity of these volatile compounds among the different species. The results showed that, 22 and 21 volatile compounds were selected using variable importance in projection (VIP > 1) and relative odor activity values (ROAV > 0.1), respectively. Partial least squares discrimnatint analysis (PLS-DA) was then employed to develop pattern recognition models for 11 species, which demonstrated strong identification performance. Furthermore, correlation heat maps, volcano plots, and Fisher linear discriminant analysis identified five volatile organic compounds, including methyl (9E)-9-octadecenoate, 2, 6-dimethylpyrazine, 1-decen-3-one, furfural, and methional as markers for distinguishing 11 boletes species. Ultimately, the rapid content prediction models of partial least squares regression (PLSR) were established by combining Fourier Transform Near-Infrared Spectroscopy (FT-NIR) with the concentrations of these five marker compounds. These findings provide a methodological strategy for the effective species identification of wild edible mushrooms and the rapid prediction of their characteristic aroma compounds.

Spectral cluster supertree: fast and statistically robust merging of rooted phylogenetic trees

The algorithms for phylogenetic reconstruction are central to computational molecular evolution. The relentless pace of data acquisition has exposed their poor scalability and the conclusion that the conventional application of these methods is impractical and not justifiable from an energy usage perspective. Furthermore, the drive to improve the statistical performance of phylogenetic methods produces increasingly parameter-rich models of sequence evolution, which worsens the computational performance. Established theoretical and algorithmic results identify supertree methods as critical to divide-and-conquer strategies for improving scalability of phylogenetic reconstruction. Of particular importance is the ability to explicitly accommodate rooted topologies. These can arise from the more biologically plausible non-stationary models of sequence evolution. We make a contribution to addressing this challenge with Spectral Cluster Supertree, a novel supertree method for merging a set of overlapping rooted phylogenetic trees. It offers significant improvements over Min-Cut supertree and previous state-of-the-art methods in terms of both time complexity and overall topological accuracy, particularly for problems of large size. We perform comparisons against Min-Cut supertree and Bad Clade Deletion. Leveraging two tree topology distance metrics, we demonstrate that while Bad Clade Deletion generates more correct clades in its resulting supertree, Spectral Cluster Supertree's generated tree is generally more topologically close to the true model tree. Over large datasets containing 10,000 taxa and ∼ 500 source trees, where Bad Clade Deletion usually takes ∼ 2 h to run, our method generates a supertree in on average 20 s. Spectral Cluster Supertree is released under an open source license and is available on the python package index as sc-supertree.

Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model

Dating phylogenetic trees to obtain branch lengths in time units is essential for many downstream applications but has remained challenging. Dating requires inferring substitution rates that can change across the tree. While we can assume to have information about a small subset of nodes from the fossil record or sampling times (for fast-evolving organisms), inferring the ages of the other nodes essentially requires extrapolation and interpolation. Assuming a distribution of branch rates, we can formulate dating as a constrained maximum likelihood (ML) estimation problem. While ML dating methods exist, their accuracy degrades in the face of model misspecification, where the assumed parametric statistical distribution of branch rates vastly differs from the true distribution. Notably, most existing methods assume rigid, often unimodal, branch rate distributions. A second challenge is that the likelihood function involves an integral over the continuous domain of the rates, often leading to difficult non-convex optimization problems. To tackle both challenges, we propose a new method called Molecular Dating using Categorical-models (MD-Cat). MD-Cat uses a categorical model of rates inspired by non-parametric statistics and can approximate a large family of models by discretizing the rate distribution into k categories. Under this model, we can use the Expectation-Maximization algorithm to co-estimate rate categories and branch lengths in time units. Our model has fewer assumptions about the true distribution of branch rates than parametric models such as Gamma or LogNormal distribution. Our results on two simulated and real datasets of Angiosperms and HIV and a wide selection of rate distributions show that MD-Cat is often more accurate than the alternatives, especially on datasets with exponential or multimodal rate distributions.

Functional and evolutionary analysis of key enzymes triacylglycerol lipase, glycogen hydrolases in the glycerol and glucose biosynthesis pathway and cellular chaperones for freeze-tolerance of the Rice stem borer, Chilo suppressalis

Freeze-tolerance is an important physiological trait for terrestrial environmental adaptation and intraspecific geographic-lineage diversification in ectothermic animals, yet there remains a lack of systematic studies on its underlying genetic mechanisms and evolution. To address this problem, we employed the widely distributed rice pest, the Chilo suppressalis, as a model to explore the genetic mechanisms and evolutionary history of freeze-tolerance. First, we systematically characterized its antifreeze mechanisms by performing functional validation of potential key genes in laboratory-reared lines. This revealed the functional roles of glycerol biosynthesis in freeze-tolerance, including the triacylglycerol-originated pathway via triacylglycerol lipase (Tgl) hydrolysis and the glycogen-originated pathway via α-amylase (Aa) and maltase (Ma) hydrolysis, as well as the roles of the cellular chaperones Hsc70 and Hsf1. Then, we investigated the evolution of freeze-tolerance by collecting representative geographical samples and performing population genetic analyses, which suggested differentiated strategies of cold adaptation in different geographic populations. Taken together, our findings demonstrate the functional basis of cold resistance in Chilo suppressalis and reveal the evolutionary history of freeze-tolerance in natural populations, providing insights into organismal freeze-tolerance and clues for pest control.

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

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

Comparative and phylogenetic analysis of the chloroplast genomes of four commonly used medicinal cultivars of Chrysanthemums morifolium

'Boju' and 'Huaiju' are cultivars of the Chrysanthemum (Chrysanthemum morifolium Ramat.) in the family Asteraceae, valued for their medicinal, tea, and ornamental properties, and valued by individuals. However, the yield and quality of medicinal chrysanthemums are limited by the characteristics of the germplasm resources, including the identification at the varieties and cultivation levels. Currently, research characterizing the chloroplast genomes of medicinal Chrysanthemum flowers is relatively limited. This study conducted chloroplast whole-genome sequencing on two cultivars of Chrysanthemum, 'Boju' and 'Huaiju', and compared them with the previously published chloroplast genomes of 'Hangbaiju' and 'Gongju'. The study analyzed the chloroplast genome structures of these four medicinal Chrysanthemums, identifying mutation hotspots and clarifying their phylogenetic relationships. The chloroplast genome sizes of four medicinal Chrysanthemum cultivation products ranged from 151,057 to 151,109 bp, with GC content ranging from 37.45% to 37.76%. A total of 134 genes were identified, including 89 protein-coding genes, 37 ribosomal RNA genes, and 8 transfer RNA genes. Comparative genomic analysis revealed 159 large repeat sequences, 276 simple sequence repeats, 1 gene, and 8 intergenic regions identified as highly variable regions. Nucleotide diversity (Pi) values were high (≥ 0.004) for the petN-psbM, trnR-UCU-trnT-GGU, trnT-GGU-psbD, ndhC-trnV-UCA, ycf1, ndhI-ndhG, trnL-UGA-rpl32, rpl32-ndhF, and ndhF-ycf1 fragments, aiding in variety identification. Phylogenetic analysis revealed consistent results between maximum likelihood and Bayesian inference trees, showing that the four medicinal Chrysanthemum cultivars, along with their wild counterparts and related species, evolved as a monophyletic group, forming a sister clade to Artemisia and Ajania. Among the six Chrysanthemum species, the wild Chrysanthemum diverged first (Posterior probability = 1, bootstrap = 1,000), followed by Ajania, while C. indicum and C. morifolium clustered together (Bootstrap = 100), indicating their closest genetic relationship. The chloroplast whole-genome data and characteristic information provided in this study can be used for variety identification, genetic conservation, and phylogenetic analysis within the family Asteraceae.

Integration of genomic and pharmacokinetic data to predict clinical outcomes in HIV-associated cryptococcal meningitis

Cryptococcal meningitis causes an estimated 112,000 global deaths per annum. Genomic and phenotypic features of the infecting strain of Cryptococcus spp. have been associated with outcomes from cryptococcal meningitis. Additionally, population-level pharmacokinetic variability is well documented in these patient cohorts. The relative contribution of these factors to clinical outcomes is unknown. Based in Malawi, we conducted a sub-study of the phase 3 Ambition-CM trial (ISRCTN72509687), collecting plasma and cerebrospinal fluid at serial time points during the first 14 days of antifungal therapy. We explored the relative contribution of pathogen genotype, drug resistance phenotype, and pharmacokinetics on clinical outcomes including lumbar opening pressure, pharmacodynamic effect, and mortality. We report remarkable genomic homogeneity among infecting strains of Cryptococcus spp., within and between patients. There was no evidence of acquisition of antifungal resistance in our isolates. Genotypic features of the infecting strain were not consistently associated with adverse or favorable clinical outcomes. However, baseline fungal burden and early fungicidal activity (EFA) were associated with mortality. The strongest predictor of EFA was the level of exposure to amphotericin B. Our analysis suggests the most effective means of improving clinical outcomes from HIV-associated cryptococcal meningitis is to optimize exposure to potent antifungal therapy.

IMPORTANCE

HIV-associated cryptococcal meningitis is associated with a high burden of mortality. Research into the different strain types causing this disease has yielded inconsistent findings in terms of which strains are associated with worse clinical outcomes. Our study suggests that the exposure of patients to potent anti-cryptococcal drugs has a more significant impact on clinical outcomes than the strain type of the infecting organism. Future research should focus on optimizing drug exposure, particularly in the context of novel anticryptococcal drugs coming into clinical use.

Morpho-phylogenetic identification and characterization of new causal agents of Fusarium species for postharvest fruit rot disease of muskmelon in northern Thailand and their sensitivity to fungicides

A significant global problem affecting muskmelon (Cucumis melo L.) is fruit rot caused by phytopathogenic fungi, which results in unsaleable products and substantial financial losses. In 2022 and 2023, fruit rot on muskmelon was found during the postharvest storage period in Phayao Province of northern Thailand. The aim of the current study was to isolate the species of fungi causing the fruit rot lesions. Out of the rot lesions on muskmelons, nine fungal isolates were received. All isolates of fungi were identified through a combination of morphological characteristics and molecular analyses. Based on their morphological traits, all isolated fungal isolate was assigned to the genus Fusarium. All the fungal isolates were determined to belong to the Fusarium incarnatum-equiseti species complex through multi-gene phylogenetic analysis employing the calmodulin (cam), RNA polymerase second largest subunit (rpb2), and translation elongation factor 1-alpha (tef1-α) genes. These isolates were identified as F. compactum (SDBR-CMU483), F. jinanense (SDBR-CMU484, SDBR-CMU485, and SDBR-CMU486), F. mianyangense (SDBR-CMU487 and SDBR-CMU488), and F. sulawesiense (SDBR-CMU489, SDBR-CMU490, and SDBR-CMU491). Moreover, pathogenicity tests were subsequently carried out, and the results indicated that all fungal isolates caused symptoms of fruit rot on inoculated muskmelon fruits. Notably, this result was consistent with the symptoms observed throughout the postharvest storage period. In the fungicide screening test, all fungal isolates showed sensitivity to copper oxychloride. However, all isolates showed insensitivity to benalaxyl-M + mancozeb, carbendazim, mancozeb, and metalaxy. To the best of our knowledge, the present study is the first to identify F. compactum, F. jinanense, and F. mianyangense as new causative agents of muskmelon fruit rot in Thailand and other regions globally. This is also the first report of postharvest fruit rot on muskmelons caused by F. sulawesiense in Thailand. Furthermore, the fungicide screening results indicate that fungicide resistance can be beneficial in developing potential management strategies against postharvest fruit rot disease of muskmelon caused by these four pathogenic Fusarium species.

A chromosome-scale genome assembly of Timorese crabgrass (Digitaria radicosa): a useful genomic resource for the Poaceae

Timorese crabgrass (Digitaria radicosa) is a grass species commonly found in Southeast Asia and Oceania. Digitaria species have high intraspecific and interspecific genetic and phenotypic diversity, suggesting their potential usefulness as a genetic resource. However, as the only high-quality reference genome available is for a tetraploid Digitaria species, a reference genome of the diploid species D. radicosa would be a useful resource for genomic studies of Digitaria and Poaceae plants. Here, we present a chromosome-level genome assembly of D. radicosa and describe its genetic characteristics; we also illustrate its usefulness as a genomic resource for Poaceae. We constructed a 441.6 Mb draft assembly consisting of 61 contigs with an N50 contig length of 41.5 Mb, using PacBio HiFi long reads. We predicted 26,577 protein-coding genes, reaching a BUSCO score of 96.5%. To demonstrate the usefulness of the D. radicosa reference genome, we investigated the evolution of Digitaria species and the genetic diversity of Japanese Digitaria plants based on our new reference genome. We also defined the syntenic blocks between D. radicosa and 2 Poaceae crops, fonio and rice, and the diverse distribution of representative resistance genes in D. radicosa. The D. radicosa reference genome presented here should help elucidate the genetic relatedness of Digitaria species and the genetic diversity of Digitaria plants. In addition, the D. radicosa genome will be an important genomic resource for Poaceae genomics and crop breeding.

Whole-genome sequencing and analysis of Streptococcus iniae strain isolated from the brain of tilapia (Oreochromis sp.)

Streptococcus iniae is a bacterium that can infect fish, mammals, and humans. In this study, the S. iniae-313 strain was isolated from the brain of an infected tilapia, and the analysis of its sequenced genome is reported. The data revealed that S. iniae-313 carried antibiotic-resistant genes and virulence factors.

The complete sequence of chloroplast genome of Baeckea frutescens Linaeus 1753 (Myrtoideae), a traditional folk medicinal plant

Baeckea frutescens Linaeus 1753, as a traditional folk medicine in South East Asia, possesses sesquiterpenes, phloroglucinols, chromones, and essential oil, and is utilized for traditional Chinese medicinal purposes. The genetic diversity of the plant must be better understood, considering its significance. The complete chloroplast (cp) genome of B. frutescens was sequenced and assembled by using Illumina paired-end data, marking a significant advancement toward comprehending its genetic composition. The complete cp genome is 158,939 bp in length and contains 128 genes, consisting of 83 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Phylogenetic analyses indicated that B. frutescens and other the 13 were clustered to the family of Myrtaceae. These findings are crucial for the conservation and utilization of this important plant species. Additionally, they underscore the potential for future research on the evolution and preservation of B. frutescens, which could be advantageous in pharmaceutical applications.

The Complete Chloroplast Genome of Meconopsis simplicifolia and Its Genetic Comparison to Other Meconopsis Species

Background: Chloroplasts, due to their high conservation and lack of recombination, serve as important genetic resources for the classification and evolutionary analysis of closely related species that are difficult to distinguish based on their morphological features. Meconopsis simplicifolia (M. simplicifolia), an endangered herb within the Meconopsis genus, has demonstrated therapeutic potential in treating various diseases. However, the highly polymorphic morphology of this species poses a challenge for accurate identification. Methods: In this study, the complete chloroplast genome of M. simplicifolia was sequenced and assembled using Illumina sequencing technology. Simple sequence repeats (SSRs) and repetitive sequences were characterized. In addition, a comparative analysis was conducted with the chloroplast genomes of six other Meconopsis species. Results: The chloroplast genome of M. simplicifolia has a quadripartite circular structure with a total length of 152,772 bp. It consists of a large single-copy region of 83,824 bp and a small single-copy region of 17,646 bp, separated by a pair of inverted repeat sequences (IRa and IRb, 25,651 bp). The genome contains 131 genes, 33 SSRs, and 27 long repetitive sequences. Comparative analysis with six other chloroplast genomes of Meconopsis revealed that M. simplicifolia is closely related to M. betonicifolia and that the rpl2 (ribosomal protein L2) gene in the IRb region has been deleted. This deletion is of significant importance for future taxonomic studies of M. simplicifolia. Conclusions: This study provides a valuable reference for the identification of M. simplicifolia and contributes to a deeper understanding of the phylogeny and evolution of the Meconopsis genus.

Genome-wide analysis tracks the emergence of intraspecific polyploids in Phragmites australis

Polyploidization plays an important role in plant speciation and adaptation. To address the role of polyploidization in grass diversification, we studied Phragmites australis, an invasive species with intraspecific variation in chromosome numbers ranging from 2n = 36 to 144. We utilized a combined analysis of ploidy estimation, phylogeny, population genetics and model simulations to investigate the evolution of P. australis. Using restriction site-associated DNA sequencing (RAD-seq), we conducted a genome-wide analysis of 88 individuals sourced from diverse populations worldwide, revealing the presence of six distinct intraspecific lineages with extensive genetic admixture. Each lineage was characterized by a specific ploidy level, predominantly tetraploid or octoploid, indicative of multiple independent polyploidization events. The population size of each lineage has declined moderately in history while remaining large, except for the North American native and the US Land types, which experienced constant population size contraction throughout their history. Our investigation did not identify direct association between polyploidization events and grass invasions. Nonetheless, we observed octoploid and hexaploid lineages at contact zones in Romania, Hungary, and South Africa, suggestively due to genomic conflicts arising from allotetraploid parental lineages.

An array of Zymoseptoria tritici effectors suppress plant immune responses

Zymoseptoria tritici is the most economically significant fungal pathogen of wheat in Europe. However, despite the importance of this pathogen, the molecular interactions between pathogen and host during infection are not well understood. Herein, we describe the use of two libraries of cloned Z. tritici effectors that were screened to identify effector candidates with putative pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI)-suppressing activity. The effectors from each library were transiently expressed in Nicotiana benthamiana, and expressing leaves were treated with bacterial or fungal PAMPs to assess the effectors' ability to suppress reactive oxygen species (ROS) production. From these screens, numerous effectors were identified with PTI-suppressing activity. In addition, some effectors were able to suppress cell death responses induced by other Z. tritici secreted proteins. We used structural prediction tools to predict the putative structures of all of the Z. tritici effectors and used these predictions to examine whether there was enrichment of specific structural signatures among the PTI-suppressing effectors. From among the libraries, multiple members of the killer protein-like 4 (KP4) and killer protein-like 6 (KP6) effector families were identified as PTI suppressors. This observation is intriguing, as these protein families were previously associated with antimicrobial activity rather than virulence or host manipulation. This data provides mechanistic insight into immune suppression by Z. tritici during infection and suggests that, similar to biotrophic pathogens, this fungus relies on a battery of secreted effectors to suppress host immunity during early phases of colonization.

Strong habitat and seasonal phenology effects on the evolution of self-compatibility, clonality and pollinator shifts in Lachenalia (Asparagaceae: Scilloideae)

Plants employ a diversity of reproductive safeguarding strategies to circumvent the challenge of pollen limitation. Focusing on southern African Lachenalia (Asparagaceae: Scilloideae), we test the hypothesis that the evolution of reproductive safeguarding traits (self-compatibility, autonomous selfing, bird pollination and clonal propagation) is favoured in species occupying conditions of low insect abundance imposed by critically infertile fynbos heathland vegetation and by flowering outside the austral spring insect abundance peak. We trace the evolution of these traits and selective regimes on a dated, multi-locus phylogeny of Lachenalia and assess their evolutionary associations using ordinary and phylogenetic regression. Ancestral state reconstructions identify an association with non-fynbos vegetation and spring flowering as ancestral in Lachenalia, the transition to fynbos vegetation and non-spring flowering taking place multiple times. They also show that self-compatibility, autofertility, bird pollination and production of multiple clonal offsets have evolved repeatedly. Regression models suggest that bird pollination and self-compatibility are selected for in fynbos and in non-spring flowering lineages, with autofertility being positively associated with non-spring flowering. These patterns support the interpretation of these traits as reproductive safeguarding adaptations under reduced insect pollinator abundance. We find no evidence to support the interpretation of clonal propagation as a reproductive safeguarding strategy.

Evolution of the pheV-tRNA integrated genomic island in Escherichia coli

Escherichia coli exhibit extensive genetic diversity at the genome level, particularly within their accessory genome. The tRNA integrated genomic islands (GIs), a part of the E. coli accessory genome, play an important role in pathogenicity. However, studies examining the evolution of GIs have been challenging due to their large size, considerable gene content variation and fragmented assembly in draft genomes. Here we examined the evolution of the GI integrated at pheV-tRNA (GI-pheV), with a primary focus on uropathogenic E. coli (UPEC) and the globally disseminated multidrug resistant ST131 clone. We show the gene content of GI-pheV is highly diverse and arranged in a modular configuration, with the P4 integrase encoding gene intP4 the only conserved gene. Despite this diversity, the GI-pheV gene content displayed conserved features among strains from the same pathotype. In ST131, GI-pheV corresponding to the reference strain EC958 (EC958_GI-pheV) was found in ~90% of strains. Phylogenetic analyses suggested that GI-pheV in ST131 has evolved together with the core genome, with the loss/gain of specific modules (or the entire GI) linked to strain specific events. Overall, we show GI-pheV exhibits a dynamic evolutionary pathway, in which modules and genes have evolved through multiple events including insertions, deletions and recombination.

Environmental Factors Shaping the Culturable Freshwater Fungi Diversity of Four Lakes in Yunnan Province, China

Our study focused on freshwater fungal diversity, an important aspect in assessing the ecology of aquatic ecosystems. We carefully explored the diversity and influencing factors of culturable fungi across Dianchi Lake, Fuxian Lake, Xingyun Lake, and Yangzonghai Lake in Yunnan Province, China. Through fungi culture, morphological characterization, and ITS sequence analysis, we identified a total of 565 isolates belonging to 405 species across 133 genera. The diversity indices viz. H′, D, and J were evaluated for fungal diversity across the lakes. Interestingly, although diversity indices were highest during summer and at Yangzonghai Lake, no significant differences in fungal community diversity were observed between seasons and regions. Water variables were analyzed and indicated that changes with rapid fluctuations in temperature, pH, and dissolved oxygen likely influence fungal diversity. These findings significantly contribute to our understanding of fungal communities within plateau lake ecosystems, thereby aiding in managing and conserving vital aquatic resources.

The first complete mitochondrial genome of the genus Laelaps with novel gene arrangement reveals extensive rearrangement and phylogenetics in the superfamily Dermanyssoidea

We collected 56 specimens of Laelaps chini from the endemic Hengduan Mountain rat species (Eothenomys miletus) and obtained the first complete mitochondrial genome of L. chini by next-generation sequencing (NGS). The L. chini mitogenome is 16,507 bp in size and contains 37 genes and a control region of 2380 bp in length. The L. chini mitogenome has a high AT content and a compact arrangement with four overlapping regions ranging from 1 to 2 bp and 16 spacer regions ranging from 1 to 48 bp. We analyzed 13 protein-coding genes of L. chini mitogenome  and found that protein-coding genes in the L. chini mitogenome preferred codons ending in A/U and codon usage pattern was mainly influenced by natural selection. Cox1 has the slowest evolution rate and cox3 has the fastest evolution rate. We combined the mitochondrial genome of eight species of gamasid mites in the superfamily Dermanyssoidea from Genbank and the L. chini mitochondrial genome to analyze its rearrangement patterns and breakpoint numbers. We found that the L. chini mitogenome showed a novel arrangement pattern and nine species of gamasid mites in the superfamily Dermanyssoidea, which have been sequenced complete mitochondrial genomes to date, all showed different degrees of rearrangement. Laelaps chini, Echinolaelaps echidninus and Echinolaelaps fukinenensis were closely related species based on genetic distance and phylogenetic analyses. Notably they are clustered with Varroa destructor of the family Varroidae, suggesting that the family Varroidae is more closely related to the family Laelapidae, but more data are needed to test whether Varroa can be classified under the family Laelapidae. The L. chini mitogenome is the first complete mitochondrial genome for the genus Laelaps, and contributes to further exploration of the mitochondrial gene rearrangements and phylogeny for the superfamily Dermanyssoidea.

Genomic epidemiology describes introduction and outbreaks of antifungal drug-resistant Candida auris

Candida auris is a globally emerged fungal pathogen causing nosocomial invasive infections. Here, we use cutting-edge genomic approaches to elucidate the temporal and geographic epidemiology of drug-resistant C. auris within the UK. We analysed a representative sample of over 200 isolates from multiple UK hospitals to assess the number and timings of C. auris introductions and infer subsequent patterns of inter- and intra-hospital transmission of azole drug-resistant isolates. We identify at least one introduction from Clade I and two from Clade III into the UK, and observe temporal and geographical evidence for multiple transmission events of antifungal drug resistant isolates between hospitals and identified local within-hospital patient-to-patient transmission events. Our study confirms outbreaks of drug-resistant C. auris are linked and that transmission amongst patients occurs, explaining local hospital outbreaks, and demonstrating a need for improved epidemiological surveillance of C. auris to protect patients and healthcare services.

Impact of pneumococcal conjugate vaccines on invasive pneumococcal disease-causing lineages among South African children

Invasive pneumococcal disease (IPD) due to non-vaccine serotypes after the introduction of pneumococcal conjugate vaccines (PCV) remains a global concern. This study used pathogen genomics to evaluate changes in invasive pneumococcal lineages before, during and after vaccine introduction in South Africa. We included genomes (N = 3104) of IPD isolates from individuals aged <18 years (2005-20), spanning four periods: pre-PCV, PCV7, early-PCV13, and late-PCV13. Significant incidence reductions occurred among vaccine-type lineages in the late-PCV13 period compared to the pre-PCV period. However, some vaccine-type lineages continued to cause invasive disease and showed increasing effective population size trends in the post-PCV era. A significant increase in lineage diversity was observed from the PCV7 period to the early-PCV13 period (Simpson's diversity index: 0.954, 95% confidence interval 0.948-0.961 vs 0.965, 0.962-0.969) supporting intervention-driven population structure perturbation. Increases in the prevalence of penicillin, erythromycin, and multidrug resistance were observed among non-vaccine serotypes in the late-PCV13 period compared to the pre-PCV period. In this work we highlight the importance of continued genomic surveillance to monitor disease-causing lineages post vaccination to support policy-making and future vaccine designs and considerations.

Carbon and Nitrogen Sources Influence Parasitic Responsiveness in Trichoderma atroviride NI-1

Parasitic species of Trichoderma use hydrolytic enzymes to destroy the host cell wall. Preferent carbon and nitrogen sources suppress the expression of genes related to parasitism. Here, different nutrients were evaluated in the parasitic isolated NI-1, which was identified as Trichoderma atroviride. The genes cbh1 and chb2 (cellobiohydrolases), bgl3.1 (endoglucanase), and pra1 and prb1 (proteinases) were poorly expressed during the interaction between NI-1 and Phytophthora capsici on PDA. However, gene expression improved on minimal medium with preferent and alternative carbon sources. Dextrin and glucose stimulated higher transcript levels than cellulose, sucrose, and glycerol. Also, ammonium stimulated a stronger parasitic responsiveness than the alternative nitrogen sources. During interaction against different phytopathogens, NI-1 detects their host differentially from a distance due to the cbh1 and cbh2 genes being only induced by P. capsici. The pra1 and ech42 genes were induced before contact with Botrytis cinerea and Rhizoctonia solani, while when confronted with P. capsici they were stimulated until contact and overgrowth. The prb1 and bgl3.1 genes were induced before contact against the three-host assayed. Overall, T. atroviride prefers to parasitize and has the capacity to distinguish between an oomycete and a fungus, but nutrient quality regulates its parasitic responsiveness.

Evolution, structure, and drug-metabolizing activity of mammalian prenylcysteine oxidases

Prenylcysteine oxidases (PCYOXs) metabolize prenylated cysteines produced by protein degradation. They utilize oxygen as a co-substrate to produce free cysteine, an aldehyde, and hydrogen peroxide through the unusual oxidation of a thioether bond. In this study, we explore the evolution, structure, and mechanism of the two mammalian PCYOXs. A gene duplication event in jawed vertebrates originated in these two paralogs. Both enzymes are active on farnesyl- and geranylgeranylcysteine, but inactive on molecules with shorter prenyl groups. Kinetics experiments outline a mechanism where flavin reduction and re-oxidation occur rapidly without any detectable intermediates, with the overall reaction rate limited by product release. The experimentally determined three-dimensional structure of PCYOX1 reveals long and wide tunnels leading from the surface to the flavin. They allow the isoprene substrate to curl up within the protein and position its reactive cysteine group close to the flavin. A hydrophobic patch on the surface mediates membrane association, enabling direct substrate and product exchange with the lipid bilayer. Leveraging established knowledge of flavoenzyme inhibition, we designed sub-micromolar PCYOX inhibitors. Additionally, we discovered that PCYOXs bind and slowly degrade salisirab, an anti-RAS compound. This activity suggests potential and previously unknown roles of PCYOXs in drug metabolism.

Isolation, characterization, and genetic manipulation of cold-tolerant, manganese-oxidizing Pseudomonas sp. strains

Manganese-oxidizing bacteria (MnOB) produce Mn oxide minerals that can be used by humans for bioremediation, but the purpose for the bacterium is less clear. This study describes the isolation and characterization of cold-tolerant MnOB strains isolated from a compost pile in Morris, Minnesota, USA: Pseudomonas sp. MS-1 and DSV-1. The strains were preliminarily identified as members of species Pseudomonas psychrophila by 16S rRNA analysis and a multi-locus phylogenetic study using a database of 88 genomes from the Pseudomonas genus. However, the average nucleotide identity between these strains and the P. psychrophila sp. CF149 type strain was less than 93%. Thus, the two strains are members of a novel species that diverged from P. psychrophila. DSV-1 and MS-1 are cold tolerant; both grow at 4°C but faster at 24°C. Unlike the mesophilic MnOB P. putida GB-1, both strains are capable of robustly oxidizing Mn at low temperatures. Both DSV-1 and MS-1 genomes contain homologs of several Mn oxidation genes found in P. putida GB-1 (mnxG, mcoA, mnxS1, mnxS2, and mnxR). Random mutagenesis by transposon insertion was successfully performed in both strains and identified genes involved in Mn oxidation that were similar to those found in P. putida GB-1. Our results show that MnOB can be isolated from compost, supporting a role for Mn oxidation in plant waste degradation. The novel isolates Pseudomonas spp. DSV-1 and MS-1 both can oxidize Mn at low temperature and likely employ similar mechanisms and regulation as P. putida GB-1.IMPORTANCEBiogenic Mn oxides have high sorptive capacity and are strong oxidants. These two characteristics make these oxides and the microbes that make them attractive tools for the bioremediation of wastewater and contaminated environments. Identifying MnOB that can be used for bioremediation is an active area of research. As cold-tolerant MnOB, Pseudomonas sp. DSV-1 and MS-1 have the potential to expand the environmental conditions in which biogenic Mn oxide bioremediation can be performed. The similarity of these organisms to the well-characterized MnOB P. putida GB-1 and the ability to manipulate their genomes raise the possibility of modifying them to improve their bioremediation ability.

Assessment of the Genetic Diversity of the Monogenean Gill Parasite Lamellodiscus echeneis (Monogenea) Infecting Wild and Cage-Reared Populations of Sparus aurata (Teleostei) from the Mediterranean Sea

The diplectanid monogenean Lamellodiscus echeneis (Wagener, 1857) is a specific and common gill parasite of the gilthead seabream Sparus aurata Linnaeus, 1758, in the Mediterranean Sea. Few isolated molecular studies of this monogenean have been conducted, and its population structure and genetic diversity are poorly understood. This study represents the first analysis of the population genetics of L. echeneis, isolated from wild and cage-reared gilthead seabream from fifteen localities in both the Southern (Tunisia) and Northern (Italy and Spain) regions of the Mediterranean Sea, using nuclear ITS rDNA markers and a partial fragment of the mitochondrial gene cytochrome oxidase subunit I (COI). The phylogenetic trees based on the newly obtained dataset and the previously published sequences of L. echeneis corroborated the spread of only a single species throughout the Mediterranean Sea. The star-like haplotypes network, inferred by COI sequences, suggested a recent population expansion of L. echeneis. This is supported by the observed high haplotype diversity (Hd = 0.918) and low nucleotide diversity (Pi = 0.01595). Population structure-based AMOVA for two groups (the Adriatic Sea and the rest of the Mediterranean Sea) attributed 35.39% of the total variation to differences within populations, 16.63% to differences among populations within groups, and 47.99% to differences among groups. Fixation indices were significant, with a high FST value (0.64612), likely related to the divergence of the parasite populations from the Adriatic Sea and other Mediterranean regions. Phylogenetic analyses grouped all samples into the main clade corresponding to L. echeneis from several localities. This study provides insight into the genetic variation between L. echeneis populations, and did not show a clear genetic structure between populations of L. echeneis throughout Tunisian, Italian, and Spanish localities, which can be attributed to the considerable gene flow between the populations favoured by the potential for host dispersion within the Mediterranean Sea. Finally, haplotypes shared between wild and cage-reared hosts provided evidence for the potential for cross-infection between wild and farmed hosts in the Mediterranean Sea.

Two new species of Nectriaceae (Hypocreales, Sordariomycetes) from Yunnan, China

Nectriaceae is a highly diverse family, and members have a worldwide distribution, particularly in warm temperate to tropical regions. During the survey of fungal diversity in different habitats in Yunnan province, China, two new species isolated from soil and air respectively, namely Atractiumyunnanense sp. nov. and Nalanthamalaxishuangbannaensis sp. nov., were proposed based on morphological comparisons and the multi-gene phylogenetic analyses of combined ITS, LSU, rpb2, and tub2 sequence data. Phylogenetically, both species clustered in a monophyletic clade within Nectriaceae with strong support. A.yunnanense is characterized by synnematous conidiophores, pale olivaceous-green, clavate to oblong-ellipsoidal, multi-septate conidia, and pale olivaceous-green chlamydospores. N.xishuangbannaensis has acremonium-like or penicillium-like conidiophores and either obovate or ellipsoidal, cylindrical or fusiform conidia. Full descriptions, illustrations, and a phylogenetic tree showing the phylogenetic position of the two new species were provided.

Characterization and phylogenetic analysis of the complete mitochondrial genome of the red alga, Gracilaria eucheumatoides Harvey 1860 (Gracilariales: Gracilariaceae) from Vietnam

The marine red alga, Gracilaria eucheumatoides, is economically significant for its agar production and pharmacologically active compounds. This study reveals its complete mitochondrial genome (mitogenome), sequenced using Illumina's next-generation technology. The mitogenome is a 25,909 bp circular molecule with a G + C content of 27.21%, comprising 24 protein-coding genes, two ribosomal RNA genes, 24 transfer RNA genes, and one open reading frame (ORF) with an unidentified function. Both gene structure and composition are highly conserved within Gracilaria. The phylogenetic analyses fully support a close relationship of G. eucheumatoides with other Gracilaria species, as well as its sister relationship with G. urvillei. This mitogenome sequencing effort of G. eucheumatoides provides crucial data for future phylogenetic research on marine red algae.

Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush

The molluskan order Neogastropoda encompasses over 15,000 almost exclusively marine species playing important roles in benthic communities and in the economies of coastal countries. Neogastropoda underwent intensive cladogenesis in the early stages of diversification, generating a "bush" at the base of their evolutionary tree, which has been hard to resolve even with high throughput molecular data. In the present study to resolve the bush, we use a variety of phylogenetic inference methods and a comprehensive exon capture dataset of 1817 loci (79.6% data occupancy) comprising 112 taxa of 48 out of 60 Neogastropoda families. Our results show consistent topologies and high support in all analyses at (super)family level, supporting monophyly of Muricoidea, Mitroidea, Conoidea, and, with some reservations, Olivoidea and Buccinoidea. Volutoidea and Turbinelloidea as currently circumscribed are clearly paraphyletic. Despite our analyses consistently resolving most backbone nodes, 3 prove problematic: First, the uncertain placement of Cancellariidae, as the sister group to either a Ficoidea-Tonnoidea clade or to the rest of Neogastropoda, leaves monophyly of Neogastropoda unresolved. Second, relationships are contradictory at the base of the major "core Neogastropoda" grouping. Third, coalescence-based analyses reject monophyly of the Buccinoidea in relation to Vasidae. We analyzed phylogenetic signal of targeted loci in relation to potential biases, and we propose the most probable resolutions in the latter 2 recalcitrant nodes. The uncertain placement of Cancellariidae may be explained by orthology violations due to differential paralog loss shortly after the whole genome duplication, which should be resolved with a curated set of longer loci.

Complete mitochondrial genome of Agropyron cristatum reveals gene transfer and RNA editing events

BACKGROUND

As an important forage in arid and semi-arid regions, Agropyron cristatum provides livestock with exceptionally high nutritional value. Additionally, A. cristatum exhibits outstanding genetic characteristics to endure drought and disease. Therefore, rich genetic diversity serves as a cornerstone for the improvement of major food crops. The purposes of this study were to systematically describe mitogenome of A.cristatum and preliminarily analyze its internal variations.

RESULT

The A. cristatum mitogenome was a single-ring molecular structure of 381,065 bp that comprised 52 genes, including 35 protein-coding, 3 rRNA and 14 tRNA genes. Among these, two pseudoprotein-coding genes and multiple copies of tRNA genes were observed. A total of 320 repetitive sequences was found to cover more than 10% of the mitogenome (105 simple sequences, 185 dispersed and 30 tandem repeats), which led to a large number of fragment rearrangements in the mitogenome of A. cristatum. Leucine was the most frequent amino acid (n = 1087,10.8%) in the protein-coding genes of A. cristatum mitogenome, and the highest usage codon was ATG (initiation codon). The number of A/T changes at the third base of the codon was much higher than that of G/C. Among 23 PCGs, the range of Pi values is from 0.0021 to 0.0539, with an average of 0.013. Additionally, 81 RNA editing sites were predicted, which were considerably fewer than those reported in other plant mitogenomes. Most of the RNA editing site base positions were concentrated at the first and second codon bases, which were C to T transitions. Moreover, we identified 95 sequence fragments (total length of 34, 343 bp) that were transferred from the chloroplast to mitochondria genes, introns, and intergenic regions. The stability of the tRNA genes was maintained during this process. Selection pressure analysis of 23 protein-coding genes shared by 15 Poaceae plants, showed that most genes were subjected to purifying selection during evolution, whereas rps4, cob, mttB, and ccmB underwent positive selection in different plants. Finally, a phylogenetic tree was constructed based on 22 plant mitogenomes, which showed that Agropyron plants have a high degree of independent heritability in Triticeae.

CONCLUSION

The findings of this study provide new data for a better understanding of A. cristatum genes, and demonstrate that mitogenomes are suitable for the study of plant classifications, such as those of Agropyron. Moreover, it provides a reference for further exploration of the phylogenetic relationships within Agropyron species, and establishes a theoretical basis for the subsequent development and utilization of A. cristatum plant germplasm resources.

Unraveling the mystery of a myxozoan parasite of the trout: redescription of Chloromyxum schurovi

Myxozoans are microscopical parasites widely distributed in fish, with over 2,600 described species, but their actual diversity is still underestimated. Among salmonids, more than 70 myxozoan species have been identified. This study focuses on species of Chloromyxum Mingazzini, 1890 that infect salmonid kidneys, particularly C. majori Yasutake et Wood, 1957 and C. schurovi Shulman et Ieshko, 2003. Despite their similar spore morphology, they exhibit distinct host preferences, tissue affinities and geographical distributions. Chloromyxum schurovi predominantly infects the renal tubules of Salmo salar Linnaues and S. trutta Linnaeus in Europe, while C. majori targets the glomeruli of Oncorhynchus mykiss (Walbaum) and O. tshawytscha (Walbaum) in North America. The sequence data for C. majori and C. schurovi have been either missing or questionable. In our study, we examined the kidneys of two salmonid species for chloromyxid infections, using both morphological and molecular data to characterise Chloromyxum species in salmonids. The sequence of C. schurovi obtained in our study did not match the previously published parasite data. Instead, it clustered as an independent lineage sister to the Paramyxidium Freeman et Kristmundsson, 2018 clade gathering the species from various fish organs, including the urinary tract. Our findings clarified the taxonomic origin of the previous C. schurovi sequence as Myxidium giardi Cépède, 1906, highlighting the risks associated with the presence of myxozoan blood stages in the bloodstream of their fish host and the challenges of non-specific PCR amplification. We redescribe C. schurovi, thus contributing to a better understanding of the diversity and phylogeny of kidney-infecting species of Chloromyxum.

Museomics help resolving the phylogeny of snowfinches (Aves, Passeridae, Montifringilla and allies)

Historical specimens from museum collections provide a valuable source of material also from remote areas or regions of conflict that are not easily accessible to scientists today. With this study, we are providing a taxon-complete phylogeny of snowfinches using historical DNA from whole skins of an endemic species from Afghanistan, the Afghan snowfinch, Pyrgilauda theresae. To resolve the strong conflict between previous phylogenetic hypotheses, we generated novel mitogenome sequences for selected taxa and genome-wide SNP data using ddRAD sequencing for all extant snowfinch species endemic to the Qinghai-Tibet Plateau (QTP) and for an extended intraspecific sampling of the sole Central and Western Palearctic snowfinch species (Montifringilla nivalis). Our phylogenetic reconstructions unanimously refuted the previously suggested paraphyly of genus Pyrgilauda. Misplacement of one species-level taxon (Onychostruthus tazcanowskii) in previous snowfinch phylogenies was undoubtedly inferred from chimeric mitogenomes that included heterospecific sequence information. Furthermore, comparison of novel and previously generated sequence data showed that the presumed sister-group relationship between M. nivalis and the QTP endemic M. henrici was suggested based on flawed taxonomy. Our phylogenetic reconstructions based on genome-wide SNP data and on mitogenomes were largely congruent and supported reciprocal monophyly of genera Montifringilla and Pyrgilauda with monotypic Onychostruthus being sister to the latter. The Afghan endemic P. theresae likely originated from a rather ancient Pliocene out-of-Tibet dispersal probably from a common ancestor with P. ruficollis. Our extended trans-Palearctic sampling for the white-winged snowfinch, M. nivalis, confirmed strong lineage divergence between an Asian and a European clade dated to 1.5 - 2.7 million years ago (mya). Genome-wide SNP data suggested subtle divergence among European samples from the Alps and from the Cantabrian mountains.

The genome of Vicia sativa ssp. amphicarpa provides insights into the role of terpenoids in antimicrobial resistance within subterranean fruits

Vicia sativa ssp. amphicarpa is a unique forage crop capable of simultaneously producing fruits above and below ground, representing a typical amphicarpic plant. In this study, we sequenced and assembled seven pseudo-chromosomes of the genome of V. sativa ssp. amphicarpa (n = 7) yielding a genome size of 1.59 Gb, with a total annotation of 48 932 protein-coding genes. Long terminal repeat (LTR) elements constituted 62.28% of the genome, significantly contributing to the expansion of genome size. Phylogenetic analysis revealed that the divergence between V. sativa ssp. amphicarpa and V. sativa was around 0.88 million years ago (MYA). Comparative transcriptomic and metabolomic analysis of aerial and subterranean pod shells showed biosynthesis of terpenoids in the subterranean pod shells indicating a correlation between the antimicrobial activity of subterranean pod shells and the biosynthesis of terpenoids. Furthermore, functional validation indicates that overexpression of VsTPS5 and VsTPS16 enhances terpenoid biosynthesis for antibacterial activity. Metabolomic analysis suggests the involvement of terpenoids in the antimicrobial properties of subterranean pod shells. Deciphering the genome of V. sativa ssp. amphicarpa elucidated the molecular mechanisms behind the antimicrobial properties of subterranean fruits in amphicarpic plants, providing valuable insights for the study of amphicarpic plant biology.

The first mitogenome of the genus Amphalius (Siphonaptera: Ceratophyllidae) and its phylogenetic implications

Amphalius spirataenius belongs to Arthropoda, Insecta, Siphonaptera, Ceratophylloidea, Ceratophyllinae, Amphalius. Only 2 species from the subfamily Ceratophyllinae have been sequenced for mitogenomes to date. The genus Amphalius mitogenome research was still blank. The A. spirataenius mitogenome was determined, annotated and analysed for the first time in this study. The 14 825 bp long genome has the typical metazoan of 37 genes with insect ancestral genome arrangement pattern. There was no significant difference in codon usage of 13 protein-coding genes: UUA, UCU, GUU, ACU and GCU were the most frequently used codons. It was found that the reason for codon preference mainly contributed to natural selection base on PR2, ENC-plot and neutrality curve analysis. Evolutionary rate, conserved sites, variable sites and nucleotide diversity analysis indicated that nad6 of A. spirataenius had the fastest evolutionary rate, while cox1 had the slowest evolutionary rate. Phylogenetic trees were reconstructed based on 13 protein-coding genes and 2 rRNA genes datasets using Bayesian inference and maximum likelihood method. The phylogenetic tree supported that both Siphonaptera and Mecoptera were monophyletic, and were sister groups to each other. This study filled gap of the genus Amphalius mitogenome sequences and was of great significance for understanding evolution of the order Siphonaptera.

Genomic analysis of Vibrio cholerae O1 isolates from cholera cases, Europe, 2022

BackgroundThe number of cholera cases reported to the World Health Organization (WHO) in 2022 was more than double that of 2021. Nine countries of the WHO European Region reported 51 cases of cholera in 2022 vs five reported cases in 2021.AimWe aimed to confirm that the Vibrio cholerae O1 isolates reported by WHO European Region countries in 2022 belonged to the seventh pandemic El Tor lineage (7PET). We also studied their virulence, antimicrobial resistance (AMR) determinants and phylogenetic relationships.MethodsWe used microbial genomics to study the 49 V. cholerae O1 isolates recovered from the 51 European cases. We also used > 1,450 publicly available 7PET genomes to provide a global phylogenetic context for these 49 isolates.ResultsAll 46 good-quality genomes obtained belonged to the 7PET lineage. All but two isolates belonged to genomic Wave 3 and were grouped within three sub-lineages, one of which, Pre-AFR15, predominated (34/44). This sub-lineage, corresponding to isolates from several countries in Southern Asia, the Middle East and Eastern or Southern Africa, was probably a major contributor to the global upsurge of cholera cases in 2022. No unusual AMR profiles were inferred from analysis of the AMR gene content of the 46 genomes.ConclusionReference laboratories in high-income countries should use whole genome sequencing to assign V. cholerae O1 isolates formally to the 7PET or non-epidemic lineages. Periodic collaborative genomic studies based on isolates from travellers can provide useful information on the circulating strains and their evolution, particularly as concerns AMR.

Disease resistance gene count increases with rainfall in Silphium integrifolium

Intracellular plant defense against pathogens is mediated by a class of disease resistance genes known as NB-LRRs or NLRs (R genes). Many of the diseases these genes protect against are more prevalent in regions of higher rainfall, which provide better growth conditions for the pathogens. As such, we expect a higher selective pressure for the maintenance and proliferation of R genes in plants adapted to wetter conditions. In this study, we enriched libraries for R genes using RenSeq from baits primarily developed from the common sunflower (Helianthus annuus) reference genome. We sequenced the R gene libraries of Silphium integrifolium Michx, a perennial relative of sunflower, from 12 prairie remnants across a rainfall gradient in the Central Plains of the United States, with both Illumina short-read (n = 99) and PacBio long-read (n = 10) approaches. We found a positive relationship between the mean effective annual precipitation of a plant's source prairie remnant and the number of R genes in its genome, consistent with intensity of plant pathogen coevolution increasing with precipitation. We show that RenSeq can be applied to the study of ecological hypotheses in non-model relatives of model organisms.

Characterization of the prevalence of Salmonella in different retail chicken supply modes using genome-wide and machine-learning analyses

Salmonella is a foodborne pathogen that causes salmonellosis, of which retail chicken meat is a major source. However, the prevalence of Salmonella in different retail chicken supply modes and the threat posed to consumers remains unclear. The prevalence, serotype distribution, antibiotic resistance, and genomic characteristics of Salmonella in three supply modes of retail chicken (live poultry, frozen, and chilled) were investigated using whole-genome sequencing (WGS) and machine learning (ML). In this study, 480 retail chicken samples from live poultry, frozen, and chilled supply modes in Guangzhou from 2020 to 2021, as well as 253 Salmonella isolates (total isolation rate = 53.1 %), were collected. The prevalence of isolates in the live poultry mode (67.5 %, 81/120) was statistically higher than in the frozen (50.0 %, 120/240) and chilled (43.3 %, 52/120) (P < 0.05) modes. Serotype identification showed significant differences in the serotype distribution of Salmonella in different supply modes. S. Enteritis (46.7 %) and S. Indiana (14.2 %) were predominant in the frozen mode. S. Agona (23.5 %) and S. Saintpaul (13.6 %) were predominant in live poultry, while S. Enteritis (40.4 %) and S. Kentucky (17.3 %) were predominant in chilled mode. Antibiotic testing showed that frozen mode isolates were more resistant; the multidrug-resistant (MDR) rate of isolates in the frozen mode reached 91.8 %, significantly higher than in the chilled (86.5 %) and live (74.1 %) (P < 0.05) modes. WGS was performed on 155 top serotypes (S. Enteritidis, S. Kentucky, S. Indiana, and S. Agona). The antibiotic resistance gene analysis showed that the abundance and carrying rate of antibiotic resistance genes of Salmonella in the frozen mode (54 types, 16.1 %) were significantly higher than in other modes (live poultry: 36 types, 9.4 %, P < 0.05; chilled: 31 types, 11.6 %). The blaNDM-1 and blaNDM-9 genes encoding carbapenem resistance were found in frozen mode isolates on a complex transposon consisting of TnAS3-IS26. Virulence factors and plasmid replicons were abundant in the studied frozen mode isolates. In addition, single nucleotide polymorphism (SNP) phylogenetic tree results showed that in the frozen supply mode, the S. Enteritidis clonal clade continued to contaminate retail chicken meat and was homologous to S. Enteritidis strains found in farm chicken embryos, slaughterhouse chicken carcasses, and patients from hospitals in China (SNP 0 = 10). Notably, the pan-genome-based ML model showed that characteristic genes in frozen and live poultry isolates differed. The narZ gene was a key characteristic gene in frozen isolates, encoding nitrate reductase, relating to anaerobic bacterial growth. The ydgJ gene is a key characteristic gene in the live mode and encodes an oxidoreductase related to oxidative function in bacteria. The high prevalence of live poultry mode Salmonella and the transmission of frozen mode MDR Salmonella in this study pose serious risks to food safety and public health, emphasizing the importance of improving disinfection and cold storage measures to reduce Salmonella contamination and transmission. In conclusion, the continued surveillance of Salmonella across different supply models and the development of an epidemiological surveillance system based on WGS is necessary.

Intergrative Taxonomic Study of the Frullania parvistipula Complex with a Modern Circumscription of the Section Trachycolea (Frullaniaceae, Marchantiphyta)

Frullania (subg. Trachycolea) sect. Trachycolea has been studied using integrative taxonomy methods and utilizing sampling from almost all areas of distribution of the species previously referred to this section. A phylogenetic analysis based on nuclear ribosomal ITS1-2 and chloroplast trnL-F sequence data and a morphological study reveal a wide range of morphological variability within specimens that has largely disguised the overall taxonomic diversity. Frullania parvistipula, previously regarded as a widespread species, has been found to represent a group of separate species within different sections of F. subg. Trachycolea: F. caucasica and F. conistipula in F. sect. Trachycolea, F. parvistipula in F. sect. Australes, and F. fukuzawana in F. sect. Integristipulae II. Illustrations of the type specimens of F. conistipula, F. fukuzawana, and F. parvistipula, as well as illustrations of the sequenced specimens belonging to two of the discussed species (F. conistipula and F. parvistipula), are provided. The morphological differences separating the highly similar F. caucasica, F. conistipula, F. fukuzawana, F. koponenii, and F. parvistipula are discussed. A dichotomous key is presented for accepted species. New combinations are provided for two taxa.

Sensing volatiles throughout the body: geographic- and tissue-specific olfactory receptor expression in the fig wasp

An essential adaptive strategy in insects is the evolution of olfactory receptors (ORs) to recognize important volatile environmental chemical cues. Our model species, Ceratosolen fusciceps, a specialist wasp pollinator of Ficus racemosa, likely possesses an OR repertoire that allows it to distinguish fig-specific volatiles in highly variable environments. Using a newly assembled genome-guided transcriptome, we annotated 63 ORs in the species and reconstructed the phylogeny of Ceratosolen ORs in conjunction with other hymenopteran species. Expression analysis showed that though ORs were mainly expressed in the female antennae, 20% were also expressed in nonantennal tissues such as the head, thorax, abdomen, legs, wings, and ovipositor. Specific upregulated expression was observed in OR30C in the head and OR60C in the wings. We identified OR expression from all major body parts of female C. fusciceps, suggesting novel roles of ORs throughout the body. Further examination of the OR expression of C. fusciceps in widely separated geographical locations, that is, South (urban) and Northeast (rural) India, revealed distinct OR expression levels in different locations. This discrepancy likely parallels the observed variation in fig volatiles between these regions and provides new insights into the evolution of insect ORs and their expression across geographical locations and tissues.

Diversity of lichen mycobionts and photobionts and their relationships in the Ny-Ålesund region (Svalbard, High Arctic)

Lichens are dual organisms, with one major mycobiont and one major photobiont in each lichen symbiosis, which can survive extreme environmental conditions in the Arctic. However, the diversity and distribution of lichen photobionts in the Arctic remain poorly understood compared to their mycobiont partners. This study explored the diversity of lichen mycobionts and photobionts in 197 lichen samples collected from the Ny-Ålesund region (Svalbard, High Arctic). The nuclear ribosomal internal transcribed spacer (ITS) regions were sequenced and phylogenetic analyses were performed. The relationships between mycobionts and photobionts, as well as the association patterns, were also investigated. A total of 48 species of lichen mycobionts (16 families, nine orders) and 31 species/lineages of photobionts were identified. These 31 photobiont species belonged to one class (Trebouxiophyceae) and five genera, including 22 species of Trebouxia, five species of Asterochloris, two species of Chloroidium, one species of Symbiochloris, and one species of Coccomyxa. The results indicated that most analyzed lichen mycobionts could associate with multiple photobiont species, and the photobionts also exhibited a similar pattern. The results provided an important reference dataset for characterizing the diversity of lichen mycobionts and photobionts in the High Arctic region.

Filamentous Fungi Associated with Disease Symptoms in Non-Native Giant Sequoia (Sequoiadendron giganteum) in Germany-A Gateway for Alien Fungal Pathogens?

Filamentous fungi associated with disease symptoms in non-native giant sequoia (Sequoiadendron giganteum) in Germany were investigated in ten cases of disease in Northwest Germany. During the study period from 2018 to 2023, a total of 81 species of Dikaria were isolated from woody tissue and needles of giant sequoia and morphotyped. Morphotypes were assigned to species designations based on ITS-sequence comparison and, in part, multi-locus phylogenetic analyses. Nine species were recognised as new reports for Germany or on giant sequoia: Amycosphaerella africana, Botryosphaeria parva, Coniochaeta acaciae, C. velutina, Muriformistrickeria rubi, Pestalotiopsis australis, P. monochaeta, Phacidiopycnis washingtonensis, and Rhizosphaera minteri. The threat posed to giant sequoia and other forest trees in Germany by certain, especially newly reported, fungal species is being discussed. The detection of a considerable number of new fungal records in the trees studied suggests that giant sequoia cultivation may be a gateway for alien fungal species in Germany.

Three new species of the genus Clavulina (Hydnaceae, Cantharellales) from North China based on morphological and phylogenetic analysis

Clavulina possesses important ecological and economic value and has attracted extensive attention from mycologists. Macrofungal diversity is high in China, but Clavulina species have not been thoroughly studied. In this study, based on morphological evidence and phylogenetic analyses of the nucleotide sequences of three loci (nrITS, nrLSU, and rpb2), three new species of Clavulina from North China were identified. Morphologically, Clavulinachengdeensis is characterized by its white to dirty white basidiomata with somewhat pale orange tips and somewhat wrinkled hymenium. Clavulinagriseoviolacea is characterized by its gray to dark grayish violet basidiomata, with a sometimes-white stipe base, monopodial or irregularly polychotomous toward branch apices. Clavulinapallida is characterized by its white to pale cream white basidiomata with somewhat orange tips. Phylogenetically, the three new species form three independent branches with high support values in the phylogenetic tree.