Parallelization of MAFFT for large-scale multiple sequence alignments

Uncovering de novo polyamine biosynthesis in the gut microbiome and its alteration in inflammatory bowel disease

Polyamines are important gut microbial metabolites known to affect host physiology, yet the mechanisms behind their microbial production remain incompletely understood. In this study, we developed a stable isotope-resolved metabolomic (SIRM) approach to track polyamine biosynthesis in the gut microbiome. Viable microbial cells were extracted from fresh human and mouse feces and incubated anaerobically with [U-13C]-labeled inulin (tracer). Liquid chromatography-high resolution mass spectrometry analysis revealed distinct 13C enrichment profiles for spermidine (SPD) and putrescine (PUT), indicating that the arginine-agmatine-SPD pathway contributes to SPD biosynthesis in addition to the well-known spermidine synthase pathway (PUT aminopropylation). Species differences were observed in the 13C enrichments of polyamines and related metabolites between the human and mouse microbiome. By analyzing the fecal metabolomics and metatranscriptomic data from an inflammatory bowel disease (IBD) cohort, we found significantly higher polyamine levels in IBD patients compared to healthy controls. Further investigations using single-strain SIRM and in silico analyses identified Bacteroides spp. as key contributors to polyamine biosynthesis, harboring essential genes for this process and potentially driving the upregulation of polyamines in IBD. Taken together, this study expands our understanding of polyamine biosynthesis in the gut microbiome and will facilitate the development of precision therapies to target polyamine-associated diseases.

Phylogenomics provides new insight into the phylogeny and diversification of Asian Lappula (Boraginaceae)

The application of omics data serves as a powerful tool for investigating the roles of incomplete lineage sorting (ILS) and hybridization in shaping genomic diversity, offering deeper insights into complex evolutionary processes. In this study, we utilized deep genome sequencing data from 76 individuals of Lappula and its closely allied genera, collected from China and Central Asia. By employing the HybPiper and Easy353 pipelines, we recovered 262-279 single-copy nuclear genes (SCNs) and 352-353 Angiosperms353 genes, respectively. We analyzed multiple datasets, including complete chloroplast genomes and a filtered set of 475 SCNs, to conduct phylogenetic analyses using both concatenated and coalescent-based methods. Furthermore, we employed Quartet Sampling (QS), coalescent simulations, MSCquartets, HyDe, and reticulate network analyses to investigate the sources of phylogenetic discordance. Our results confirm that Lappula is polyphyletic, with L. mogoltavica clustering with Pseudolappula sinaica and forming a sister relationship with other taxa included in this study. Additionally, three Lepechiniella taxa nested within distinct clades of Lappula. Significant gene tree discordance was observed at several nodes within Lappula. Coalescent simulations and hybrid detection analyses suggest that both ILS and hybridization contribute to these discrepancies. Flow cytometry (FCM) analyses confirmed the presence of both diploid and tetraploid taxa within Lappula. Phylogenetic network analyses further revealed that Clades IV and VII likely originated through hybridization, with the tetraploids in Clade IV arising from two independent hybridization events. Additionally, the "ghost lineage" identified as sister to Lappula redowskii serves as one of the donors in allopolyploidization. In conclusion, our study provides new insights into the deep phylogenetic relationships of Asian Lappula and its closely allied genera, contributing to a more comprehensive understanding of the evolution and diversification of Lappula.

Characterization of the family-level Borreliaceae pan-genome and development of an episomal typing protocol

The Borreliaceae family includes many obligate parasitic bacterial species etiologically associated with a myriad of zoonotic borrelioses, including Lyme disease and vector-borne relapsing fevers. Borreliaceae infections are difficult to detect by both direct and indirect methods, often leading to delayed and missed diagnoses. Efforts to improve diagnostics center around the development of molecular diagnostics (MDx), but due to deep tissue sequestration and the lack of persistent bacteremias, even MDx assays suffer from a lack of sensitivity. Additionally, the extensive genomic heterogeneity among isolates, even within the same species, contributes to the lack of assay sensitivity, as single target assays, whether nucleic acid-based or serologically based, cannot provide universal coverage. This within-species heterogeneity is partly due to differences in replicon repertoires and genomic structures that have likely arisen to support the complex Borreliaceae life cycle necessary for these parasites to survive in multiple hosts, each with unique immune responses. We constructed a Borreliaceae family-level pan-genome and characterized the phylogenetic relationships among the constituent taxa, which supports the recent, although contested, taxonomy of splitting the family into at least two genera. Gene content profiles were created for the majority of the Borreliaceae replicons, providing for the first time their unambiguous molecular typing. Our characterization of the Borreliaceae pan-genome supports the splitting of the former Borrelia genus into two genera and provides for the phylogenetic placement of several non-species designated isolates. Mining this family-level pan-genome will enable the development of precision diagnostics corresponding to gene content-driven clinical outcomes while also providing targets for interventions.

IMPORTANCE

Using whole genome sequencing, we demonstrated that the bacteria that are transmitted by ticks and other arthropod vectors that cause Lyme disease and relapsing fevers, while related, do not belong within the same genus classification. In addition, through characterization of their highly atypical genomic structure, we were able to develop a genetic typing system that will help with future studies of how they cause disease while also providing targets for medical interventions.

Evolutionary trajectories of Nipah virus: Evaluating the antiviral efficacy of Kabasura Kudineer Chooranam

Nipah virus (NiV) is a highly contagious zoonotic pathogen causing severe encephalitis and respiratory illnesses in humans. With a high fatality rate and no FDA-approved treatments, NiV poses a significant public health threat. This study conducts a comprehensive Bayesian phylogenetic analysis of all publicly available NiV genomes since the first human case. Additionally, a protein-protein interaction (PPI) network analysis focusing on Pteropus species was performed to identify potential therapeutic targets. High-throughput virtual screening assessed the inhibitory potential of Kabasura Kudineer Chooranam phytocompounds against these targets. Molecular dynamic simulations (MDS) were conducted to evaluate the stability and dynamic characteristics of NiV proteins bound to specific inhibitors. Bayesian phylogenetic analysis of 280 NiV genomes revealed two distinct clades among Indian isolates, highlighting significant regional diversity. Notably, the latest strain, OM135495, along with other NiV variants in Kerala, underscores the virus's rapid genetic evolution since 2015. The PPI network identified NiV-F, NiV-G, and NiV-N as key therapeutic targets. Among the tested phyto compounds, Vasicinone and Piperine exhibited strong binding affinities (-4.51 to -5.96 kcal/mol) and enhanced stability during MDS, suggesting their potential as antiviral agents. These findings indicate that phyto compounds may serve as viable alternatives for NiV treatment, paving the way for novel drug development. However, further validation through laboratory and animal studies is essential. This study enhances our understanding of NiV evolution, informs public health strategies, and contributes to preparedness for future outbreaks.

Integrated single-cell transcriptome and comparative genome analysis reveals the origin of intermuscular bones in zebrafish

The evolutionary process of intermuscular bones (IBs) is complex, the molecular regulatory mechanisms of their development are not clear, and even the genes involved in the evolution and development of IBs are poorly understood. In this study, comparative genomic analysis of four fish species with IBs and eleven fish species without IBs identified 106 genes that are more conservatively evolved in fish species with IBs, but highly variable in fish species without IBs. These genes are mainly involved in swimming behavior and BMP signaling pathways. We performed single-cell transcriptome sequencing of IBs origin tissues in zebrafish before and after IBs formation and found that osteoblasts and mesenchymal stem cells (MSCs) increased significantly after IBs formation. RNA velocity analysis showed that osteoblasts in IBs differentiate from MSCs, and the differentiation trajectory of MSCs into osteoblasts was successfully constructed by pseudo-time analysis. Combined with the results of multi-omics analysis, seven candidate genes associated with IBs development were screened and knocked out in zebrafish. It was found that foxn3 mutation resulted in a delay in IB development, whereas bmp6 mutation resulted in a total loss of IB. By comparing the transcriptome of IBs tissues between bmp6+/+ zebrafish and bmp6-/- zebrafish, we found that bmp6 deletion may inhibit the differentiation of MSCs into osteoblasts while promoting the formation of osteoclasts and ultimately inhibiting the formation of IBs. This study provides new insights into the molecular regulatory mechanisms and evolutionary processes of IB development.

Outbreak of Enterovirus D68 in Young Children, Brescia, Italy, August to November 2024

Enterovirus D68 (EV-D68) is responsible for a plethora of clinical manifestations ranging from asymptomatic infections to severe respiratory symptoms and neurological disorders. EV-D68 was first detected in children with pneumonia in 1962 and, from then, only sporadic cases were reported until 2014, when outbreaks were notified across the world. After the withdrawal of preventive measures against SARS-CoV-2, a significant increase in EV-D68 infections has been reported in 2021-2022. A surveillance program to evaluate the incidence of enterovirus/rhinovirus (EV/RV) infections was implemented at the Brescia Civic Hospital, Italy. Fifty-five EV/RV-positive respiratory samples, belonging to pediatric patients, were subjected to NGS. We observed that 61.8% of samples were positive for EV, with EV-D68 as the most prevalent genotype predominantly detected between August and November 2024. Phylogenetic analysis revealed that EV-D68 sequences formed two monophyletic clades corresponding to the A2 and B3 lineages, highlighting their recent introduction in Italy. Interestingly, 40% of pediatric EV-D68 infections were detected with at least one other EV/RV. Our study highlights the crucial role played by genomic surveillance of respiratory infections to monitor the circulation of emerging and re-emerging viruses, as well as their evolution. This will be fundamental to enable prompt intervention strategies.

Genome-Wide Characterization, Comparative Analysis, and Expression Profiling of SWEET Genes Family in Four Cymbidium Species (Orchidaceae)

The SWEET (Sugar Will Eventually be Exported Transporters) protein family plays a key role in plant growth, adaptation, and stress responses by facilitating soluble sugar transport. However, their functions in Cymbidium remain poorly understood. This study identified 59 SWEET genes across four Cymbidium species, encoding conserved MtN3/saliva domains. Despite variations in exon-intron structures, gene motifs and domains were highly conserved. Phylogenetic analysis grouped 95 SWEET proteins from six species into four clades, with gene expansion driven by whole-genome, segmental, and tandem duplications. Cis-element analysis and expression profiling across 72 samples revealed diverse regulatory patterns. Notably, SWEET genes showed peak expression in floral development, leaf morph variations, and diurnal rhythms. qRT-PCR and transcription factor binding analysis further highlighted their regulatory roles in floral patterning, leaf variation, and metabolic rhythms. These findings provide a foundation for future studies on SWEET gene function and their potential molecular breeding value in orchids.

Mediterranean monk seal (Monachus monachus) and leopard seal (Hydrurga leptonyx) de novo genomes to study the demographic history and genetic diversity of southern seals

BACKGROUND

The Monachinae, or southern seals, are one of two subfamilies within the Phocidae and are home to iconic pinnipeds such as the leopard seal, a fierce Antarctic top predator, and the Mediterranean monk seal, one of the world's most endangered mammals. These two species are difficult to study and sample, due to their hidden lives in extreme environments or, in case of the monk seal, their critically reduced population sizes; consequently, genetic data from these two species is scarce. However, cost developments and advances in genome sequencing have made it possible to generate continuous genome assemblies from DNA of even stranded individuals, allowing to assemble the first reference genomes of such rarely observed species.

RESULTS

In this study, we have sequenced the genomes of the leopard seal and the Mediterranean monk seal using PacBio's CCS technology to assemble the very first genomes for these species. Four additional Mediterranean monk seal individuals were sequenced using Illumina short-read technology. These data allowed analysis of their demography and genomic diversity based on whole-genome data, confirming low genetic variability and small numbers of individuals for the Mauritanian population of the Mediterranean monk seal. In contrast, the relatively abundant leopard seal shows a high degree of heterozygosity, comparable in the range of other common carnivores.

CONCLUSIONS

The first genome assemblies for these seals will lay the groundwork for population-level and other studies to better understand their evolutionary history and biology and to aid conservation efforts.

Decoding G-Quadruplexes Sequence in Vitis vinifera: Regulatory Region Enrichment, Drought Stress Adaptation, and Sugar-Acid Metabolism Modulation

G-quadruplexes play a crucial role in transcription, translation, and DNA replication in plant genomes. Here, we comprehensively examined the prevalence and functions of G-quadruplexes in Vitis vinifera. A total of 467,813 G-quadruplexes were identified in grapevine genome, with enrichment in the promoter (0.54/kbp) and near transcription start sites (TSSs, 1.00/kbp), and showed conservative strand preference. The G-quadruplex density in centromeres exhibited heterogeneity. The differentially expressed genes (DEGs) under two-day drought stress manifested high G-quadruplex density in the promoter and TSS regions. The upregulated DEGs showed template strand-biased G-quadruplex enrichment, while downregulated DEGs displayed coding strand dominance linked to metal ion homeostasis and sugar-acid metabolism pathways, respectively. G-quadruplexes were enriched in key sugar-acid metabolism genes, including pyruvate kinase and sucrose synthase. The number of G-quadruplexes in sucrose transferase VINV genes was higher than that in the CWINV and NINV genes. This study revealed G-quadruplexes as regulatory elements of stress response and berry development, providing abundant genetic targets for precision breeding and the quality improvement of grapevines.

Validating a Target-Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals

In the last three decades, DNA sequencing of ancient animal osteological assemblages has become an important tool complementing standard archaeozoological approaches to reconstruct the history of animal domestication. However, osteological assemblages of key archaeological contexts are not always available or do not necessarily preserve enough ancient DNA for a cost-effective genetic analysis. Here, we develop an in-solution target-enrichment approach, based on 80-mer species-specific RNA probes (ranging from 306 to 1686 per species) to characterise (in single experiments) the mitochondrial genetic variation from eight domesticated animal species of major economic interest: cattle, chickens, dogs, donkeys, goats, horses, pigs and sheep. We also illustrate how our design can be adapted to enrich DNA library content and map the Y-chromosomal diversity within Equus caballus. By applying our target-enrichment assay to an extensive panel of ancient osteological remains, farm soil, and cave sediments spanning the last 43 kyrs, we demonstrate that minimal sequencing efforts are necessary to exhaust the DNA library complexity and to characterise mitogenomes to an average depth-of-coverage of 19.4 to 2003.7-fold. Our assay further retrieved horse mitogenome and Y-chromosome data from Late Pleistocene coprolites, as well as bona fide mitochondrial sequences from species that were not part of the probe design, such as bison and cave hyena. Our methodology will prove especially useful to minimise costs related to the genetic analyses of maternal and paternal lineages of a wide range of domesticated and wild animal species, and for mapping their diversity changes over space and time, including from environmental samples.

A core Plasmopara viticola effector attenuates the DNA-binding activity of bZIP transcription factor to compromise plant immunity

Grapevine (Vitis vinifera L.) frequently faces challenges from various pathogens, among which Plasmopara viticola is the most devastating one hindering grape production. During infection, P. viticola secretes a series of effectors into host cells to manipulate plant immune responses. Here, an RXLR effector of P. viticola, PvRXLR13, was identified as one that could disrupt immune processes and thus promote pathogen colonization. PvRXLR13 contained a functional signal peptide and was highly conserved across different destructive oomycetes. PvRXLR13 was significantly induced during P. viticola infection and could suppress elicitor chitin-induced reactive oxygen species (ROS), callose deposition, and INF1-triggered cell death. Furthermore, PvRXLR13 could also inhibit P. viticola- and P. capsici-triggered H2O2 accumulation and promote pathogen colonization in both grapevine and Nicotiana benthamiana, respectively. VvHY5, a basic leucine zipper (bZIP) transcription factor, was found to be the host target of PvRXLR13. Further analysis revealed that overexpression of VvHY5 enhanced grapevine resistance to P. viticola and P. viticola-triggered H2O2 accumulation. Furthermore, we found that VvHY5 directly bound to the promoter of the positive immune factor VvEDS1 and activated its expression, whereas PvRXLR13 attenuated the DNA-binding activity of VvHY5 during P. viticola infection. Further analysis revealed that other members of grape bZIPs, VvbZIP6/9/21/32/34/37, were also involved in the defense response against P. viticola invasion. Just like HY5/HYH, all these bZIP family members were targeted by the effector PvRXLR13. Collectively, our findings suggest that P. viticola secretes a key effector PvRXLR13 to compromise the function in immune regulation of bZIP transcription factors to promote infection in grapevine.

A species-level identification pipeline for human gut microbiota based on the V3-V4 regions of 16S rRNA

16S rRNA gene sequencing is pivotal for identifying bacterial species in microbiome studies, especially using the V3-V4 hypervariable regions. A fixed 98.5% similarity threshold is often applied for species-level identification, but this approach can cause misclassification due to varying thresholds among species. To address this, our study integrated data from SILVA, NCBI, and LPSN databases, extracting V3-V4 region sequences and supplementing them with 16S rRNA sequences from 1,082 human gut samples. This resulted in a non-redundant amplicon sequence variants (ASVs) database specific to the V3-V4 regions (positions 341-806). Utilizing this database, we identified flexible classification thresholds for 674 families, 3,661 genera, and 15,735 species, finding clear thresholds for 87.09% of families and 98.38% of genera. For the 896 most common human gut species, we established precise taxonomic thresholds. To leverage these findings, we developed the asvtax pipeline, which applies flexible thresholds for more accurate taxonomic classification, notably improving the identification of new ASVs. The asvtax pipeline not only enhances the precision of species-level classification but also provides a robust framework for analyzing complex microbial communities, facilitating more reliable ecological and functional interpretations in microbiome research.

Biodegradation of isoprene by soil Actinomycetota from coffee-tea integrated plantations in a tropical evergreen forest

Isoprene, a biogenic volatile compound emitted largely by plants, can form greenhouse gases when it reacts with atmospheric radicals. A significant amount of isoprene is absorbed into soil and can be degraded by soil microorganisms, but our understanding of the microbial biodegradation of isoprene in tropical ecosystems remains limited. This study investigated isoprene degradation by soil microbes indigenous to a tropical evergreen forest, focusing on those associated with coffee and tea plants grown as integrated crops and their genome characteristics in relation to their biodegradation capabilities. Following a 96-hour incubation with 7.2 × 10⁵ parts per billion by volume (ppbv) of isoprene, soil samples exhibited degradation levels ranging from 11.95 % to 36.54 %. From these soils, bacterial isolates belonging to the genera Rhodococcus and Gordonia (Actinomycetota) were recovered. These isolates demonstrated high isoprene biodegradation activity (50.3 %-69.1 % over seven days) and carried the isoA gene associated with isoprene metabolism. According to genome analysis, the organization of genes in the iso cluster was homologous, and the encoded amino acid sequences were highly similar to those of previously known isoprene-degrading members of the same genera. These findings emphasized the contribution of these widespread isoprene-degrading bacterial genera in the biodegradation of isoprene and the role of their isoprene monooxygenases in modulating atmospheric isoprene flux.

Altered oral health and microbiota in drug-free patients with schizophrenia

BACKGROUND

The oral microbiota is associated with neuro-psychiatric disorders. However, there is presently inadequate comprehension regarding the correlation between schizophrenia and the oral microbiota. Moreover, patients with schizophrenia frequently exhibit poor oral health, potentially influencing research outcomes. Therefore, this study aims to investigate changes in the oral microbiota and oral health status in drug-free schizophrenia patients.

METHODS

Oral microbiota samples were collected from 50 drug-free patients with schizophrenia and 50 healthy controls (HCs). The downstream microbiota analysis was based on Illumina sequencing of the V3-V4 hypervariable region of the 16 S rRNA gene.

RESULTS

The alpha diversity of SCZ group is increased, such as the Shannon index (p < 0.001) and Simpson index (p = 0.004), while the community structure also displays variance compared to the HC group (p < 0.001). Key discriminative taxa were found in LEfSe analysis, including the phyla Fusobacteriota, Firmicutes, and Actinobacteriota. The differential taxa and microbial functions showed a strong correlation with clinical oral conditions. Further analysis demonstrated that models based on the entire oral microbiota effectively distinguished SCZ patients from HC (AUC = 0.97).

CONCLUSIONS

The significant changes in the microbiota of Drug-free SCZ patients appear to be closely associated with the poor oral environment.

Metrics of Genomic Complexity in the Evolution of Bacterial Endosymbiosis

Endosymbiosis can be considered a regressive or degenerative evolutionary process characterized at the genomic level by genome erosion and degeneration due to high mutational pressure toward AT (adenine and thymine) bases. The genomic and biological complexity of endosymbionts must be lower than that of the free-living bacteria from which they evolved. In the present work, we contrasted whether two proposed metrics for measuring genomic complexity in both types of bacteria, GS and BB, reflect their complexity, expecting higher values in free-living bacteria than in endosymbionts. On the other hand, we endeavored to delve into the factors that contribute to the reduction in metric values in endosymbionts, as well as their eventual relationship with six genomic parameters associated with functionality. This study aimed to test the robustness of these proposed metrics in a well-known biological scenario, such as the endosymbiosis process.

Description of two novel bacteriophages of the class Caudoviricetes that infect Ralstonia solanacearum and Ralstonia pseudosolanacearum

Here, we describe the isolation and characterization of two novel phages from Brazilian soil that infect Ralstonia solanacearum and Ralstonia pseudosolanacearum, which we have named "RS phage AB1 and RS phage CA1. Genome sequencing and phylogenetic analysis revealed that RS phage AB1 is a novel member of the family Peduoviridae, while RS phage CA1 could not be classified as part of any established family. Thus, we propose a new viral family, "Anamaviridae", with two subfamilies, "Kantovirinae" and "Mascarenevirinae", with the latter including RS phage CA1. We propose the species names "Cocadavirus alagoinhas" and "Acarajevirus bahia" for RS phage CA1 and RS phage AB1, respectively. These findings increase our understanding of the diversity of phages infecting plant pathogens of the genus Ralstonia.

aurora: a machine learning gwas tool for analyzing microbial habitat adaptation

A primary goal of microbial genome-wide association studies is identifying genomic variants associated with a particular habitat. Existing tools fail to identify known causal variants if the analyzed trait shaped the phylogeny. Furthermore, due to inclusion of allochthonous strains or metadata errors, the stated sources of strains in public databases are often incorrect, and strains may not be adapted to the habitat from which they were isolated. We describe a new tool, aurora, that identifies autochthonous strains and the genes associated with habitats while acknowledging the potential role of the habitat adaptation trait in shaping phylogeny.

Epidemiological and phylogenetic analyses of public SARS-CoV-2 data from Malawi

The COVID-19 pandemic has had varying impacts across different regions, necessitating localised data-driven responses. SARS-CoV-2 was first identified in a person in Wuhan, China, in December 2019 and spread globally within three months. While there were similarities in the pandemic's impact across regions, key differences motivated systematic quantitative analysis of diverse geographical data to inform responses. Malawi reported its first COVID-19 case on 2 April 2020 but had significantly less data than Global North countries to inform its response. Here, we present a modelling analysis of SARS-CoV-2 epidemiology and phylogenetics in Malawi between 2 April 2020 and 19 October 2022. We carried out this analysis using open-source tools and open data on confirmed cases, deaths, geography, demographics, and viral genomics. R was used for data visualisation, while Generalised Additive Models (GAMs) estimated incidence trends, growth rates, and doubling times. Phylogenetic analysis was conducted using IQ-TREE, TreeTime, and interactive tree of life. This analysis identifies five major COVID-19 waves in Malawi, driven by different lineages: (1) Early variants, (2) Beta, (3) Delta, (4) Omicron BA.1, and (5) Other Omicron. While the Alpha variant was present, it did not cause a major wave, likely due to competition from the more infectious Delta variant, since Alpha circulated in Malawi when Beta was phasing out and Delta emerging. Case Fatality Ratios were higher for Delta, and lower for Omicron, than for earlier lineages. Phylogeny reveals separation of the tree into major lineages as would be expected, and early emergence of Omicron, as is consistent with proximity to the likely origin of this variant. Both variant prevalence and overall rates of confirmed cases and confirmed deaths were highly geographically heterogeneous. We suggest that real-time analyses should be considered in Malawi and other countries, where similar computational and data resources are available.

Prevalence and Molecular Characterization of Cryptosporidium Species in Diarrheic Children in Cameroon

Cryptosporidiosis remains a major cause of diarrhea-related childhood death, particularly in developing countries. Although effective anti-retroviral therapy has significantly reduced the cryptosporidiosis burden in western nations, the situation in developing countries remains alarming due to limited therapeutic options and a lack of preventive measures. To better control disease transmission and develop effective prevention strategies, a thorough understanding of the genetic diversity of circulating species is crucial. While cryptosporidiosis has previously been reported in Cameroon, information on the genetic diversity of parasite strains is lacking. In a large cross-sectional study conducted between March 2020 and March 2021 in four regions of Cameroon, Southwest, Littoral, Center and West, a total of 1119 fecal samples of children (n = 1119) were collected and genetically analyzed. This study aimed to assess the genetic diversity of Cryptosporidium strains circulating in this patient cohort in Cameroon. Using modified Ziehl-Neelsen fecal smear staining, an overall prevalence of 8.5% (96/1119) was recorded. PCR analysis revealed a prevalence of 15.4% in the Center, 7.2% in the Littoral, 10.5% in the West, and 13.1% in the Southwest regions. Molecular analysis identified Cryptosporidium. hominis and Cryptosporidium parvum as circulating species, with all subtype families suggesting anthroponotic transmission. No zoonotic subtypes of C. parvum were detected. These findings confirm that cryptosporidiosis transmission in Cameroon is primarily anthroponotic. Nonetheless, much larger epidemiological surveys, including other patient cohorts, are necessary for final confirmation of this statement.

Analyses of Transposable Elements in Arbuscular Mycorrhizal Fungi Support Evolutionary Parallels With Filamentous Plant Pathogens

Transposable elements are repetitive DNA sequences that excise or create copies that are inserted elsewhere in the genome. Their expansion shapes genome variability and evolution by impacting gene expression and rearrangement rates. Arbuscular mycorrhizal fungi are beneficial plant symbionts with large, transposable element-rich genomes, and recent findings showed these elements vary significantly in abundance, evolution, and regulation among model strains. Here, we aimed to obtain a more comprehensive understanding of transposable element function and evolution in arbuscular mycorrhizal fungi by investigating assembled genomes from representatives of all known families. We uncovered multiple, family-specific bursts of insertions in different species, indicating variable past and ongoing transposable element activity contributing to the diversification of arbuscular mycorrhizal fungi lineages. We also found that transposable elements are preferentially located within and around candidate effectors/secreted proteins, as well as in proximity to promoters. Altogether, these findings support the role of transposable elements in promoting the diversity in proteins involved in molecular dialogs with hosts and, more generally, in driving gene regulation. The mechanisms of transposable element evolution we observed in these prominent plant symbionts bear striking similarities to those of many filamentous plant pathogens.

The Mitochondrial Genome of the Springtail Semicerura bryophila (Collembola): New Data Call into Question the Relevance of the Subfamilies of the Isotomidae

Background: Semicerura bryophila Potapov & Sun, 2020 is a soil-dwelling springtail belonging to the family Isotomidae. The phylogenetic relationships among species of this group remain controversial due to a lack of molecular data. Therefore, in this study, we sequenced the mitochondrial genome of S. bryophila, analyzed the characterization of the mitochondrial genome, and investigated the phylogenetic relationships of Isotomidae. Methods: The mitochondrial genome of S. bryophila was sequenced and assembled. We analyzed the sequence length, nucleotide composition, and evolutionary relationships within the Isotomidae family, incorporating data from twelve previously published mitochondrial genomes. Results: The length of the S. bryophila mitogenome is 15,247 bp and comprises 13 protein-coding genes, 22 tRNAs, and two rRNAs, arranged in a typical order. Its base composition is as follows: A = 38.05%, T = 33.64%, G = 10.17%, and C = 15.03%. Phylogenetic analysis based on the mitogenome revealed that the monophyly of Isotomidae and the paraphyletic grouping of Semicerura and Folsomotoma, supporting their closer relationship with the subfamily Anurophorinae rather than to Isotominae. The analysis validated subfamily Anurophorinae, identified Pachyotominae as a part of Anurophorinae, and suggested that Isotominae is paraphyletic. Conclusions: The present study provides valuable mitochondrial information for the classification of S. bryophila and offers new insights into the taxonomic and evolutionary studies within the genus Semicerura.

Generating multiple alignments on a pangenomic scale

MOTIVATION

Since novel long read sequencing technologies allow for de novo assembly of many individuals of a species, high-quality assemblies are becoming widely available. For example, the recently published draft human pangenome reference was based on assemblies composed of contigs. There is an urgent need for a software-tool that is able to generate a multiple alignment of genomes of the same species because current multiple sequence alignment programs cannot deal with such a volume of data.

RESULTS

We show that the combination of a well-known anchor-based method with the technique of prefix-free parsing yields an approach that is able to generate multiple alignments on a pangenomic scale, provided that large-scale structural variants are rare. Furthermore, experiments with real world data show that our software tool PANgenomic Anchor-based Multiple Alignment significantly outperforms current state-of-the art programs.

AVAILABILITY AND IMPLEMENTATION

Source code is available at: https://gitlab.com/qwerzuiop/panama, archived at swh:1:dir:e90c9f664995acca9063245cabdd97549cf39694.

Backbone phylogeny of Salix based on genome skimming data

The genus Salix is a common component of the Northern Hemisphere dendroflora with important ecological and economic value. However, taxonomy and systematics of Salix is extremely difficult and relationships between main lineages, especially deep phylogenies, remain largely unresolved. In this study, we used genome-skimming, plastome assembly, and single-copy orthologs (SCOs) from 66 Salix accessions, along with publicly available plastome and sequence read archive (SRA) datasets to obtain a robust backbone phylogeny of Salix, clarify relationships between its main lineages, and gain a more precise understanding of the origin and diversification of this species-rich genus. The plastome and SCO datasets resolved Salix into two robust clades, with plastome-based phylogenies lacking inner resolution and SCO offering fully resolved phylogenies. Our results support the classification of Salix into five subgenera: Salix, Urbaniana, Triandrae, Longifoliae and Vetrix. We observed a significant acceleration in the diversification rate within the Chamaetia-Vetrix clade, while Salix exhibited increased rates of diversification spanning from the early Oligocene to the late Miocene. These changes coincided with contemporaneous tectonic and climate change events. Our results provide a foundation for future systematic and evolutionary studies of Salix. Additionally, we showed that genome skimming data is an efficient, rapid, and reliable approach for obtaining extensive genomic data for phylogenomic studies, enabling the comprehensive elucidation of Salix relationships.

Majority of the Highly Variable NLRs in Maize Share Genomic Location and Contain Additional Target-Binding Domains

Nucleotide-binding, leucine-rich repeat (LRR) proteins (NLRs) are a major class of immune receptors in plants. NLRs include both conserved and rapidly evolving members; however, their evolutionary trajectory in crops remains understudied. Availability of crop pan-genomes enables analysis of the recent events in the evolution of this highly complex gene family within domesticated species. Here, we investigated the NLR complement of 26 nested association mapping (NAM) founder lines of maize. We found that maize has just four main subfamilies containing rapidly evolving highly variable NLR (hvNLR) receptors. Curiously, three of these phylogenetically distinct hvNLR lineages are located in adjacent clusters on chromosome 10. Members of the same hvNLR clade show variable expression and methylation across lines and tissues, which is consistent with their rapid evolution. By combining sequence diversity analysis and AlphaFold2 computational structure prediction, we predicted ligand-binding sites in the hvNLRs. We also observed novel insertion domains in the LRR regions of two hvNLR subfamilies that likely contribute to target recognition. To make this analysis accessible, we created NLRCladeFinder, a Google Colaboratory notebook, that accepts any newly identified NLR sequence, places it in the evolutionary context of the maize pan-NLRome, and provides an updated clade alignment, phylogenetic tree, and sequence diversity information for the gene of interest. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Draft genome of pin nematode Paratylenchus projectus recovered from rhizosphere of blueberry

BACKGROUND

The pin nematode, belonging to the genus Paratylenchus, parasitizes higher plants, often causing reduced or inhibited root tip development.

METHODS

Pin nematodes were isolated from the roots and rhizosphere of blueberry plants and subsequently identified as representatives of Paratylenchus projectus based on morphological characteristics and molecular barcoding. The P. projectus draft genome was sequenced using the Illumina platform.

RESULTS

Phylogenetic analysis based on 18S, 28S and ITS rRNA placed this species in highly supported clades alongside other P. projectus specimens. The draft genome of P. projectus was sequenced and assembled, representing the first genomic data for both the genus Paratylenchus and the family Tylenchulidae. The assembled genome, though fragmented, had a total length of 191.36 Mb and an estimated genome size of 64.9 Mb. Protein-coding genes were predicted using four different databases, with particular focus on carbohydrate-active enzymes from the GH5 and GH18 families. The recovered GH5 genes were distributed among three distinct clades: one forming a basal group relative to other nematodes, one as a sister clade to the fungivorous nematode Aphelenchus avenae and one nested within a fungal clade. The GH18 chitinase genes were grouped into two clades: one closely related to sedentary plant-parasitic nematodes of the genera Heterodera and Globodera and the other closely related to the fungivorous nematode Ditylenchus.

CONCLUSIONS

The draft genome of Paratylenchus projectus was sequenced and assembled, representing the first genomic data for both the genus Paratylenchus and the family Tylenchulidae to our knowledge.

CamITree: a streamlined software for phylogenetic analysis of viral and mitochondrial genomes

BACKGROUND

Over the past decade, the continuous and rapid advances in bioinformatics have led to an increasingly common use of molecular sequence comparison for phylogenetic analysis. However, the use of multi-software and cross-platform strategies has increased the complexity of phylogenetic tree estimation. Therefore, the development and application of streamlined phylogenetic analysis tools are growing in significance in the field of biology. Particularly for genomes with relatively short sequences, there is a lack of simple and integrative tools for phylogenetic analysis.

RESULTS

In this study, we present CamlTree (Concatenated alignments maximum-likelihood tree), a user-friendly desktop software designed to simplify phylogenetic analysis for viral and mitochondrial genomes, ultimately facilitating related research. CamlTree provides a workflow including gene concatenation (or coalescence), sequence alignment, alignment optimization, and the estimation of phylogenetic trees using both maximum-likelihood (ML) and Bayesian inference (BI) methods. CamlTree was written in TypeScript and developed using the Electron framework. It offers a primarily user-friendly interface based on the React framework.

CONCLUSIONS

CamlTree software has been released for the Windows OS. It integrates several popular analysis tools to optimize and simplify the process of estimating polygenic phylogenetic trees. The establishment of software can assist researchers in reducing their workload and enhancing data processing efficiency, enabling them to expedite their research progress. The software, along with a detailed user manual, is available at https://github.com/BioCrossCoder/camltree .

Plastome-based subgenus-level phylogenetic backbone of hawthorns: insights into the maternal position and taxonomic synopsis of Crataegusshandongensis (Rosaceae, Maleae)

The recent recognition of the five-subgenera classification within Crataegus has prompted discussion about the maternal phylogenetic relationships among these subgenera, with inconsistencies in taxon sampling, marker selection, and inference methods contributing to differing interpretations. In this study, we performed deep genome skimming sequencing and assembled 63 whole plastomes, including 58 from Crataegus and five from related genera as the outgroups. We employed multiple phylogenetic inference methods (Maximum Likelihood and Bayesian Inference) to reconstruct an accurate phylogeny. The whole plastome-based, maternally inherited trees consistently supported two major clades within Crataegus: one comprising C.subg.Crataegus and C.subg.Brevispinae, the other encompassing the remaining three subgenera. Within the latter clade, C.subg.Sanguineae and C.subg.Americanae formed a sister group, which together were sister to C.subg.Mespilus. Our analysis also revealed a close maternal relationship between C.shandongensis and C.pinnatifidavar.major, suggesting the shared maternal ancestry. Furthermore, we updated the description of C.shandongensis based on extensive specimen examination and designated the lectotype for this species. This comprehensive taxonomic synopsis, supported by both phylogenomic and morphological analyses, provides a robust foundation for future taxonomic and evolutionary studies of the Shandong hawthorn.

Comparative Genomic Analysis of Two Monokaryons of Auricularia heimuer Hei29

Auricularia heimuer is a valuable traditional Chinese fungus used as food and medicine. Hei29 is a strain derived from wild A. heimuer through systematic domestication and selection. It has been the primary A. heimuer variety in Northeast China for 30 years and offers the advantages of high yield, good commercial property, and stable traits. This study used protoplast nucleation on Hei29 to produce two amiable and paired monokaryons, Hei29-D1 and Hei29-D2. The genome of Hei29 was sequenced utilizing the Illumina PE150 and PacBio Sequel sequencing platforms. Hei29-D1 and Hei29-D2 had genomic sizes of 47.54 Mb and 47.49 Mb, GC contents of 56.95% and 56.99%, and an N50 of 2.37 Mb and 4.28 Mb, respectively. Hei29's genome possessed two phytoene synthase (PSY) protein genes, one of which-PSY encoded by g894-has a transmembrane domain. The phylogenetic tree showed that Hei29 shared the closest evolutionary relationship with Auricularia subglabra TFB-10046 SS5. Collinearity analysis showed that the correlation between the two monokaryons was as high as 90.81%. Cluster analysis revealed that Hei29 contains 12,362 core genes, 223 unique genes in Hei29-D1, and 228 unique genes in Hei29-D2. This study is the first to sequence two related and paired monokaryons from A. heimuer, which is critical for fully understanding the genetic composition and information of the characteristic strain of A. heimuer in Northeast China. It establishes the data and theoretical foundation for gene mining, usage, and molecular breeding. It further promotes the genetic breeding and active substance utilization of A. heimuer.

An Expanding Universe of Mutational Signatures and Its Rapid Evolution in Single-Stranded RNA Viruses

The study of mutational processes in somatic genomes has gained recent momentum, uncovering a wide array of endogenous and exogenous factors associated with somatic changes. However, the overall landscape of mutational processes in germline mutations across the tree of life and associated evolutionary driving forces are rather unclear. In this study, we analyzed mutational processes in single-stranded RNA (ssRNA) viruses which are known to jump between different hosts with divergent exogenous environments. We found that mutational spectra in different ssRNA viruses differ significantly and are mainly associated with their genetic divergence. Surprisingly, host environments contribute much less significantly to the mutational spectrum, challenging the prevailing view that the exogenous cellular environment is a major determinant of the mutational spectrum in viruses. To dissect the evolutionary forces shaping viral spectra, we selected two important scenarios, namely the inter-host evolution between different viral strains as well as the intra-host evolution. In both scenarios, we found mutational spectra change significantly through space and time, strongly correlating with levels of natural selection. Combining the mutations across all ssRNA viruses, we identified a suite of mutational signatures with varying degrees of similarity to somatic signatures in humans, indicating universal and divergent mutational processes across the tree of life. Taken together, we unraveled an unprecedented dynamic landscape of mutational processes in ssRNA viruses, pinpointing important evolutionary forces shaping fast evolution of mutational spectra in different species.

Subcellular Enrichment Patterns of New Genes in Drosophila Evolution

The evolutionary patterns of proteins within subcellular compartments underlie the innovation and diversification foundation of the living eukaryotic organism. The location of proteins in subcellular compartments promotes the formation of network interaction modules, which in turn reshape the architecture of higher-level protein-protein interaction networks. Here, we conducted the most up-to-date gene age dating of Drosophila melanogaster by employing recently available long-read sequencing genomes as references. We found that an elevated gene fixation in the most recent common ancestor of Drosophila genus predated the divergence between two Drosophila subgenera, and a significant tendency of these genes in D. melanogaster encode proteins that localize to the extracellular matrix, accompanying the adaptive radiation of Drosophila species. Proteins encoded by genes located in the extracellular space exhibit higher sequence divergence, suggesting a rapid evolutionary process. We also observed that proteins encoded by genes originating from the same evolutionary branches tend to co-localize in the same subcellular compartments, and proteins in the same subcellular compartment tend to interact with each other. The proteins encoded by genes that have persisted through deeper branches exhibit broader localization across multiple subcellular compartments, enhancing the likelihood of their integration into various protein or gene regulatory networks, thereby increasing functional diversity. These evolutionary patterns not only contribute to understanding the evolution of subcellular localization in proteins encoded by genes originating from different branches, but also provide insights into the evolution of protein-protein networks driven by the emergence of new genes.

Unveiling hidden diversity: Phylogenomics of neotomine rodents and taxonomic implications for the genus Peromyscus

Neotomine rodents (Cricetidae, Neotominae) represent one of the most commonly encountered and diverse group of rodents in North America, yet phylogenetic relationships within this group remain uncertain. This subfamily is known for its rapid evolution, adding more complexity to our efforts to unravel their evolutionary history. The main debate revolves around the recognition of the genus Peromyscus as monophyletic or paraphyletic due to its relationship with other genera such as Habromys, Megadontomys, Podomys, Neotomodon, and Osgoodomys. Here, we aim to resolve phylogenetic relationships within Neotominae, to further explore their evolutionary history and taxonomic boundaries. We used target capture and high-throughput sequencing of complete mitogenomes and thousands of genome-wide ultraconserved elements loci (UCEs). Our comprehensive analyses encompassed 53 species of Neotominae spanning 12 previously described genera, along with one yet-undescribed genus. We also investigated 12 out of the 13 species groups within Peromyscus. Our analyses, including Maximum Likelihood and Bayesian Inference with both mitogemomes and UCEs, as well as the coalescent species-tree-based approach with UCEs, consistently recovered concordant and well-resolved phylogenies with high levels of nodal support. We identified seven main clades within Neotominae that could potentially be recognized at the generic level, mostly to categorize the genus Peromyscus as a monophyletic group, including one species group within "Peromyscus". Furthermore, our divergence dating estimates place the crown age of Neotominae to be around the late Miocene at ca. 7.9 - 10.7 mya. While generic level diversification continued through the Pliocene, species level diversification predominantly occurred during the late Pliocene, extending through the Pleistocene and Holocene. These epochs have been recognized as periods with significant changes in flora and fauna, driving ecological transformations on a global scale. We hypothesized that climatic and vegetation shifts during the Neogene and Quaternary, coupled with geological events, topographical features, and the presence of biogeographical corridors played a pivotal role in the speciation and diversification of Neotominae. Recognizing the importance of generating genomic-scale data coupled with a broad taxonomic sampling, our study, for the first time, offers resolution of the relationships among the main lineages of Neotominae. We expect that the phylogeny presented here will serve as a foundational resource for future systematic and evolutionary studies. This includes facilitating a proper comprehensive taxonomic revision of the group and the formal description and naming of new genera.

High-fidelity annotated triploid genome of the quarantine root-knot nematode, Meloidogyne enterolobii

Root-knot nematodes (RKN) of the genus Meloidogyne are obligatory plant endoparasites that cause substantial economic losses to agricultural production and impact the global food supply. These plant parasitic nematodes belong to the most widespread and devastating genus worldwide, yet few measures of control are available. The most efficient way to control RKN is deployment of resistance genes in plants. However, current resistance genes that control other Meloidogyne species are mostly inefficient on Meloidogyne enterolobii. Consequently, M. enterolobii was listed as a European Union quarantine pest requiring regulation. To gain insight into the molecular characteristics underlying its parasitic success, exploring the genome of M. enterolobii is essential. Here, we report a high-quality genome assembly of M. enterolobii using the high-fidelity long-read sequencing technology developed by Pacific Biosciences, combined with a gap-aware sequence transformer, DeepConsensus. The resulting triploid genome assembly spans 285.4 Mb with 556 contigs, a GC% of 30 ± 0.042 and an N50 value of 2.11 Mb, constituting a useful platform for comparative, population and functional genomics.

Chromosome-Level Genome Assembly and Comparative Genomic Analysis of Planiliza haematocheilus: Insights into Environmental Adaptation and Hypoxia Tolerance Mechanisms

Planiliza haematocheilus, a teleostan species noted for its ecological adaptability and economic significance, thrives in both freshwater and marine environments. This study presents a novel chromosome-level genome assembly through Hi-C, PacBio CCS, and Illumina sequencing methods. The assembled genome has a final size of 651.58 Mb, with 24 chromosomes anchoring 91.94% of contigs. Contig N50 and scaffold N50 are respectively measured at 25.52 Mb and 28.59 Mb. Of the 22,476 protein-coding genes identified in the genome, 21,834 have functional annotations. BUSCO (Benchmarking Universal Single-Copy Orthologs) genome and gene annotation assessments yielded scores of 96% and 96.6%, respectively. The genome of P. haematocheilus revealed 228 expanded and 1433 contracted gene families. Comparative genomic analyses highlight adaptations and hypoxia tolerance, linked to protein synthesis, immune response, and metabolic regulation. The high-quality genome assembly supports advanced studies on gene expression patterns under different environmental stressors, contributing to genetic enhancement efforts for this economically important aquaculture species.

Genetic tracking of Crimean-Congo haemorrhagic orthonairovirus in Hyalomma population infesting cattle in Nigeria

Crimean-Congo haemorrhagic fever virus (CCHFV), a Biosafety level 4 pathogen transmitted by ticks, causes severe haemorrhagic diseases in humans but remains clinically silent in animals. Over the past forty years, Nigeria lacks comprehensive genetic data on CCHFV in livestock and ticks. This study aimed to identify and characterize CCHFV strains in cattle and their Hyalomma ticks, the primary vector, in Kwara State, Nigeria. Blood samples and Hyalomma ticks were collected from cattle, with ticks identified to species, pooled, and homogenized for RNA extraction. The CCHFV S-segment was detected using specific primers via reverse transcriptase polymerase chain reaction, followed by sequencing of amplicons. Among 318 cattle, 318 sera samples and 2855 Hyalomma ticks (H. dromedarii (49.0%), H. truncatum (44.5%), and H. rufipes (6.5%)) were obtained. Only two tick pools of H. truncatum tested (2/319 pools) were positive for CCHFV, with no positive cattle sera detected. The sequenced positive pools, denoted as CCHFV/NGR/ILN/2021/F22_S-segment (1228 bp) and CCHFV/NGR/ILN/2021/F101_S-segment (863 bp), showed 98.21% nucleotide identity with 15 variations. These strains shared 98.13% and 98.93% nucleotide identity with CCHFV IbAr10200/UCCR4401 isolated from Nigerian ticks, but only 93.88% and 93.63% similarity with CCHFV isolated in 2016 from humans in Nigeria. Additionally, compared to CCHFV isolate IbAr10200 (KY484036), sequences from this study exhibited 9-23 nucleotide variable positions with 3-4 non-synonymous amino acid replacements. Phylogenetic analysis revealed clustering of these strains around IbAr10200, suggesting ongoing circulation. This study underscores the need for broader surveillance to understand the full spectrum of CCHFV strains and clades circulating in Nigeria.

Evolutionary diversification and succession of soil huge phages in glacier foreland

BACKGROUND

Huge phages (genome size ≥ 200 kb) have been detected in diverse habitats worldwide, infecting a variety of prokaryotes. However, their evolution and adaptation strategy in soils remain poorly understood due to the scarcity of soil-derived genomes.

RESULTS

Here, we conduct a size-fractioned (< 0.22 μm) metagenomic analysis across a 130-year chronosequence of a glacier foreland in the Tibetan Plateau and discovered 412 novel viral operational taxonomic units (vOTUs) of huge phages. The phylogenomic and gene-shared network analysis gained insights into their unique evolutionary history compared with smaller phages. Their communities in glacier foreland revealed a distinct pattern between the early (≤ 41 years) and late stages (> 41 years) based on the macrodiveristy (interspecies diversity) analysis. A significant increase in the diversity of huge phages communities following glacier retreat were observed according to current database. The phages distributed across sites within late stage demonstrated a remarkable higher microdiversity (intraspecies diversity) compared to other geographic range such as the intra early stage, suggesting that glacial retreat is key drivers of the huge phage speciation. Alongside the shift in huge phage communities, we also noted an evolutionary and functional transition between the early and late stages. The identification of abundant CRISPR-Cas12 and type IV restriction-modification (RM) systems in huge phages indicates their complex mechanisms for adaptive immunity.

CONCLUSIONS

Overall, this study unravels the importance of climate change in shaping the composition, evolution, and function of soil huge phage communities, and such further understanding of soil huge phages is vital for broader inclusion in soil ecosystem models. Video Abstract.

Orogeny and High Pollen Flow as Driving Forces for High Genetic Diversity of Endangered Acer griseum (Franch.) Pax Endemic to China

Acer griseum (Franch.) Pax is an endangered species endemic to China, mainly scattered in the Qinling-Daba Mountains. The genetic diversity of 17 natural populations were analyzed by nuclear DNA (nDNA) and chloroplast DNA (cpDNA) to explore the driving forces for its microevolution. A high level of genetic diversity (nDNA: He = 0.296, cpDNA: Ht = 0.806) was found in A. griseum. Genetic variation was mainly within populations (92.52%) based on nDNA, while it was mainly among populations (96.26%) based on cpDNA. The seventeen populations were divided into two groups, corresponding to the subtropical zone (Group I) and temperate zone (Group II), with haplotype 4 (Hap4) and Hap5 being the most common haplotypes, respectively. Consequently, genes associated with heat and heavy metal stress were identified in Group I, while genes related to salt and drought stress were identified in Group II. Haplotype differentiation was driven by the heterogeneous microenvironment caused by the uplifting of the Qinling-Daba Mountains, which was a vital source of its high genetic diversity. Furthermore, the uplifted Qinling-Daba mountains may bridge high pollen flow among populations, whereas rivers can result in low seed flow among populations, which has led to the incongruent genetic structure between nDNA and cpDNA. This study represents a new perspective that geological events, especially orogeny, play an important role in plant microevolution through the establishment of maternal genetic structure and provides a meaningful conservation strategy for A. griseum. Overall, the Qinling-Daba Mountains not only are cradles for the genetic diversity of A. griseum but also provided refugia for it during the Quaternary glacial period.

De novo assembly of the mitochondrial genome of Glycyrrhiza glabra and identification of two types of homologous recombination configurations caused by repeat sequences

BACKGROUND

Glycyrrhiza glabra, which is widely used in medicine and therapy, is known as the 'king of traditional Chinese medicine'. In this study, we successfully assembled and annotated the mitochondrial and chloroplast genomes of G. glabra via high-throughput sequencing technology, combining the advantages of short-read (Illumina) and long-read (Oxford Nanopore) sequencing.

RESULTS

We revealed the ring structure of the mitochondrial genome, which spans 421,293 bp with 45.1% GC content and 56 annotated genes. Notably, we identified 514 repetitive sequences, including 123 Simple sequence repeats (SRs), 3 Tndem sequence repeats (TSRs), and 388 Dispersed sequence repeats (DSRs). We identified 79 out of the 388 DSRs as potentially involved in homologous recombination. We identified five forward repeats and four palindromic repeats that facilitate homologous recombination and induce alterations in the mitochondrial genome structure. We corroborated this finding via polymerase chain reaction (PCR). Furthermore, we identified chloroplast-derived sequence fragments within the mitochondrial genome, offering novel insights into the evolutionary history of plant mitochondrial genomes. We predicted 460 potential RNA editing sites, primarily involving cytosine-to-uracil transitions. This study reveals the complexity of repetitive sequence-mediated homologous recombination in the mitochondrial genome of G. glabra and provides new insights into its structure, function, and evolution.

CONCLUSIONS

These findings have important implications for conservation biology, population genetics, and evolutionary studies, underscoring the role of repetitive sequences in genome dynamics and highlighting the need for further research on mitochondrial genome evolution and function in plants.

Phylogenomic analyses shed new light on the spatiotemporal evolution of global larches: Implications for the dynamics of boreal forests

As the Earth warms, understanding the long-term dynamics of forest ecosystems is essential for guiding forest management and biodiversity conservation. Insights from past dynamics may provide valuable lessons for managing today's forests. Here, we investigated the spatiotemporal evolution of global larches to gain further insights into how boreal forests change over time. We first reconstructed a highly resolved and robust phylogeny of Larix covering all widely recognized species, using both transcriptome-based 1,301 orthologous genes (OGs) and plastid genomes. In sharp contrast to previous studies, an unexpected deep split between the circumboreal and Qinghai-Tibetan Plateau (QTP) larches was revealed in our study. Within each lineage, two geographically distinct clades were further resolved. Biogeographical analyses suggest that Larix might have an origin of Eocene in high-latitude uplands, and during the Miocene, all extant species have appeared. Cenozoic climate- and orogeny-triggered vicariance likely played a major role in the divergence of global larches. Our results also demonstrate that the proto-boreal forest biome may have a relatively old origin back to the early Miocene, and significant winnowing and species alteration would have occurred as the climate shifted to much colder and drier conditions during the Neogene. Ecological niche analyses show various responses of the circumboreal and QTP larches under different climate scenarios, but both lineages are negatively impacted by warming climates. These findings have important conservation implications given the sensitivity of boreal forests in the face of global warming. Our work further emphasizes the importance of a solid phylogenetic framework for evolutionary and biogeographical inferences.

The planktonic freshwater ciliate Balanion planctonicum (Ciliophora, Prostomatea): A cryptic species complex or a "complex species"?

The globally distributed ciliate Balanion planctonicum is a primary consumer of phytoplankton spring blooms. Due to its small size (~20 μm), identification and quantification by molecular tools is preferable as an alternative to the laborious counting of specimen in quantitative protargol stains. However, previous sequencing of the 18S rDNA V9 region of B. planctonicum from Lake Zurich (Switzerland) and subsequent quantification by fluorescence in situ hybridization yielded significantly lower cell numbers than using morphotype counting. This raised the question of whether B. planctonicum shows a cryptic diversity or whether it is just a 'complex species' with intra-clonal polymorphisms. Over three years, we established numerous monoclonal cultures, and long-read sequencing of rDNA operons revealed four distinct dominant haplotypes (BpHs 1-4). The gene sequences of BpHs 1 and 3 differed by 6% and did not share intra-clonal polymorphisms, providing evidence for two distinct clades. Furthermore, phylogenetic analyses corroborate the sister relationship between Balanion and Askenasia (plus Hexasterias and Radiosperma). Morphologically, the two Balanion clades are nearly indistinguishable with small differences in macronucleus size and in the cell length to width ratio. CARD-FISH analyses indicated that the diversity of B. planctonicum is even more extensive with still unidentified clades.

Three Novel Spider Genomes Unveil Spidroin Diversification and Hox Cluster Architecture: Ryuthela nishihirai (Liphistiidae), Uloborus plumipes (Uloboridae) and Cheiracanthium punctorium (Cheiracanthiidae)

Spiders are a hyperdiverse taxon and among the most abundant predators in nearly all terrestrial habitats. Their success is often attributed to key developments in their evolution such as silk and venom production and major apomorphies such as a whole-genome duplication. Resolving deep relationships within the spider tree of life has been historically challenging, making it difficult to measure the relative importance of these novelties for spider evolution. Whole-genome data offer an essential resource in these efforts, but also for functional genomic studies. Here, we present de novo assemblies for three spider species: Ryuthela nishihirai (Liphistiidae), a representative of the ancient Mesothelae, the suborder that is sister to all other extant spiders; Uloborus plumipes (Uloboridae), a cribellate orbweaver whose phylogenetic placement is especially challenging; and Cheiracanthium punctorium (Cheiracanthiidae), which represents only the second family to be sequenced in the hyperdiverse Dionycha clade. These genomes fill critical gaps in the spider tree of life. Using these novel genomes along with 25 previously published ones, we examine the evolutionary history of spidroin gene and structural hox cluster diversity. Our assemblies provide critical genomic resources to facilitate deeper investigations into spider evolution. The near chromosome-level genome of the 'living fossil' R. nishihirai represents an especially important step forward, offering new insights into the origins of spider traits.

First report of Penicillium brevicompactum causing disease in Pleurotus ostreatus

Oyster mushroom (Pleurotus ostreatus) is the second most produced mushroom globally, but increased production is linked to new diseases. This study reports the first occurrence of Penicillium brevicompactum on P. ostreatus mushrooms. Symptoms, identified in the primordia, include atrophy, malformation, drying, and sporulation, causing up to 100% losses. The pathogen was confirmed with 99% identity via ITS region analysis and phylogenetic comparison. The research highlights P. brevicompactum's infection of mushroom primordia, emphasizing the need for pathogen identification and preventive measures to mitigate production losses.

A trivalent mucosal vaccine encoding phylogenetically inferred ancestral RBD sequences confers pan-Sarbecovirus protection in mice

The continued emergence of SARS-CoV-2 variants and the threat of future Sarbecovirus zoonoses have spurred the design of vaccines that can induce broad immunity against multiple coronaviruses. Here, we use computational methods to infer ancestral phylogenetic reconstructions of receptor binding domain (RBD) sequences across multiple Sarbecovirus clades and incorporate them into a multivalent adenoviral-vectored vaccine. Mice immunized with this pan-Sarbecovirus vaccine are protected in the upper and lower respiratory tracts against infection by historical and contemporary SARS-CoV-2 variants, SARS-CoV, and pre-emergent SHC014 and Pangolin/GD coronavirus strains. Using genetic and immunological approaches, we demonstrate that vaccine-induced protection unexpectedly is conferred principally by CD4+ and CD8+ T cell-mediated anamnestic responses. Importantly, prior mRNA vaccination or SARS-CoV-2 respiratory infection does not alter the efficacy of the mucosally delivered pan-Sarbecovirus vaccine. These data highlight the promise of a phylogenetic approach for antigen and vaccine design against existing and pre-emergent Sarbecoviruses with pandemic potential.

The whole chromosome-level genome provides resources and insights into the endangered fish Percocypris pingi evolution and conservation

BACKGROUND

Percocypris pingi (Tchang) was classified as Endangered on the Red List of China's Vertebrates in 2015 and is widely distributed in the Upper Yangtze River. Although breeding and release into wild habitats have been performed for this commercially important fish in recent years, low genetic diversity has been found in wild populations. Genomic resources are strongly recommended before formulating and carrying out conservation strategies for P. pingi. Thus, there is an urgent need to conserve germplasm resources and improve the population diversity of P. pingi. To date, the whole genome of P. pingi has not been reported.

RESULTS

In our study, we constructed the first chromosome-level genome of P. pingi by high-throughput chromosome conformation capture (Hi-C) technology and PacBio long-read sequencing. The assembled genome was 1.7 Gb in size, with an N50 of 17,692 bp and a GC content from circular consensus sequencing of 37.67%. The Hi-C results again demonstrated that P. pingi was tetraploid (n = 98), with the genome consisting of 24-type and 25-type chromosomes. Chr.19 of the 24-type chromosomes in P. pingi resulted from the fusion of chr.19 and chr.22 in zebrafish. The divergence times between 24-type and 25-type chromosomes was around 6.1 million years ago. A total of 25,198 and 25,291 protein-coding genes were obtained from the 24-type and 25-type chromosomes, respectively. The ploidy of P. pingi is an allotetraploid. A total of 8,741 genes of P. pingi were clustered into 4,378 gene families that were shared with 14 other species, and the P. pingi genome had 68 unique gene families. Phylogenetic analyses indicated that P. pingi was most closely related to Schizothorax oconnori, and the genes were clustered on one branch. We identified 166 significantly expanded gene families and 173 significantly contracted gene families in P. pingi. The most enriched positive protein-coding genes, such as Bmp-4, Etfdh, homeobox protein HB9, and ATG3, were screened.

CONCLUSION

Our study provides a high-quality chromosome-anchored reference genome for P. pingi and provides sufficient information on the chromosomes, which will lead to valuable resources for genetic, genomic, and biological studies of P. pingi and for improving the genetic diversity, population size, and scientific conservation of endangered fish and other key cyprinid species in aquaculture.

Transglutaminase mediates the hardening of fish egg envelope produced by duplication of factor XIIIA gene during the evolution of Teleostei

During the fertilization of fish eggs, the hardening of the egg envelope is mediated by transglutaminase (hTGase). After fertilization, TGase undergoes processing. We isolated hTGase from extracts of unfertilized and water-activated rainbow trout eggs. Rainbow trout hTGase (Rt-hTGase) appeared as an 80 kDa protein, and its processed form was 55 kDa. Their N-terminal amino acid sequences were nearly identical, suggesting processing in the C-terminal region. The specific activities were not significantly different, indicating that C-terminal processing does not activate the enzyme itself. We cloned the cDNA by reverse transcription polymerase chain reaction (RT-PCR) using degenerate primers followed by RACE-PCR. The deduced amino acid sequence of the cDNA was similar to that of factor XIII subunit A (FXIIIA). Molecular phylogenetic and gene syntenic analyses clearly showed that hTGase was produced by duplication of FXIIIA during the evolution to Teleostei. The 55 kDa processed form of Rt-hTGase is predominantly composed of an enzyme domain predicted from the amino acid sequence of the cDNA. It is hypothesized that the C-terminal domain of Rt-hTGase binds to egg envelope proteins, and that processing allows the enzyme to move freely within the egg envelope, increasing substrate-enzyme interaction and thereby accelerating hardening.

Molecular Epidemiology, Transmission, and Evolution of Rubella Virus Circulating in Tianjin, China, Between 2009 and 2020

Rubella is listed as a disease that needs to be eliminated worldwide by the World Health Organization. This study aimed to investigate rubella epidemiology and genetic characteristics based on data from 12 years of laboratory-based surveillance (2009-2020) in Tianjin and to provide baseline genotype data for monitoring future rubella control efforts. We collected RV-positive throat swab samples from confirmed rubella cases during 2009-2020 in Tianjin to isolate RV, amplify and sequence target gene fragments, construct phylogenetic trees, and analyze nucleotide homologies. Four rubella isolates were chosen for whole genome sequencing. The epidemiological data of rubella cases were collected to describe and analyze the epidemiological characteristics of the rubella outbreak. Most cases (87.6%) occurred between March and June, and the peak incidence was observed in May. The age of the reported rubella cases ranged from almost 1 month to 82 years, most were between 10 and 29 years old (83.3%). Almost half (48.3%) of the confirmed rubella cases were from just four districts (Beichen District, Binhai New Area, Hebei District, and Nankai District). A total of 211 rubella virus strains were obtained during 2009-2020, phylogenetic analyses identified four lineages, including 1E-L1, 1E-L2, 2B-L1, and 2B-L2c, with high homologies of nucleotide sequences compared with RV strains from other provinces of China. Recombination analysis indicated that strain RVi/Tianjin.CHN/37.19/1 a possible recombination strain by 7 analysis methods, with p-values of 4.993 × 10-28-2.922 × 10-4. Our study provided comprehensive data on rubella epidemiology and the first information on rubella genotypes in Tianjin. Clear evidence of recombination was found, indicating that RV has the potential to continually mutate, so close monitoring of the genetic variations of wild-type rubella virus strains is necessary. Rubella viruses were highly conserved at the genomic level, the incidence of rubella in Tianjin, as well as in China, has sustains at a low level, which gives us the idea that the rubella control and elimination goal could be achieved in the near future if strengthened RV surveillance continues and vaccine immunization coverage maintaining at the high level.

Genetic diversity of dengue virus circulating in the Philippines (2014-2019) and comparison with dengue vaccine strains

Dengue virus has four distinct serotypes and the genetic diversity within each of the four serotypes contribute to its complexity. An important aspect of dengue molecular evolutionary studies has been the dissection of the extent and structure of genetic variation among major genotypes within each serotype. It is important to understand the role of dengue genetic variability and its potential role and impact in the effectiveness of the dengue vaccine. Demographic data and blood were collected from patients seen at a tertiary hospital in the Philippines and clinically diagnosed with dengue from 2014-2019. Dengue virus (DENV) RT-PCR was used to confirm infection and positive samples underwent whole genome sequencing. Phylogenetic analysis was performed on 127 samples (25 DENV-1, 19 DENV-2, 70 DENV-3, and 13 DENV-4). We observed a serotype shift in 2014 and 2022. We detected the following genotypes per serotype for the wild-type (WT) DENV sequences: genotype IV (DENV-1), cosmopolitan (DENV-2), genotype I (DENV-3) and genotype IIa (DENV-4). WT DENV belonged to different genotypes versus the QDENGA strains and except for DENV-4, belonged to different genotypes versus the Dengvaxia strains. Comparing Dengvaxia vaccine sequences with WT DENV, we observed 23, 24, 34, and 9 positions with amino acid changes in the entire envelope protein, with 1, 5, 1, and 2 positions with amino acid changes identified among the important human monoclonal antibodies (mAbs) targeted epitope positions. We detected 24, 25, 36 and 12 positions with amino acid changes in the E protein with 0, 5, 1, and 2 positions with amino acid changes among the important mAbs targeted epitope positions for DENV-1, DENV-2, DENV-3, and DENV-4, respectively when comparing QDENGA vaccine sequences with the WT DENV. We showed low genotype complexity, genetically distinct clades and local evolution for DENV circulating in the Philippines.

Phylotranscriptomic and ecological analyses reveal the evolution and morphological adaptation of Abies

Coniferous forests are under severe threat of the rapid anthropogenic climate warming. Abies (firs), the fourth-largest conifer genus, is a keystone component of the boreal and temperate dark-coniferous forests and harbors a remarkably large number of relict taxa. However, the uncertainty of the phylogenetic and biogeographic history of Abies significantly impedes our prediction of future dynamics and efficient conservation of firs. In this study, using 1,533 nuclear genes generated from transcriptome sequencing and a complete sampling of all widely recognized species, we have successfully reconstructed a robust phylogeny of global firs, in which four clades are strongly supported and all intersectional relationships are resolved, although phylogenetic discordance caused mainly by incomplete lineage sorting and hybridization was detected. Molecular dating and ancestral area reconstruction suggest a Northern Hemisphere high-latitude origin of Abies during the Late Cretaceous, but all extant firs diversified during the Miocene to the Pleistocene, and multiple continental and intercontinental dispersals took place in response to the late Neogene climate cooling and orogenic movements. Notably, four critically endangered firs endemic to subtropical mountains of China, including A. beshanzuensis, A. ziyuanensis, A. fanjingshanensis and A. yuanbaoshanensis from east to west, have different origins and evolutionary histories. Moreover, three hotspots of species richness, including western North America, central Japan, and the Hengduan Mountains, were identified in Abies. Elevation and precipitation, particularly precipitation of the coldest quarter, are the most significant environmental factors driving the global distribution pattern of fir species diversity. Some morphological traits are evolutionarily constrained, and those linked to elevational variation (e.g., purple cone) and cold resistance (e.g., pubescent branch and resinous bud) may have contributed to the diversification of global firs. Our study sheds new light on the spatiotemporal evolution of global firs, which will be of great help to forest management and species conservation in a warming world.

Genomic Landscape of Chromosome X Factor VIII: From Hemophilia A in Males to Risk Variants in Females

BACKGROUND

Variants within factor VIII (F8) are associated with sex-linked hemophilia A and thrombosis, with gene therapy approaches being available for pathogenic variants. Many variants within F8 remain variants of uncertain significance (VUS) or are under-explored as to their connections to phenotypic outcomes.

METHODS

We assessed data on F8 expression while screening the UniProt, ClinVar, Geno2MP, and gnomAD databases for F8 missense variants; these collectively represent the sequencing of more than a million individuals.

RESULTS

For the two F8 isoforms coding for different protein lengths (2351 and 216 amino acids), we observed noncoding variants influencing expression which are also associated with thrombosis risk, with uncertainty as to differences in females and males. Variant analysis identified a severe stratification of potential annotation issues for missense variants in subjects of non-European ancestry, suggesting a need for further defining the genetics of diverse populations. Additionally, few heterozygous female carriers of known pathogenic variants have sufficiently confident phenotyping data, leaving researchers unable to determine subtle, less defined phenotypes. Using structure movement correlations to known pathogenic variants for the VUS, we determined seven clusters of likely pathogenic variants based on screening work.

CONCLUSIONS

This work highlights the need to define missense variants, especially those for VUS and from subjects of non-European ancestry, as well as the roles of these variants in women's physiology.

The tetraploid Camellia oleifera genome provides insights into evolution, agronomic traits, and genetic architecture of oil Camellia plants

Camellia oleifera is an economically important woody oil plant. Complex ploidy and lack of genomic information have seriously hindered the molecular breeding of C. oleifera. Here, we present an 11.43-Gb haplotype-resolved, chromosome-level genome assembly of tetraploid C. oleifera (COL-tetra). Methods employed in this study support the conclusion that COL-tetra is an autotetraploid and probably originates from genome doubling of the diploid C. brevistyla. In addition, DNA methylation plays a significant role in imbalanced allelic expression and seed development. Genetic divergence analyses reveal significant differentiation signals for flowering time between spring-flowering and autumn-flowering oil Camellia species, which probably account for reproductive isolation between species with distinct flowering times. Strong introgression signals are detected between COL-tetra and C. sasanqua and between C. vietnamensis and COL-hexa, which might affect the development of agronomic traits and environmental adaptability. This study provides valuable insights into the evolution, agronomic trait development, and genetic architecture of oil Camellia plants.