Genome Research Articles

Comprehensive Analysis of Codon Usage Bias in Human Papillomavirus Type 51.

Human papillomavirus type 51 (HPV-51) is associated with various cancers, including cervical cancer. Examining the codon usage bias of the organism can offer valuable insights into its evolutionary patterns and its relationship with the host. This study comprehensively analyzed codon usage bias in HPV-51 by examining 64 complete genome sequences sourced from the NCBI GenBank database. Our analysis revealed no noteworthy preference for codon usage in HPV-51 overall. However, there was a noticeable bias towards A/T-ending codons, accompanied by GC3s below 32%. Dinucleotide frequency analysis revealed reduced frequencies for ApA, CpG, and TpC dinucleotides, while CpA and TpG dinucleotides were more frequent than others. Relative Synonymous Codon Usage analysis revealed 30 favored codons, primarily concluding with A/T nucleotides. Further analysis using Parity Rule 2, Effective Number of Codons plot, and neutrality plot indicated a balance between mutational pressure and natural selection, with natural selection being the primary force shaping codon usage bias. The Isoacceptor tRNA Pool analysis indicates that HPV-51 has a higher translation efficiency within the human cellular translational system. Moreover, the Codon Adaptation Index and Relative Codon Deoptimization Index analyses suggested a moderate adaptation of HPV-51 to human codon preferences. Our discoveries offer valuable perspectives on how HPV-51 evolves and uses genetic codes, contributing to a deeper comprehension of its endurance and disease-causing potential.

Multiple Acquisitions of XopJ2 Effectors in Populations of Xanthomonas perforans.

Type III effectors (T3Es) are major determinants of Xanthomonas virulence and targets for resistance breeding. XopJ2 (synonym AvrBsT) is a highly conserved YopJ-family T3E acquired by X. perforans, the pathogen responsible for bacterial spot disease of tomato. In this study, we characterized a new variant (XopJ2b) of XopJ2, which is predicted to have a similar three-dimensional (3D) structure as the canonical XopJ2 (XopJ2a) despite sharing only 70% sequence identity. XopJ2b carries an acetyltransferase domain and the critical residues required for its activity, and the positions of these residues are predicted to be conserved in the 3D structure of the proteins. We demonstrated that XopJ2b is a functional T3E and triggers a hypersensitive response (HR) when translocated into pepper cells. Like XopJ2a, XopJ2b triggers HR in Arabidopsis that is suppressed by the deacetylase, SOBER1. We found xopJ2b in genome sequences of X. euvesicatoria, X. citri, X. guizotiae, and X. vasicola strains, suggesting widespread horizontal transfer. In X. perforans, xopJ2b was present in strains collected in North America, Africa, Asia, Australia, and Europe, whereas xopJ2a had a narrower geographic distribution. This study expands the Xanthomonas T3E repertoire, demonstrates functional conservation in T3E evolution, and further supports the importance of XopJ2 in X. perforans fitness on tomato. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Isolation and characterisation of novel lytic bacteriophages for therapeutic applications in biofilm-associated prosthetic joint infections

Abstract Prosthetic joint infections are devastating complications of joint arthroplasties. Without effective management, they can lead to limb amputation and even death. A significant proportion of these infections is caused by the primarily commensal Coagulase-negative Staphylococci pathogens, which form thick, antibiotic-resistant biofilms at the site of infection. Combinatorial therapy involving antibiotics and bacteriophages may represent a strategy to overcome resistance. Previous research indicates that as bacteria develop resistance to antibiotics, they often become more susceptible to bacteriophages. In this study, we produced a cocktail of novel bacteriophages and assessed their viability to eradicate nosocomial staphylococcal biofilms. Here, we used clinical isolates from prosthetic joint infections to isolate and identify four new bacteriophages from sewage effluent. These novel phages were characterized through electron microscopy and full genome sequencing. Subsequently, we combined them into a phage cocktail, which effectively re-sensitized biofilms to vancomycin and flucloxacillin. Notably, this phage cocktail demonstrated low cytotoxicity in vitro to human epithelial cells, even when used alongside antibiotic treatments. These findings highlight the potential of the phage cocktail as a tool to increase antibiotic treatment success in prosthetic joint infections.

Multiple genotypes of a quarantine plant pathogen detected in New Zealand indigenous plants located in a botanical garden overseas

AbstractXylella fastidiosa is a xylem‐limited bacterial plant pathogen transmitted by insect vectors. It infects a wide range of plant species and causes devastating diseases. Botanical gardens are global repositories of plant diversity exposed to local biotic and abiotic stresses. We used molecular diagnostic tools for the detection of X. fastidiosa in a collection of New Zealand indigenous plants grown in a X. fastidiosa‐infected Californian area to determine if any species were infected with this bacterial pathogen and to help inform biosecurity responses. To this end, 130 New Zealand indigenous plant species comprising 72 genera, growing in the University of California Botanical Garden at Berkeley, California, were screened for X. fastidiosa. Multiple PCR‐based methods were used to detect the pathogen at the subspecies and sequence‐type levels directly from plant material; nine plant species tested positive by at least two PCR‐based methods. All nine infections were identified as X. fastidiosa subsp. multiplex sequence types 6 or 7 by the amplification of seven housekeeping genes. Three strains were cultured in vitro and their whole genome sequences were obtained; these strains belonged to three distinct clades within subspecies multiplex, indicating that the infections were not transmitted among these New Zealand indigenous plant species. The information gathered in this study will help to assess the risk of X. fastidiosa to New Zealand indigenous flora and the potential spillover to crops of agricultural importance. The work also shows the applied value of botanical garden collections as sentinels for international plant pathogen biosecurity risk assessment.

Genome Sequencing Identifies 13 Novel Candidate Risk Genes for Autism Spectrum Disorder in a Qatari Cohort

Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by deficits in social communication, restricted interests, and repetitive behaviors. Despite considerable research efforts, the genetic complexity of ASD remains poorly understood, complicating diagnosis and treatment, especially in the Arab population, with its genetic diversity linked to migration, tribal structures, and high consanguinity. To address the scarcity of ASD genetic data in the Middle East, we conducted genome sequencing (GS) on 50 ASD subjects and their unaffected parents. Our analysis revealed 37 single-nucleotide variants from 36 candidate genes and over 200 CGG repeats in the FMR1 gene in one subject. The identified variants were classified as uncertain, likely pathogenic, or pathogenic based on in-silico algorithms and ACMG criteria. Notably, 52% of the identified variants were homozygous, indicating a recessive genetic architecture to ASD in this population. This finding underscores the significant impact of high consanguinity within the Qatari population, which could be utilized in genetic counseling/screening program in Qatar. We also discovered single nucleotide variants in 13 novel genes not previously associated with ASD: ARSF, BAHD1, CHST7, CUL2, FRMPD3, KCNC4, LFNG, RGS4, RNF133, SCRN2, SLC12A8, USP24, and ZNF746. Our investigation categorized the candidate genes into seven groups, highlighting their roles in cognitive development, including the ubiquitin pathway, transcription factors, solute carriers, kinases, glutamate receptors, chromatin remodelers, and ion channels.

Universal newborn screening using genome sequencing: early experience from the GUARDIAN study.

For more than 20 years there has been speculation about a future in which newborns are routinely screened at birth for genetic disorders using genome sequencing, but prospective large-scale studies assessing this vision have only recently begun. Genome sequencing may provide a means of expanding the scope of conditions included in newborn screening programs and improving the positive predictive value of traditional newborn screening. However, the use of genome sequencing for newborn screening has also raised concerns including acceptability, equity, and scalability. By reviewing the initial results of the GUARDIAN study and contrasting them with other pilot studies investigating the use of genome sequencing for large-scale newborn screening, we highlight how the lessons learned from these studies are shaping the future for the implementation of truly universal and equitable newborn genomic screening.

Bla SED-1 beta-lactamase-producing Citrobacter sedlakii isolated from horses and genomic comparison with human-derived isolates.

We aim to detect beta-lactamase-producing Citrobacter sedlakii from horses and compare the genomic characteristics with isolates from humans.Methods and Result: We characterized phenotypically and genotypically nine C. sedlakii isolates from the feces of horses and then compared them to human-derived isolates using whole genome sequencing and phylogenomic methods. Seven isolates (7/9) were ampicillin-resistant, while at least one isolate was resistant to ceftriaxone, gentamicin, meropenem, and streptomycin. All nine isolates were carriers of the chromosomal-mediated blaSED-1 beta-lactamase gene which confer resistance to ampicillin. One isolate was positive for the mcr-9 gene that confers resistance to colistin, and another isolate had the aac(6')-lid gene that confers resistance to aminoglycosides. Seven isolates (7/9) were carriers of genes that confer metal resistance to copper, silver, and arsenic. Phylogenetically, two horse-derived isolates clustered together with two human-derived isolates from the NDARO database. The results from our study provide insight into the antimicrobial susceptibility of C. sedlakii in horses which was previously lacking, and the specific beta-lactamase gene mediating resistance.

DGCNN approach links metagenome-derived taxon and functional information providing insight into global soil organic carbon

Metagenomics can provide insight into the microbial taxa present in a sample and, through gene identification, the functional potential of the community. However, taxonomic and functional information are typically considered separately in downstream analyses. We develop interpretable machine learning (ML) approaches for modelling metagenomic data, combining the biological representation of species with their associated genetically encoded functions within models. We apply our methods to investigate soil organic carbon (SOC) stocks. First, we combine a diverse global set of soil microbiome samples with environmental data, improving the predictive performance of classic ML and providing new insights into the role of soil microbiomes in global carbon cycling. Our network analysis of predictive taxa identified by classical ML models provides context for their ecological significance, extending the focus beyond just the most predictive taxa to ‘hidden’ features within the model that might be considered less predictive using standard methods for explainability. We next develop unique graph representations for individual microbiomes, linking microbial taxa to their associated functions directly, enabling predictions of SOC via deep graph convolutional neural networks (DGCNNs). Interpretation of the DGCNNs distinguished between the importance of functions of key individual species, providing genome sequence differences, e.g., gene loss/acquisition, that associate with SOC. These approaches identify several members of the Verrucomicrobiaceae family and a range of genetically encoded functions, e.g., related to carbohydrate metabolism, as important for SOC stocks and effective global SOC predictors. These relatively understudied but widespread organisms could play an important role in SOC dynamics globally.

Genomic landscape of adult testicular germ cell tumours in the 100,000 Genomes Project

Testicular germ cell tumours (TGCT), which comprise seminoma and non-seminoma subtypes, are the most common cancers in young men. In this study, we present a comprehensive whole genome sequencing analysis of adult TGCTs. Leveraging samples from participants recruited via the UK National Health Service and data from the Genomics England 100,000 Genomes Project, our results provide an extended description of genomic elements underlying TGCT pathogenesis. This catalogue offers a comprehensive, high-resolution map of copy number alterations, structural variation, and key global genome features, including mutational signatures and analysis of extrachromosomal DNA amplification. This study establishes correlations between genomic alterations and histological diversification, revealing divergent evolutionary trajectories among TGCT subtypes. By reconstructing the chronological order of driver events, we identify a subgroup of adult TGCTs undergoing relatively late whole genome duplication. Additionally, we present evidence that human leukocyte antigen loss is a more prevalent mechanism of immune disruption in seminomas. Collectively, our findings provide valuable insights into the developmental and immune modulatory processes implicated in TGCT pathogenesis and progression.

Global invasion history with climate-related allele frequency shifts in the invasive Mediterranean fruit fly (Diptera, Tephritidae: Ceratitis capitata)

The Mediterranean fruit fly (Ceratitis capitata) is a globally invasive species and an economically significant pest of fruit crops. Understanding the evolutionary history and local climatic adaptation of this species is crucial for developing effective pest management strategies. We conducted a comprehensive investigation using whole genome sequencing to explore (i) the invasion history of C. capitata with an emphasis on historical admixture and (ii) local climatic adaptation across African, European, Central, and South American populations of C. capitata. Our results suggest a stepwise colonization of C. capitata in Europe and Latin America in which Mediterranean and Central American populations share an ancestral lineage. Conversely, South American invasion history is more complex, and our results partly suggest an old secondary invasion into South America from Europe or a colonization of South America directly from Africa, followed by admixture with an European lineage. Throughout its invasive range, C. capitata is challenged with diverse climatic regimes. A genome wide association study identified a relationship between allele frequency changes and specific bioclimatic variables. Notably, we observed a significant allele frequency shift related to adaptation to cold stress (BIO6), highlighting the species’ ability to rapidly adapt to seasonal variations in colder climates.

Identifying DNA Variants in a Turkish Cohort with Inner Ear Anomalies.

To determine the genetic causes of sensorineural hearing loss (SNHL) associated with inner ear anomalies, 11 unrelated Turkish individuals diagnosed with SNHL and an inner ear anomaly using temporal bone computed tomography and inner ear magnetic resonance imaging underwent exome or whole genome sequencing to identify underlying genetic defects. None of the individuals was diagnosed with a recognized syndrome. Four of the 11 probands were homozygous for SLC26A4 variants, c.283G>A, c.845G>A, c.1061T>C, and c.1198delT. Another proband was homozygous for a TECTA variant, c.4163G>A. Patients with variants of the SLC26A4 gene had bilateral enlarged vestibular aqueduct, bilateral incomplete partition type 2 anomaly, bilateral hypoplastic cochlea and bilateral enlarged vestibular aqueduct plus hypoplastic cochlea anomaly. Patients with the variant TECTA gene had bilateral hypoplastic cochlea. This study identified variants of SLC26A4 in 36% of probands with inner ear anomalies. While we identified a variant of the TECTA gene in a proband with cochlear hypoplasia, further studies are needed to see if TECTA variants can cause cochlear malformations.

A comprehensive map of copy number variations in dromedary camels based on whole genome sequence data

Copy number variants (CNVs) are structural variants within the eukaryotic genome that vary among individuals of a species. These variants have been associated with different phenotypic traits, making them a valuable consideration as markers for designing breeding programmes. In this study, whole genome sequence data of 60 dromedary camel samples originating from the Arabian Peninsula were analyzed to construct a comprehensive dromedary CNV map. Utilizing four CNV callers employing read-depth, split-read and paired-end mapping approaches, a total of 37,519 CNV events (17,847 deletions and 19,672 duplications) were called on the dromedary autosomes. These CNV events were merged into 2,557 regions, categorized as 1,322 losses, 122 gains, and 1,113 “mixed regions” comprising both types. The cumulative size of the CNV regions amounted to 22.5 Mb, covering roughly 1.16% of the dromedary autosomes. Approximately 32% of the defined CNV regions (comprising 60% losses, 18% gains, and 0.27% mixed regions) were found in ≥ 90% of the dromedary samples, classifying them as prevalent regions. Genes with biological functions related to the different adaptive physiologies of dromedary camels, such as fertility, heat stress, musculoskeletal development, and fat metabolism, were overlapping with or in close proximity to ~ 68% of the defined CNV regions, demonstrating their potential role in dromedaries’ physiology. This study presents the first comprehensive CNV map of dromedary camels and builds on the present knowledge in understanding the genetic structure of this species.

Isolation and identification of a novel goose-origin reovirus GD218 and its pathogenicity experiments

Since 2020, a novel goose-derived reovirus, characterized by goose hemorrhagic hepatitis, has emerged in the goose breeding industry of Guangdong province, China, leading to significant economic losses in the poultry sector. To study the genetic variation of novel goose reovirus (NGRV) in Guangdong province, this experiment utilized goose embryonic fibroblast cells for virus isolation. RT-PCR was conducted to identify, amplify, clone, and sequence the complete genome of the NGRV isolated from Zhaoqing. The genomic sequences were compared with reference strains to construct a phylogenetic tree. Moreover, animal pathogenicity, excretion patterns, and pathological sections were examined. The results showed that liver and spleen samples from geese suspected of NGRV infection were used for isolation, resulting in the identification of a reovirus presumed to originate from geese, designated as GD218. In terms of genomic structure and sequence homology, GD218 closely resembles the novel duck reovirus, differing significantly from earlier isolated NDRV strains (J18, NP03, SD12, etc.) in genetic composition (nt: 80.6–97.9%, aa: 94.3–98.9%). However, it is similar to strains isolated after 2018, such as XT18, SY, QR, YL, LY20, etc. (nt: 95.3–98.9%, aa: 98.6–99.7%). Therefore, based on phylogenetic analysis, GD218 is hypothesized to be a novel type of goose-origin reovirus homologous to the novel duck reovirus.

Whole genome sequencing of M. tuberculosis for disease control in high-burden settings: study protocol for a cluster randomized controlled trial evaluating different community-wide intervention strategies in rural Madagascar

BackgroundRetrospective and descriptive molecular epidemiology studies have shown that Mycobacterium tuberculosis whole genome sequencing can identify outbreaks and disease transmission events with higher resolution than conventional epidemiological investigations. Those studies have strengthened our understanding of genomic polymorphisms correlating with person-to-person transmission and helped resolve putative transmission clusters. To date, systematic genomic surveillance programs implemented for M. tuberculosis were only implemented in low-incidence settings. The purpose of this study is to determine whether there is an impact of routine M. tuberculosis whole genome sequencing on tuberculosis case detection in a high-incidence setting.MethodsA cluster randomized controlled trial will be performed. Forty-eight rural village groups (or Fokontany) in the Vohibato district of Madagascar will be randomized to one of three interventions arms. Arm 1 (standard of care) involves healthcare facility-based passive case detection with smear microscopy testing. Arm 2 (best practice) consists of active case finding and Xpert MTB/RIF Ultra PCR testing followed by household contact investigations. Arm 3 (novel intervention) includes the same interventions as arm 2, with addition of sputum culture and M. tuberculosis whole genome sequencing for all newly diagnosed cases. In arm 3, molecular suggested putative outbreaks are investigated, and additional TB suspects are appropriately tested. The intervention observational period will be 2 years. The primary outcome will be the number of detected cases/100,000/year in each arm after 1 year of intervention.DiscussionThis study is designed to determine whether there is an impact of prospective whole genome sequencing-based molecular typing on tuberculosis case detection in high-incidence settings. Investigating potential outbreaks and focusing active case finding in spatiotemporal settings where disease transmission is suggested by genomic typing is hypothesized to improve case detection in rural communities.Trial registrationClinicalTrials.gov NCT05406453. Retrospectively registered on June 6, 2022.

Genomic characterization of Pantoea dispersa A003 isolated from a clinical patient

IntroductionPantoea dispersa is a Gram-negative bacterium generally considered as a plant pathogen and rarely causes human infections. To date, there have been 13 studies that have documented clinical infections linked to P. dispersa, with a primary emphasis on the initial identification of this pathogen. The genomic features and the mechanisms underlying the pathogenesis of P. dispersa remain largely uninvestigated. In the present study, we describe a clinical infection caused by P. dispersa and provide the first genomic analysis of this bacterium.MethodsThe bacterial strain designated A003 was isolated from blood samples. Preliminary identification of strain A003 was conducted using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) technology (VITEK® MS, bioMérieux, France). Biochemical and antimicrobial susceptibility assessments were carried out utilizing the VITEK-2 compact automated microbial analysis system (bioMérieux, France). Additionally, whole genome sequencing and subsequent analysis were performed to further elucidate the potential pathogenicity.ResultsThe bacterial isolate was cultured overnight at 35°C in a CO2-enriched environment on Columbia blood agar, resulting in the appearance of a white, smooth, Gram-negative rod-shaped bacterium with diameters ranging from 1 to 2 mm. Identification of strain A003 was achieved with a high confidence level of 99.9% as P. dispersa using MALDI-TOF mass spectrometry. The average nucleotide identity (ANI) value between strain A003 and the reference strain P. dispersa DSM 30073T was 98.08%, while the DNA–DNA hybridization (DDH) value was 84.10% (Formula 2) based on genome sequencing data, which further confirmed that A003 belonged to the P. dispersa species. Comprehensive analysis revealed the presence of 372 virulence factors, 15 antibiotic resistance genes, 222 carbohydrate-active enzymes, and 666 genes related to Type III secretion system (T3SS) effector proteins, as identified through the core databases of VFDB (Virulence Factors of Pathogenic Bacteria), CARD (Comprehensive Antibiotic Resistance Database), CAZY (Carbohydrate-Active enZYmes Database), and T3SS. The virulence factors included type IV pili (TFP), type VI secretion system, flagella, iron uptake system, and ompA, which are implicated in bacterial pathogenicity. The antibiotic resistance profile indicated resistance to fluoroquinolones, cephalosporins, penams, macrolides, and aminoglycosides, as annotated by the CARD database.ConclusionThe draft genome sequenced represents the inaugural genomic sequence of P. dispersa derived from clinical sources. This advancement may enhance clinical practitioners’ comprehension of the organism’s clinical attributes and serve as a foundational resource for future research into its virulence, antibiotic resistance, and host–pathogen interactions.

GTasm: a genome assembly method using graph transformers and HiFi reads

MotivationGenome assembly aims to reconstruct the whole chromosome-scale genome sequence. Obtaining accurate and complete chromosome-scale genome sequence serve as an indispensable foundation for downstream genomics analyses. Due to the complex repeat regions contained in genome sequence, the assembly results commonly are fragmented. Long reads with high accuracy rate can greatly enhance the integrity of genome assembly results.ResultsHere we introduce GTasm, an assembly method that uses graph transformer network to find optimal assembly results based on assembly graphs. Based on assembly graph, GTasm first extracts features about vertices and edges. Then, GTasm scores the edges by graph transformer model, and adopt a heuristic algorithm to find optimal paths in the assembly graph, each path corresponding to a contig. The graph transformer model is trained using simulated HiFi reads from CHM13, and GTasm is compared with other assembly methods using real HIFI read set. Through experimental result, GTasm can produce well assembly results, and achieve good performance on NA50 and NGA50 evaluation indicators. Applying deep learning models to genome assembly can improve the continuity and accuracy of assembly results. The code is available from https://github.com/chu-xuezhe/GTasm.

Global research landscape on the genetics of congenital heart disease: A bibliometric and visualized analysis via VOSviewer and CiteSpace.

Genetic factors play a significant role in the development of congenital heart disease (CHD). Many studies on the genetics of CHD have been published worldwide; however, no research has assessed and mapped the global research landscape of these studies. This bibliometric and visualized study aimed to delineate research hotspots and trends in the field of CHD genetics. Scientific papers on the genetics of CHD from January 1, 1950, to December 31, 2023, were obtained by searching the Web of Science Core Collection. The bibliometric metadata of each chosen research paper were extracted, analyzed, and visualized using tools such as Microsoft Excel 2021, VOSviewer, and CiteSpace. The final analysis included 5317 papers discussing the genetics of CHD. The countries and journals that published the highest number of papers were the United States (n = 2118), and American Journal of Medical Genetics Part A (n = 332), respectively. In addition to CHD and genetics, keywords such as tetralogy of Fallot, ventricular septal defect, and atrial septal defect appeared most frequently among 8365 keywords. Eight clusters were formed to categorize the keywords. Keywords such as case-control study, whole genome sequencing, and whole exome sequencing in clusters 6, 7, and 8, respectively, had the latest average publication year among all clusters. To the best of our knowledge, this is the first bibliometric analysis of CHD genetics studies. Tetralogy of Fallot, ventricular septal defect, and atrial septal defect are global research topics. The interactions between environmental and genetic factors in the pathogenesis of CHD, genetic etiology of CHD-associated pulmonary arterial hypertension, and molecular genetics of CHD via high-throughput genomic technology are possible areas of future research on the genetics of CHD.

Isolation and degradation characterization of a 1, 4-dioxane-degrading bacterial strain

To address the potential pollution caused by the carcinogen 1, 4-dioxane in aquatic environments, we isolated a highly efficient 1, 4-dioxane-degrading bacterial strain, designated as DXTK-010, from the groundwater contaminated by 1, 4-dioxane. According to the morphological characteristics, the phylogenetic tree established based on the 16S rRNA gene sequence, and the whole genome sequence, we identified DXTK-010 as Aminobacter aminovorans. This strain demonstrated robust degradation capacity within a temperature range of 20 ℃ to 37 ℃ and a pH range of 5.0 to 8.0. Furthermore, single-factor experiments indicated the optimal degradation conditions at 30 ℃ and pH 7.5. Under the optimal conditions, the strain completely degraded 200 mg/L of 1, 4-dioxane within 24 h, achieving a maximum degradation rate of 9.367 mg/(L·h). The Monod equation was adopted to fit the degradation kinetics of 1, 4-dioxane at different initial concentrations, which revealed a maximum specific degradation rate of 0.224 mg 1, 4-dioxane/(mg protein·h), a half-saturation constant (Ks) of 41.350 mg/L, and a cell yield of 0.130 mg protein/(mg 1, 4-dioxane). Whole genome sequencing revealed a circular chromosome and three plasmids within DXTK-010. Functional gene annotation and analysis underscored the significance of the propane monooxygenase gene cluster and alcohol dehydrogenase gene in facilitating the efficient degradation of 1, 4-dioxane by this strain. DXTK-010 outperformed the existing degraders for 1, 4-dioxane, expanding the strain resources for the bioremediation of 1, 4-dioxane pollution. This study provides a theoretical basis for the practical application of DXTK-010 in the remediation of 1, 4-dioxane pollution.

Whole genome sequencing of Castanea mollissima and molecular mechanisms of sugar and starch synthesis

The chestnut tree exhibits self-incompatibility, where the selection of the male parent (pollen xenia) significantly affects seed starch metabolism, as well as fruit yield and quality. Despite its importance, the molecular mechanisms underlying pollen xenia remains largely unknown. In this study, we utilized the ‘Lan You’ variety of C. mollissima to construct a high-quality reference genome. As a result, a first Telomere-to-telomere (T2T) gap-free genome for this species was successfully assembled. A total of 560 transcription factors and 22 structural genes were identified as consistent across the TO-GCNs, indicating a consistent regulation pattern in the co-expression of genes involved in starch accumulation. These networks were further divided into three sub-networks: T1, T2, and T3. Among these, the T1 and T2 sub-networks exhibited a higher number of structural genes with consistent regulation patterns and were closely associated with sugar biosynthesis. The gene SBE (Camol08G0254600) was identified as the hub gene with the highest degree of connectivity, encoding a key rate-limiting enzyme in the amylopectin biosynthesis pathway. This study provides a foundation for further research on C. mollissima population genetics, genetic improvement, and strategies aimed at enhancing yield and quality.

Janibacter alittae sp. nov., an actinobacterium isolated from the gut of marine sandworm (Alitta virens).

A novel Gram-stain-positive, facultatively anaerobic, non-motile, catalase-positive, oxidase-negative and ovoid cocci, designated as A1S7T, was isolated from the gut of a marine sandworm (Alitta virens). Strain A1S7T exhibited optimal growth at temperatures of 20-30 ℃, pH 6-8 and in the presence of 2-4% (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain A1S7T belonged to the genus Janibacter, exhibiting a similarity of 99.0% to Janibacter cremeus KCTC 49873T, followed by Janibacter anophelis KCTC 19282T (98.8%), Janibacter hoylei KCTC 49872T (98.4%), Janibacter limosus KACC 20518T (98.2%) and Janibacter corallicola KACC 21120T (97.2%). The complete genome sequence of strain A1S7T revealed a genome size of 3360920 bp with a genomic G+C content of 70.1 mol%. The orthologous average nucleotide identity and the digital DNA-DNA hybridization values between strain A1S7T and Janibacter cremeus KCTC 49873T were determined to be 89.5 and 37.2%, respectively. The major respiratory quinone was MK-8(H4). The predominant fatty acids (>10%) included iso-C16:0, C17:1 ω8c, C18:1 ω9c and C17:0. Polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown phosphoglycolipid and three unknown polar lipids. The cell-wall peptidoglycan type was A1γ. The major whole-cell sugars were ribose, mannose and glucose. Based on phenotypic, phylogenetic, genotypic and chemotaxonomic properties, strain A1S7T represents a novel species in the genus Janibacter, for which the name Janibacter alittae sp. nov. is proposed. The type strain is A1S7T (=KCTC 49714T = JCM 36706T).