The ectomycorrhizal fungus Laccaria bicolor is a key symbiotic mutualist in forest ecosystems, where it enhances nutrient uptake and promotes the growth of host trees. Here, we present genome assemblies of 14 geographically distinct strains and progeny of L. bicolor, providing new insights into the intraspecific genomic diversity. Pangenome analysis revealed substantial variation in assembly size (42-96 Mbp), gene content (16,084-26,800 genes), and single nucleotide polymorphism (SNP) density (0.04-12.08 SNPs/kb). This variation likely reflects genuine biological differences among strains adapted to diverse environmental conditions, although differences in assembly quality and repeat content may also play a role. These genomic resources, comprising draft genome assemblies with comprehensive annotations, will facilitate comparative studies of the genetic diversity and functional traits underlying the ecological success of this model ectomycorrhizal fungus.
The Myanmar puddle frog, Phrynoglossus myanhessei, is a recently described, small dicroglossid frog distributed across central and southern Myanmar, typically inhabiting areas adjacent to small stagnant water bodies. With that new species description, rudimentary genome data from 30-fold Illumina sequencing were published as a novel approach in taxonomy to routinely publish genome data for new holotypes. While the data allowed to assemble the entire mitochondrial genome, it was not possible to extract basic population genetic data. Therefore, we present a de novo PacBio CLR genome assembly of P. myanhessei, to aid population genomic, evolutionary and taxonomic studies. The assembled genome has a size of 2.28 Gbp, with a scaffold N50 of 44 kbp and largest scaffold being 270 kbp long. BUSCO analysis indicates a completeness score of 49%, with 26.9% complete and 22.3% fragmented BUSCOs. Approximately 43% of the genome consists of repetitive elements and about 22,500 genes could be predicted. While not an optimal assembly, the new P. myanhessei genome is a valuable resource for follow-up studies and for closing the gap in amphibian genome representation.
Anopheles gambiae or the African malaria mosquito is the main vector of human malaria. G3, is an Anopheles gambiae strain, that was isolated from Gambiae in 1975, We report here a 216.3 Mbp draft genome sequence and assembly for Anopheles gambiae strain G3, with almost 82 thousand scaffold, 53X coverage and a G+C content of 44.5%.
Anopheles stephensi, one of the main mosquito vectors for malaria in Asia. It belongs to the same complex species of Anopheles gambiae. A genome assembly was performed on female Anopheles stephensi, the resulting genome was 201Mbp in size and consisted of 32,280 contigs with an N50 of 21,1 kb and a GC content of 45%.
The molecular basis of parental behavior in burying beetles is not well understood. This study is a first attempt to evaluate the extent of alternative splicing (AS) as a source of transcriptome diversity that may facilitate flexible parenting behavior in this species. RNA-seq datasets from beetle parents exhibiting high or low care behavior and a newly available Nicrophorus orbicollis genome were used to perform AS analysis by AStalavista to comprehensively classify AS events, and specific patterns of splicing variation within and across parental groups were evaluated. Towards functional characterization, AS genes were annotated via protein family analysis. Transcriptome-wide AS profiles for each parental group were established, revealing no specific splicing patterns associated with either sex or parenting phenotype (high or low care behavior). Among simple types of AS events, intron retention was the most common (13%), while mutually exclusive exons were the least common (0.4%), with alternative acceptor (6%) and alternative donor (5%) occurring slightly more often than exon skipping (3%). Functional annotation highlighted AS genes belonging to protein families broadly linked to chemoreception, neuromodulation and JH function, all biological processes essential for the regulation of reproductive behavior and physiology. This analysis was successful in generating a large catalogue of AS events associated with parenting behavior in burying beetles. Additional analyses could expand upon this dataset to include tissue, development and species-specific splice variants, as well as functionally validate AS transcripts via RT-PCR to further clarify the role of functional AS in behavioral regulation in this species.
Discovery, development, and production of new antibiotic drugs in a form safe for human consumption have become increasingly difficult, expensive, and time-consuming, especially with an increase in antibiotic-resistant pathogens. The ESKAPE pathogens are a group of six pathogenic bacteria that can be highly virulent and are likely to, or already have, developed antibiotic resistance to many of the currently available antibiotics. New antibiotics or new activities of existing natural products are needed to combat these multi-drug resistant pathogens. Our approach was to search for soil microbes that produce antimicrobial compounds that could potentially inhibit the growth of the ESKAPE pathogens. We report one draft genome of Chromobacterium and one draft genome of Alcaligenes cultured from soil with antimicrobial activity against Staphylococcus epidermidis, a relative of ESKAPE pathogen Staphylococcus aureus. The lengths of the genomes were 5.2 and 4.0 Mbps and GC content was at 64.4% and 56.1% for Chromobacterium sp. HL1 and Alcaligenes parafaecalis HL2, respectively. Chromobacterium sp. HL1 has not been assigned to any previously known species. Phylogenetic analysis revealed that Chromobacterium sp. HL1 may be closely related to Chromobacterium fluminis and Chromobacterium alkanivorans. A. parafaecalis HL2 is likely related to Alcaligenes faecalis subsp. parafaecalis. Functional analysis revealed biosynthetic gene clusters related to betalactone, terpene, isocyanide, and T1PKS in one or both genomes analyzed. Antimicrobial properties were previously reported from the products of these gene clusters that could further aid our search for the active component of the analyzed strains.
In a prior study, adoptive cell transfer (ACT) of Dexamethasone (DEX)-induced M2c macrophages with positive expression of MerTK receptor mitigated acute allograft rejection, which was observed in the presence of apoptotic lymphocytes, while simultaneously reducing MHC-II and CD8+ T cells in the recipients. However, there has been limited exploration of the properties of adoptive M2c cells, leaving their potential for other applications unclear. In this study, we aimed to characterize the transcriptome profile of DEX-induced MerTK+/high M2c macrophages. Notably, through the analysis of differentially expressed genes (DEGs), no significant pathway could be constructed from the upregulated DEGs. Only downregulated DEGs could facilitate KEGG construction, encompassing the role of DEX-induced MerTK+/high M2c in immune tolerance. The expression of T-cell activation, pro- and anti-inflammatory cytokines modulation, leukocyte recruitment and adjustment of MHC-I/II-related proteins were entirely diminished. Nonetheless, association of these traits suggests the potential of MerTK+/high M2c macrophages for use in ACT, particularly for autoimmune conditions such as rheumatoid arthritis, inflammatory bowel disease, type-I diabetes mellitus, and AGE/RAGE signaling pathway in diabetic complications. In summary, the preference for downregulated gene expression profiles in DEX-induced MerTK+/high M2c macrophages affirms their potential for immunosuppressive adoptive cell therapy.
High microbial diversity offers extensive benefits to both the environment and human health, contributing to ecosystem stability, nutrient cycling, and pathogen suppression. In built environments, factors such as building design, human activity, and cleaning protocols influence microbial communities. This study investigates the impact of landscape design on microbial diversity and function within the "Visionary Lab" exhibition in Tokyo, Japan, using 16S rRNA gene amplicon sequencing and shallow shotgun sequencing. Despite the limited sample size, the study suggests that the Visionary Lab samples may exhibit higher microbial diversity compared to other museum areas. Potential distinct microbial community structures may be correlated with sampling locations. However, despite this, no consistent patterns were observed in virulence factors or antimicrobial resistance genes across the samples. Metabolic function analysis showed varied profiles, suggesting diverse ecological interactions influenced that may be by the curated landscape. This suggest that the curated landscape design may have the potential to enhance microbial diversity, highlighting a possible avenue to create healthier and more sustainable built environments. However, the lack of consistent patterns in virulence factors and antimicrobial resistance genes underscores the complexity of microbial community dynamics.
The earthball Scleroderma, an ectomycorrhizal basidiomycete belonging to the Sclerodermataceae family, serves as a significant mutualistic tree symbiont globally. Originally, two genetically sequenced strains of this genus were obtained from fruiting bodies collected under chestnut trees (Castanea mollissima). These strains were utilized to establish in vitro ectomycorrhizal roots of chestnut seedlings. The genome sequences of these strains share characteristics with those of other ectomycorrhizal species in Boletales order, including a restricted set of genes encoding carbohydrate-active enzymes. The genome sequences presented here will aid in further exploring the factors contributing to the establishment of ectomycorrhizal symbiosis in chestnut trees.
Purpose: Genetic variants encoding both low COMT and MTHFR activity are associated with idiopathic scoliosis. The combined impact of COMT and MTHFR on progression of adolescent idiopathic scoliosis (AIS) is unknown. This study investigated if COMT and MTHFR low activity variants are associated with AIS progression. Methods: Patients with AIS, at least two Cobb angle measurements in adolescence, and those with both low COMT (rs4680 AA) and low MTHFR (A1298C AC and C677T CT; A1298C AA and C677T TT) activity (Group 1) or those with intermediate or high COMT (rs4680 AG or GG) and MTHFR (A1298C AA and C677T CT; A1298C AC and C677T CC; A1298C AA and C677T CC) activity (Group 2) were included. Those with neuromuscular or syndromic scoliosis were excluded. The primary outcome was progression of scoliosis, defined as a Cobb angle increase of at least 20 degrees or spinal surgery between the time of diagnosis and skeletal maturity. The primary outcome was analyzed via a Chi-square test. Results: Seventy-two patients with AIS diagnosis and required Cobb angle measurements had both COMT and MTHFR results that met criteria for Group 1 (n=41) or Group 2 (n=31). Regarding the primary outcome, 78.0% (32/41) in Group 1 progressed versus 48.4% (15/31) of patients in Group 2 (p=0.009). Conclusion: Significantly more patients with both low COMT and low MTHFR activity variants had progression of AIS than those with intermediate or normal activity variants of COMT and MTHFR. Further understanding the role of COMT and MTHFR may inform research regarding treatment modalities.
Monilinia vacccinii-corymbosi (phylum Ascomycota, family Sclerotiniaceae) causes fruit disease 'mummy berry' on berry crops and responsible for yield losses and quality of fruits. We reported mummy berry disease of black huckleberry (Vaccinium membranaceum) first time in British Columbia, Canada. We have performed sequencing and genome assembly of M. vacccinii-corymbosi from infected fruits of huckleberry. The resulting genome was 33.8 Mbp in size and consisted of 2,437 scaffolds with an N50 of 33,816 bp. To our best knowledge, this is the first report of resource announcement of whole genome sequence of mummy berry pathogen (M. vacccinii-corymbosi) infecting black huckleberry. The genome resource will be valuable for future studies to understand the genomic structure of pathogen, and mechanisms associated with black huckleberry-M. vacccinii-corymbosi interactions.
Phytophthora citrophthora is an oomycete pathogen that infects citrus. Its occurrence in citrus-growing regions worldwide is considered a major contributor to crop losses. This study presents a high-quality genome resource for P. citrophthora, which was generated using PacBio HiFi long-read high-throughput sequencing technology. We successfully assembled a 48.5 Mb genome containing 16,409 protein-coding genes from high-quality reads. This marks the first complete genome assembly of P. citrophthora, providing a valuable resource to enhance the understanding of pathogenic behaviour and fungicide sensitivity of this destructive citrus pathogen.
Quality control (QC) is primordial for determining the efficiency in any downstream genomic applications. There are several steps in the verification of the quality of RNA samples destined for genomic studies. The aim of this research was to determine whether RNA should be discarded at the level of the field lab if it fails preliminary quality control using Optical Density (OD) measurements. In this study, all samples were submitted to rigorous quality control in every stage of work. RNA samples showing poor OD values still gave excellent results in downstream QC and genomic applications. At the end of the quality control exercise, it was observed that the original samples were the same and had not undergone any deterioration along the different stages of handling and manipulation. This paper shows the different and most important stages of quality control on RNA samples (RIN) for an effective down stream application in genomic studies. RNA samples should not be discarded based on preliminary QC from our field labs.
The emergence of antimicrobial-resistant and mastitis-associated Staphylococcus aureus is of great concern due to the huge economic losses worldwide. Here, we report draft genome sequences of two Staphylococcus aureus strains which were isolated from raw milk samples obtained from mastitis-infected cows in Bangladesh. The strains were isolated and identified using conventional microbiological and molecular polymerase chain reaction (PCR) methods. Antibiotic susceptibility testing was performed. Genomic DNA of the two strains was extracted and the strains were sequenced using the Illumina NextSeq 550 platform. The assembled contigs were analyzed for virulence determinants, antimicrobial resistance genes, extra-chromosomal plasmids, and multi-locus sequence type (MLST). The genomes of the two strains were compared with other publicly available genome sequences of Staphylococcus aureus strains. The raw read sequences were downloaded and all sequence files were analyzed identically to generate core genome phylogenetic trees. The genome of BR-MHR281strain did not harbour any antibiotic resistance determinants, however BR-MHR220 strain harbored mecA and blaZ genes. Analysis of BR-MHR220 strain revealed that it was assigned to sequence type (ST-6), clonal complex (CC) 5 and spa type t304, while BR-MHR281 strain belonged to ST-2454, CC8, and harbored the spa type t7867. The findings of the present study and the genome sequences of BR-MHR220 and BR-MHR281 strains will provide data on the detection and genomic analysis and characterization of mastitis-associated Staphylococcus aureus in Bangladesh. In addition, the findings of the present study will serve as reference genomes for future molecular epidemiological studies and will provide significant data which help understand the prevalence, pathogenesis and antimicrobial resistance of mastitis-associated Staphylococcus aureus.
Favolaschia claudopus, a wood-inhabiting basidiomycete of the Mycenaceae family, is considered an invasive species that has recently spread from Oceania to Europe. The CIRM-BRFM 2984 strain of this fungus was originally isolated from a basidiome collected from the fallen limb of a decayed oak tree in Southwest France. The genome sequence of this strain shared characteristics with other Mycenaceae species, including a large genome size and enriched content of protein-coding genes. The genome sequence provided here will facilitate further investigation on the factors that contribute to the successful global dissemination of F. claudopus.
Enterobacter asburiae is a species of Gram-negative bacteria that is found in soil, water, and sewage. E. asburiae is generally considered to be an opportunistic pathogen, but has also been reported as a plant growth-promoting bacterium (PGPB), which may have beneficial effects on plant growth and development. However, genetic analysis of E. asburiae has been limited, possibly due to its redundant enzymes that digest exogenous DNA in the cell. Here, an E. asburiae strain i6 was isolated from soil in Nara, Japan. This strain was amenable to transformation and the one-step gene inactivation method based on λ Red recombinase. The transformation efficiency of the i6 strain with the 10 kb plasmid DNA pCF430 was at least four orders of magnitude higher than that of the previously sequenced E. asburiae strain ATCC 35953, which could not be transformed with the same plasmid DNA. A draft genome sequence of the i6 strain was determined and deposited into the database, allowing several factors that may determine transformation efficiency to be perturbed and tested. Together with the amenability of the i6 strain to genetic manipulation, the information from the i6 genome will facilitate characterization and fine-tuning of the beneficial and detrimental traits of this species.
Phytophthora gonapodyides is a newly reported oomycetes pathogen associated with root rot of red raspberry. We generated high-quality whole genome resource for P. gonapodyides, which was pathogenic on red raspberry. The genome size was 88,717,598 bp with a BUSCO completeness score of 93.9%. This genome resource provides insight on pathogen biology of Phytophthora spp. causing root rot of raspberry. To our best knowledge, this is the first complete genome assembly of plant pathogenic P. gonapodyides.
The complete genome of Annamia dubia was sequenced.The genome size is 4.02 Mbp, including 3886286 bp circular chromosome and four circular plasmids (31516, 42453, 38085 and 24903 bp).It included 3718 protein-coding sequences, 45 tRNA genes, three sets of rRNA genes, a microcystin biosynthesis gene cluster and six CRISPR (clustered regularly interspaced short palindromic repeat).Annamia is the only one genus in the Chroococcales that makes filamentous colonies.FraC and FraG were identified in the genome.These genes are required for the integrity of cell junctions and influencing filament integrity and are thought to be related to colony formation.These genes are first reported from Chroococcales, and may play a significant role in the colony formation of this species.In the phylogenetic tree of the FraC gene, A. dubia was located in the basal position of Oscillatoriales.The GC ratio of FraC gene of A. dubia is very low from the genome and the FraC gene of Microcoleaceae.The presence of these genes in the basal region and the low GC ratio suggests that the FraC gene in this species was introduced by horizontal gene transfer.Since the filamentous colony is a fundamental and important taxonomic feature for the classification of cyanobacteria, the possibility of horizontal transmission of genes involved in filamentous cyanobacterial colonies is an important discovery for the classification of cyanobacteria.
INTRODUCTION:Metagenomic sequencing is a powerful tool that is widely used in laboratories worldwide for taxonomic characterization of microorganisms in clinical and environmental samples. In this study, we utilized metagenomics to investigate comprehensively the microbial diversity in fecal samples of children over a four-year period. Our methods were carefully designed to ensure accurate and reliable results. MATERIAL AND METHODS:Validated and analyzed were metagenomic data obtained from sequencing 27 fecal samples from children under 10 years old with gastroenteritis over a four-year period (2012-2016). The fecal specimens were collected from patients who received care at public health facilities in the northern region of Brazil. Sequencing libraries were prepared from cDNA and sequenced on the Illumina HiSeq. Kraken-2 was utilized to classify bacterial taxonomy based on the 16S rRNA gene, using the Silva rRNA database. Additionally, the Diamond program was used for mapping to the non-redundant protein database (NR database). Phylogenomic analyses were conducted using Geneious R10 and MEGA X software, and Bayesian estimation of phylogeny was performed using the MrBayes program. The results indicate significant heterogeneity among norovirus strains, with evidence of recombination and point mutations. This study presents the first complete genome of parechovirus 8 in the region. Additionally, it describes the bacterial populations and bacteriophages present in feces, with a high abundance of Firmicutes and Proteobacteria, including an increased proportion of the Enterobacteriaceae family. The presented data demonstrate the genetic diversity of microbial populations and provide a comprehensive report on viral molecular characterization. These findings are relevant for genomic studies in gastrointestinal infections. The metagenomic approach is a powerful tool for investigating microbial diversity in children with gastroenteritis. However, further studies are imperative to conduct genomic analysis of identified bacterial strains and thoroughly analyze antimicrobial resistance genes.
Streptomyces Strain San01 is isolated from the soil of ant-nest found in the tea estate of Darjeeling, India. The morphology, biochemical, as well as the molecular characteristics, proved that San01 belonged to the genus Streptomyces. The average nucleotide identity (ANI) value between the genome sequence of the studied strain and its closest phylogenetic neighbors were very low and also could be distinguished from its closest neighbour with broad range of phenotypic data. The draft genome sequence of isolate San01 (NZ_RZYA00000000.1) was estimated to be 9.12 Mbp in size with 71.2% of GC content and it encompasses 39 biosynthetic gene clusters that emphasize the biotechnological potential of this isolate.Based on the phenotypic, genetic and genomic data, isolate San01 (=JCM 34633 = NCTC 14543) merits to be recognized as a type strain of a novel species and hereby propose the name Streptomyces antnestii sp. nov. Incidentally, this is the first report on Streptomyces genomes from Darjeeling, India.
