Journal of Genomics最新文献

{"title":"COMT and MTHFR Genetic Variants Combined Effects on Adolescent Idiopathic Scoliosis Progression.","authors":"Jessica Wright, Adrijana Kekic, Ann Vincent, Jana Kay Lacanlale, Razan El Melik, Eric Matey, Mark Morningstar","doi":"10.7150/jgen.104110","DOIUrl":"https://doi.org/10.7150/jgen.104110","url":null,"abstract":"<p><p><b>Purpose:</b> Genetic variants encoding both low COMT and MTHFR activity are associated with idiopathic scoliosis. The combined impact of <i>COMT</i> and <i>MTHFR</i> on progression of adolescent idiopathic scoliosis (AIS) is unknown. This study investigated if <i>COMT</i> and <i>MTHFR</i> low activity variants are associated with AIS progression. <b>Methods:</b> Patients with AIS, at least two Cobb angle measurements in adolescence, and those with both low <i>COMT</i> (rs4680 AA) and low <i>MTHFR</i> (A1298C AC and C677T CT; A1298C AA and C677T TT) activity (Group 1) or those with intermediate or high <i>COMT</i> (rs4680 AG or GG) and <i>MTHFR</i> (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. <b>Results:</b> Seventy-two patients with AIS diagnosis and required Cobb angle measurements had both <i>COMT</i> and <i>MTHFR</i> 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). <b>Conclusion:</b> Significantly more patients with both low <i>COMT</i> and low <i>MTHFR</i> activity variants had progression of AIS than those with intermediate or normal activity variants of <i>COMT</i> and <i>MTHFR</i>. Further understanding the role of <i>COMT</i> and <i>MTHFR</i> may inform research regarding treatment modalities.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"13 ","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11704681/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142950015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Draft genomes and assemblies of the ectomycorrhizal basidiomycetes <i>Scleroderma citrinum</i> hr and <i>S. yunnanense</i> jo associated with chestnut trees.","authors":"Haolin Zhang, Jiayi Han, Richard D Hayes, Kurt LaButti, Igor Shabalov, Anna Lipzen, Kerrie Barry, Igor V Grigoriev, Qing Zhang, Qingqin Cao, Huchen Li, Francis M Martin","doi":"10.7150/jgen.103481","DOIUrl":"https://doi.org/10.7150/jgen.103481","url":null,"abstract":"<p><p>The earthball <i>Scleroderma</i>, 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 (<i>Castanea mollissima</i>). These strains were utilized to establish <i>in vitro</i> 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.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"13 ","pages":"6-9"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11704682/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142949963","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First Report and Genome Resource of <i>Monilinia vaccinii-corymbosi</i>, causal agent of Mummy Berry Disease of Black Huckleberry (<i>Vaccinium membranaceum</i>).","authors":"Rishi R Burlakoti, Sanjib Sapkota, Mark Lubberts, Mehdi Sharifi","doi":"10.7150/jgen.97432","DOIUrl":"10.7150/jgen.97432","url":null,"abstract":"<p><p><i>Monilinia vacccinii-corymbosi</i> (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 <i>M. vacccinii-corymbosi</i> 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 (<i>M. vacccinii-corymbosi</i>) 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-<i>M. vacccinii-corymbosi</i> interactions.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"12 ","pages":"71-74"},"PeriodicalIF":0.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11317209/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141972535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The impact of <i>Elaeagnus angustifolia</i> root exudates on <i>Parafrankia soli</i> NRRL B-16219 exoproteome.","authors":"Ikram Kammoun, Guylaine Miotello, Karim Ben Slama, Jean Armengaud, Faten Ghodhbane-Gtari, Maher Gtari","doi":"10.7150/jgen.93243","DOIUrl":"10.7150/jgen.93243","url":null,"abstract":"<p><p>Root exudates from host plant species are known to play a critical role in the establishment and maintenance of symbiotic relationships with soil bacteria. In this study, we investigated the impact of root exudates from compatible host plant species; <i>Elaeagnus angustifolia</i> on the exoproteome of <i>Parafrankia soli</i> strain NRRL B-16219. A total of 565 proteins were evidenced as differentially abundant, with 32 upregulated and 533 downregulated in presence of the plant exudates. Analysis of the function of these proteins suggests that the bacterial strain is undergoing a complex metabolic reprogramming towards a new developmental phase elicited in presence of host plant root exudates. The upregulation of Type II/IV secretion system proteins among the differentially expressed proteins indicates their possible role in infecting the host plant, as shown for some rhizobia. Additionally, EF-Tu, proteins upregulated in this study, may function as an effector for the T4SSs and trigger plant defense responses. These findings suggest that <i>Parafrankia soli</i> may use EF-Tu to infect the actinorhizal host plant and pave the way for further investigations of the molecular mechanisms underlying the establishment of symbiotic relationships.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"12 ","pages":"58-70"},"PeriodicalIF":0.0,"publicationDate":"2024-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11093716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140946812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome Resource of Raspberry Root Rot Pathogen <i>Phytophthora gonapodyides</i>.","authors":"Rishi R Burlakoti, Sanjib Sapkota, Mark Lubberts","doi":"10.7150/jgen.94500","DOIUrl":"10.7150/jgen.94500","url":null,"abstract":"<p><p><i>Phytophthora gonapodyides</i> is a newly reported oomycetes pathogen associated with root rot of red raspberry. We generated high-quality whole genome resource for <i>P. gonapodyides</i>, 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 <i>Phytophthora</i> spp. causing root rot of raspberry. To our best knowledge, this is the first complete genome assembly of plant pathogenic <i>P. gonapodyides</i>.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"12 ","pages":"55-57"},"PeriodicalIF":0.0,"publicationDate":"2024-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11093715/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140946811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial Diversity in Children with Gastroenteritis in the Amazon Region of Brazil: Development and Validation of a Molecular Method for Complete Sequencing of Viral Genomes.","authors":"Juliana Merces Hernandez, Giovanna Brunetta SantAna Almeida, Ana Caroline Rodrigues Portela, Jedson Ferreira Cardoso, Edivaldo Costa Sousa Junior, Maria Silvia Sousa Lucena, Márcio Roberto Teixeira Nunes, Yvone Benchimol Gabbay, Luciana Damascena Silva","doi":"10.7150/jgen.94116","DOIUrl":"10.7150/jgen.94116","url":null,"abstract":"<p><strong>Introduction: </strong>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.</p><p><strong>Material and methods: </strong>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 <i>Enterobacteriaceae</i> 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.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"12 ","pages":"47-54"},"PeriodicalIF":0.0,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11024607/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140865160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quality control on oil palm RNA samples for efficient genomic downstream applications.","authors":"Ardha Apryianto, Primadiyanti Arsela, Foncha Felix, Walter Ajambang","doi":"10.7150/jgen.92209","DOIUrl":"10.7150/jgen.92209","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"12 ","pages":"35-43"},"PeriodicalIF":0.0,"publicationDate":"2024-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10905253/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140021957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Draft genome sequencing and assembly of <i>Favolaschia claudopus</i> CIRM-BRFM 2984 isolated from oak limbs.","authors":"David Navarro, Elodie Drula, Delphine Chaduli, Robert Cazenave, Steven Ahrendt, Jie Wang, Anna Lipzen, Chris Daum, Kerrie Barry, Igor V Grigoriev, Anne Favel, Marie-Noëlle Rosso, Francis Martin","doi":"10.7150/jgen.92255","DOIUrl":"10.7150/jgen.92255","url":null,"abstract":"<p><p><i>Favolaschia claudopus</i>, 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 <i>F. claudopus</i>.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"12 ","pages":"44-46"},"PeriodicalIF":0.0,"publicationDate":"2024-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10905254/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140021956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Isolation and draft genome sequence of <i>Enterobacter asburiae</i> strain i6 amenable to genetic manipulation.","authors":"Akinori Kato","doi":"10.7150/jgen.91337","DOIUrl":"10.7150/jgen.91337","url":null,"abstract":"<p><p><i>Enterobacter asburiae</i> is a species of Gram-negative bacteria that is found in soil, water, and sewage. <i>E. asburiae</i> 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 <i>E. asburiae</i> has been limited, possibly due to its redundant enzymes that digest exogenous DNA in the cell. Here, an <i>E. asburiae</i> 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 <i>E. asburiae</i> 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.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"12 ","pages":"26-34"},"PeriodicalIF":0.0,"publicationDate":"2024-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10845240/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139697634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular identification and whole genome sequence analyses of methicillin-resistant and mastitis-associated <i>Staphylococcus aureus</i> sequence types 6 and 2454 isolated from dairy cows.","authors":"Mohammad H Rahman, Mohamed E El Zowalaty, Linda Falgenhauer, Mohammad F R Khan, Jahangir Alam, Najmun N Popy, Hossam M Ashour, Md Bahanur Rahman","doi":"10.7150/jgen.90833","DOIUrl":"10.7150/jgen.90833","url":null,"abstract":"<p><p>The emergence of antimicrobial-resistant and mastitis-associated <i>Staphylococcus aureus</i> is of great concern due to the huge economic losses worldwide. Here, we report draft genome sequences of two <i>Staphylococcus aureus</i> 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 <i>Staphylococcus aureus</i> 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 <i>mecA</i> and <i>blaZ</i> genes. Analysis of BR-MHR220 strain revealed that it was assigned to sequence type (ST-6), clonal complex (CC) 5 and <i>spa</i> type t304, while BR-MHR281 strain belonged to ST-2454, CC8, and harbored the <i>spa</i> 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 <i>Staphylococcus aureus</i> 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 <i>Staphylococcus aureus</i>.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"12 ","pages":"19-25"},"PeriodicalIF":0.0,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10845239/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139697635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}