Journal of Genomics最新文献_第3页

Draft Genomes of Halophilic Chromohalobacter and Halomonas Strains Isolated from Brines of The Carpathian Foreland, Poland. 波兰喀尔巴阡边疆区卤水中分离的嗜盐嗜色盐杆菌和嗜盐单胞菌的基因组草案。

Journal of Genomics Pub Date : 2023-03-21 eCollection Date: 2023-01-01 DOI: 10.7150/jgen.80829

Jakub Lach, Dominik Strapagiel, Agnieszka Matera-Witkiewicz, Paweł Stączek

{"title":"Draft Genomes of Halophilic Chromohalobacter and Halomonas Strains Isolated from Brines of The Carpathian Foreland, Poland.","authors":"Jakub Lach, Dominik Strapagiel, Agnieszka Matera-Witkiewicz, Paweł Stączek","doi":"10.7150/jgen.80829","DOIUrl":"10.7150/jgen.80829","url":null,"abstract":"Chromohalobacter and Halomonas are genera of bacterial microorganisms belonging to the group of halophiles. They are characterized by high diversity and the ability to produce bioproducts of biotechnological importance, such as ectoine, biosurfactants and carotenoids. Here, we report three draft genomes of Chromohalobacter and two draft genomes of Halomonas isolated from brines. The length of the genomes ranged from 3.6 Mbp to 3.8 Mbp, and GC content was in the 60.11%-66.46% range. None of the analysed genomes has been assigned to any previously known species of the genus Chromohalobacter or Halomonas. Phylogenetic analysis revealed that Chromohalobacter 296-RDG and Chromohalobacter 48-RD10 belonged to the same species, and Chromohalobacter 11-W is more distantly related to the other two analysed strains than to Chromohalobacter canadensis. Halomonas strains 11-S5 and 25-S5 were clustered together and located close to Halomonas ventosae. Functional analysis revealed BGCs related to ectoine production in all genomes analysed. This study increases our overall understanding of halophilic bacteria and is also consistent with the notion that members of this group have significant potential as useful natural product producers.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"11 ","pages":"14-19"},"PeriodicalIF":0.0,"publicationDate":"2023-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10093197/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9418858","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}

引用次数: 1

Draft Genomes of Frankia strains AiPa1 and AiPs1 Retrieved from Soil with Monocultures of Picea abies or Pinus sylvestris using Alnus incana as Capture Plant. 以银杉为捕获植物，从云杉或樟子松单体培养的土壤中检索到Frankia菌株AiPa1和AiPs1的基因组草案。

Journal of Genomics Pub Date : 2023-01-01 DOI: 10.7150/jgen.77880

Philippe Normand, Petar Pujic, Danis Abrouk, Spandana Vemulapally, Trina Guerra, Camila Carlos-Shanley, Dittmar Hahn

{"title":"Draft Genomes of Frankia strains AiPa1 and AiPs1 Retrieved from Soil with Monocultures of Picea abies or Pinus sylvestris using Alnus incana as Capture Plant.","authors":"Philippe Normand, Petar Pujic, Danis Abrouk, Spandana Vemulapally, Trina Guerra, Camila Carlos-Shanley, Dittmar Hahn","doi":"10.7150/jgen.77880","DOIUrl":"10.7150/jgen.77880","url":null,"abstract":"The genomes of two nitrogen-fixing Frankia strains, AiPa1 and AiPs1, are described as representatives of two novel candidate species. Both strains were isolated from root nodules of Alnus incana, used as capture plants in bioassays on soils from a reforested site at Karttula, Finland, that was devoid of actinorhizal plants but contained 25 year-old monocultures of spruce (Picea abies (L.) Karsten) or pine (Pinus sylvestris L.), respectively. ANI analyses indicate that each strain represents a novel Frankia species, with genome sizes of 6.98 and 7.35 Mb for AiPa1 and AiPs1, respectively. Both genomes harbored genes typical for many other symbiotic frankiae, including genes essential for nitrogen-fixation, for synthesis of hopanoid lipids and iron-sulfur clusters, as well as clusters of orthologous genes, secondary metabolite determinants and transcriptional regulators. Genomes of AiPa1 and AiPs1 had lost 475 and 112 genes, respectively, compared to those of other cultivated Alnus-infective strains with large genomes. Lost genes included one hup cluster in AiPa1 and the gvp cluster in AiPs1, suggesting that some genome erosion has started to occur in a different manner in the two strains.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"11 ","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9760358/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9472553","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}

引用次数: 0

Draft genome sequencing and assembly of Risso's dolphin, Grampus griseus. 里索海豚Grampus griseus的基因组测序和组装草案。

Journal of Genomics Pub Date : 2023-01-01 DOI: 10.7150/jgen.78761

Jayan D M Senevirathna, Ryo Yonezawa, Taiki Saka, Yuka Hiramatsu, Ashley Rinka Smith, Yoji Igarashi, Kazutoshi Yoshitake, Shigeharu Kinoshita, Noriko Funasaka, Shuichi Asakawa

{"title":"Draft genome sequencing and assembly of Risso's dolphin, Grampus griseus.","authors":"Jayan D M Senevirathna, Ryo Yonezawa, Taiki Saka, Yuka Hiramatsu, Ashley Rinka Smith, Yoji Igarashi, Kazutoshi Yoshitake, Shigeharu Kinoshita, Noriko Funasaka, Shuichi Asakawa","doi":"10.7150/jgen.78761","DOIUrl":"10.7150/jgen.78761","url":null,"abstract":"The Risso's dolphin (Grampus griseus) is one of the migratory marine mammals and they have commonly dispersed in tropical and temperate seas. It is a least concerned species in the IUCN red list of threatened species. However, their population size and factors affecting their population structure are unknown. Due to the wide distribution of this species, their populations might be genetically stable and less structured. To support genetic studies on dolphins and other marine mammals, we assembled the draft genome of Risso's dolphin that was found in Japan. The tissue samples were used to extract high molecular DNA and subjected to sequencing by Illumina HiSeq X, Oxford Nanopore MinION, and Bionano Saphyr. The assembled hybrid genome was 75.9% of complete eukaryotic BUSCOs and the genome size was 2.256 Gb with 2.042 Mb of scaffold N50. De novo assembly of this genome by Bionano Saphyr recovered 2.036 Gb total genome map length and structural variations. The gene structures of this draft genome were identified by BRAKER2, and 9947 genes were recovered. The data will be useful for future studies of cetaceans.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"11 ","pages":"9-13"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9830294/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9416786","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}

引用次数: 1

Draft Genomes Sequences of 11 Geodermatophilaceae Strains Isolated from Building Stones from New England and Indian Stone Ruins found at historic sites in Tamil Nadu, India. 从新英格兰的建筑石块和印度泰米尔纳德邦历史遗址中发现的印度石遗址中分离出的 11 个嗜地肤菌株的基因组序列草案。

Journal of Genomics Pub Date : 2022-09-21 eCollection Date: 2022-01-01 DOI: 10.7150/jgen.76121

Nathaniel J Ennis, Dhanasekaran Dharumadurai, Joseph L Sevigny, Ryan Wilmot, Sulaiman M Alnaimat, Julia G Bryce, W Kelley Thomas, Louis S Tisa

{"title":"Draft Genomes Sequences of 11 Geodermatophilaceae Strains Isolated from Building Stones from New England and Indian Stone Ruins found at historic sites in Tamil Nadu, India.","authors":"Nathaniel J Ennis, Dhanasekaran Dharumadurai, Joseph L Sevigny, Ryan Wilmot, Sulaiman M Alnaimat, Julia G Bryce, W Kelley Thomas, Louis S Tisa","doi":"10.7150/jgen.76121","DOIUrl":"10.7150/jgen.76121","url":null,"abstract":"Metagenomic analysis of stone microbiome from samples collected in New England, USA and Tamil Nadu, India identified numerous Actinobacteria including Geodermatphilaceae. A culture-dependent approach was performed as a companion study with this culture-independent metagenomic analysis of these stone samples and resulted in the isolation of eleven Geodermatphilaceae strains (2 Geodermatophilus and 9 Blastococcus strains). The genomes of the 11 Geodermatphilaceae strains were sequenced and analyzed. The genomes for the two Geodermatophilus isolates, DF1-2 and TF2-6, were 4.45 and 4.75 Mb, respectively, while the Blastococcus genomes ranged in size from 3.98 to 5.48 Mb. Phylogenetic analysis, digital DNA:DNA hybridization (dDDH), and comparisons of the average nucleotide identities (ANI) suggest the isolates represent novel Geodermatophilus and Blastococcus species. Functional analysis of the Geodermatphilaceae genomes provides insight on the stone microbiome niche.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":" ","pages":"69-77"},"PeriodicalIF":0.0,"publicationDate":"2022-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9516006/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40385325","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}

引用次数: 0

Draft Genomes of Symbiotic Frankia Strains AgB32 and AgKG'84/4 from Root Nodules of Alnus Glutinosa growing under Contrasted Environmental Conditions. 对比环境条件下生长的桤木根瘤共生菌株AgB32和AgKG'84/4的基因组绘制

Journal of Genomics Pub Date : 2022-08-08 eCollection Date: 2022-01-01 DOI: 10.7150/jgen.75779

Philippe Normand, Petar Pujic, Danis Abrouk, Spandana Vemulapally, Trina Guerra, Camila Carlos-Shanley, Dittmar Hahn

{"title":"Draft Genomes of Symbiotic Frankia Strains AgB32 and AgKG'84/4 from Root Nodules of Alnus Glutinosa growing under Contrasted Environmental Conditions.","authors":"Philippe Normand, Petar Pujic, Danis Abrouk, Spandana Vemulapally, Trina Guerra, Camila Carlos-Shanley, Dittmar Hahn","doi":"10.7150/jgen.75779","DOIUrl":"https://doi.org/10.7150/jgen.75779","url":null,"abstract":"The genomes of two nitrogen-fixing Frankia strains, AgB32 and AgKG'84/4, were isolated from spore-containing (spore+) and spore-free (spore-) root nodules of Alnus glutinosa, but they did not sporulate upon reinfection. The two strains are described as representatives of two novel candidate species. Phylogenomic and ANI analyses indicate that each strain represents a novel species within cluster 1, with genome sizes of 6.3 and 6.7 Mb smaller than or similar to those of other cultivated Alnus-infective cluster 1 strains. Genes essential for nitrogen-fixation, clusters of orthologous genes, secondary metabolite clusters and transcriptional regulators analyzed by comparative genomic analyses were typical of those from Alnus-infective cluster 1 cultivated strains in both genomes. Compared to other cultivated Alnus-infective strains with large genomes, those of AgB32 and AgKG'84/4 had lost 380 or 409 genes, among which one hup cluster, one shc gene and the gvp cluster, which indicates genome erosion is taking place in these two strains.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":" ","pages":"61-68"},"PeriodicalIF":0.0,"publicationDate":"2022-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9379372/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40622187","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}

引用次数: 3

Draft Genomes of Six Wild Poisonous Mushrooms. 六种野生毒蘑菇的基因组草图。

Journal of Genomics Pub Date : 2022-08-01 eCollection Date: 2022-01-01 DOI: 10.7150/jgen.75652

Sittiporn Parnmen, Nattakarn Nooron, Sujitra Sikaphan, Chutimon Uttawichai, Dutsadee Polputpisatkul, Sriprapa Phatsarapongkul, Rungsaeng Chankunasuka, Unchalee Nitma, Chidkamon Thunkhamrak, Nisakorn Palakul, Khwanruan Naksuwankul, Onanong Pringsulaka, Achariya Rangsiruji

引用次数: 1

Draft Genomes of Nitrogen-fixing Frankia Strains Ag45/Mut15 and AgPM24 Isolated from Root Nodules of Alnus Glutinosa 固氮菌株Ag45/Mut15和AgPM24的基因组图谱

Journal of Genomics Pub Date : 2022-06-06 DOI: 10.7150/jgen.74788

P. Normand, P. Pujić, Danis Abrouk, Spandana Vemulapally, Trina M Guerra, Camila Carlos-Shanley, D. Hahn

引用次数: 4

Identification of the c.829_832delAATA Deletion Variants in the BRCA1 Gene Associated with Hereditary Breast/Ovarian Cancer ˗ Case Report 与遗传性乳腺癌/卵巢癌相关的BRCA1基因c.829_832delAATA缺失变异体的鉴定——病例报告

Journal of Genomics Pub Date : 2022-02-14 DOI: 10.7150/jgen.68220

M. Ostrowska, Karolina Olszewska-Bożek, J. Podlodowska, J. Sierocińska-Sawa, J. Wojcierowski

{"title":"Identification of the c.829_832delAATA Deletion Variants in the BRCA1 Gene Associated with Hereditary Breast/Ovarian Cancer ˗ Case Report","authors":"M. Ostrowska, Karolina Olszewska-Bożek, J. Podlodowska, J. Sierocińska-Sawa, J. Wojcierowski","doi":"10.7150/jgen.68220","DOIUrl":"https://doi.org/10.7150/jgen.68220","url":null,"abstract":"Determination of the BRCA1/BRCA2 mutation status in patients with breast and/or ovarian cancer is commonly performed using various molecular techniques. The use of targeted PCR-based tests only may not be sufficient, as not all possible variants are investigated. In the present study, we used next-generation sequencing (NGS) techniques to identify novel pathogenic variants in BRCA1 and BRCA2. In this study, material (blood and FFPE) collected from a 67-year-old patient with ovarian cancer was used. The presence of hereditary mutations characteristic for the Polish population was examined using Sanger sequencing. BRCA1 and BRCA2 gene exons were amplified using the Devyser BRCA kit and sequenced on the Miniseq. No germline mutations characteristic for the Polish population were detected. However, 12 single nucleotide variants and 2 indels were identified. We found a new deleterious mutation of gene BRCA1 (c.829_832delAATA). To our knowledge, this mutation has not been reported yet in the Polish population and elsewhere. The use of the NGS technique increases the possibility of detecting mutational changes in patients with ovarian and/or breast cancer. Quick determination of pathogenic variants is important to facilitate specific therapy, in addition to the identification of familial predisposition to cancer.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"10 1","pages":"33 - 38"},"PeriodicalIF":0.0,"publicationDate":"2022-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47506628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Complete Genome Sequence of Four Strains of Leptospira borgpetersenii serovar Hardjo isolated from Cattle in the Central United States 从美国中部牛身上分离的四株博格彼得森钩端螺旋体血清型Hardjo的全基因组序列

Journal of Genomics Pub Date : 2022-02-14 DOI: 10.7150/jgen.69822

E. Putz, D. Bayles, D. Alt, J. Nally

引用次数: 3

GTQC: Automated Genotyping Array Quality Control and Report. GTQC：自动基因分型阵列质量控制和报告。

Journal of Genomics Pub Date : 2022-02-14 eCollection Date: 2022-01-01 DOI: 10.7150/jgen.69860

Shilin Zhao, Limin Jiang, Hui Yu, Yan Guo

{"title":"GTQC: Automated Genotyping Array Quality Control and Report.","authors":"Shilin Zhao, Limin Jiang, Hui Yu, Yan Guo","doi":"10.7150/jgen.69860","DOIUrl":"10.7150/jgen.69860","url":null,"abstract":"Genotyping array is the most economical approach for conducting large-scale genome-wide genetic association studies. Thorough quality control is key to generating high integrity genotyping data and robust results. Quality control of genotyping array is generally a complicated process, as it requires intensive manual labor in implementing the established protocols and curating a comprehensive quality report. There is an urgent need to reduce manual intervention via an automated quality control process. Based on previously established protocols and strategies, we developed an R package GTQC (GenoTyping Quality Control) to automate a majority of the quality control steps for general array genotyping data. GTQC covers a comprehensive spectrum of genotype data quality metrics and produces a detailed HTML report comprising tables and figures. Here, we describe the concepts underpinning GTQC and demonstrate its effectiveness using a real genotyping dataset. R package GTQC streamlines a majority of the quality control steps and produces a detailed HTML report on a plethora of quality control metrics, thus enabling a swift and rigorous data quality inspection prior to downstream GWAS and related analyses. By significantly cutting down on the time on genotyping quality control procedures, GTQC ensures maximum utilization of available resources and minimizes waste and inefficient allocation of manual efforts. GTQC tool can be accessed at https://github.com/slzhao/GTQC.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"10 ","pages":"39-44"},"PeriodicalIF":0.0,"publicationDate":"2022-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8922302/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10340276","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}

引用次数: 0