Genomics Data最新文献

{"title":"Genome sequences of 12 isolates of the EU1 lineage of Phytophthora ramorum, a fungus-like pathogen that causes extensive damage and mortality to a wide range of trees and other plants","authors":"Judith Turner ,&nbsp;Paul O'Neill ,&nbsp;Murray Grant ,&nbsp;Rick A. Mumford ,&nbsp;Richard Thwaites ,&nbsp;David J. Studholme","doi":"10.1016/j.gdata.2017.02.006","DOIUrl":"10.1016/j.gdata.2017.02.006","url":null,"abstract":"<div><p>Here we present genome sequences for twelve isolates of the invasive pathogen <em>Phytophthora ramorum</em> EU1. The assembled genome sequences and raw sequence data are available <em>via</em> BioProject accession number PRJNA177509. These data will be useful in developing molecular tools for specific detection and identification of this pathogen.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 17-21"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.02.006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34770090","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":"Synaptic vesicles isolated from the electric organ of Torpedo californica and from the central nervous system of Mus musculus contain small ribonucleic acids (sRNAs)","authors":"Huinan Li,&nbsp;Cheng Wu,&nbsp;Rodolfo Aramayo,&nbsp;Matthew S. Sachs,&nbsp;Mark L. Harlow","doi":"10.1016/j.gdata.2017.02.015","DOIUrl":"10.1016/j.gdata.2017.02.015","url":null,"abstract":"<div><p>Synaptic vesicles (SVs) are presynaptic organelles that load and release small molecule neurotransmitters at chemical synapses. In addition to classic neurotransmitters, we have demonstrated that SVs isolated from the Peripheral Nervous Systems (PNS) of the electric organ of <em>Torpedo californica,</em> a model cholinergic synapse, and SVs isolated from the Central Nervous System (CNS) of <em>Mus musculus</em> (mouse) contain small ribonucleic acids (sRNAs; ≤<!--> <!-->50 nucleotides) (Scientific Reports, 5:1–14(14918) Li et al. (2015) [1]). Our previous publication provided the five most abundant sequences associated with the <em>T. californica</em> SVs, and the ten most abundant sequences associated with the mouse SVs, representing 59% and 39% of the total sRNA reads sequenced, respectively). We provide here a full repository of the SV sRNAs sequenced from <em>T. californica</em> and the mouse deposited in the NCBI as biosamples. Three data studies are included: SVs isolated from the electric organ of <em>T. californica</em> using standard techniques, SVs isolated from the electric organ of <em>T. californica</em> using standard techniques with an additional affinity purification step, and finally, SVs isolated from the CNS of mouse. The three biosamples are available at <span>https://www.ncbi.nlm.nih.gov/biosample/</span><svg><path></path></svg> SRS1523467, SRS1523466, and SRS1523472 respectively.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 52-53"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.02.015","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34878759","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-centric evaluation of Burkholderia sp. strain SRS-W-2-2016 resistant to high concentrations of uranium and nickel isolated from the Savannah River Site (SRS), USA","authors":"Ashish Pathak ,&nbsp;Ashvini Chauhan ,&nbsp;Paul Stothard ,&nbsp;Stefan Green ,&nbsp;Mark Maienschein-Cline ,&nbsp;Rajneesh Jaswal ,&nbsp;John Seaman","doi":"10.1016/j.gdata.2017.02.011","DOIUrl":"10.1016/j.gdata.2017.02.011","url":null,"abstract":"<div><p>Savannah River Site (SRS), an approximately 800-km² former nuclear weapons production facility located near Aiken, SC remains co-contaminated by heavy metals and radionuclides. To gain a better understanding on microbially-mediated bioremediation mechanisms, several bacterial strains resistant to high concentrations of Uranium (U) and Nickel (Ni) were isolated from the Steeds Pond soils located within the SRS site. One of the isolated strains, designated as strain SRS-W-2-2016, grew robustly on both U and Ni. To fully understand the arsenal of metabolic functions possessed by this strain, a draft whole genome sequence (WGS) was obtained, assembled, annotated and analyzed. Genome-centric evaluation revealed the isolate to belong to the <em>Burkholderia</em> genus with close affiliation to <em>B</em>. <em>xenovorans</em> LB400, an aggressive polychlorinated biphenyl-degrader. At a coverage of 90<!--> <!-->×, the genome of strain SRS-W-2-2016 consisted of 8,035,584 bases with a total number of 7071 putative genes assembling into 191 contigs with an N50 contig length of 134,675 bases. Several gene homologues coding for resistance to heavy metals/radionuclides were identified in strain SRS-W-2-2016, such as a suite of outer membrane efflux pump proteins similar to nickel/cobalt transporter regulators, peptide/nickel transport substrate and ATP-binding proteins, permease proteins, and a high-affinity nickel-transport protein. Also noteworthy were two separate gene fragments in strain SRS-W-2-2016 homologous to the <em>spoT</em> gene; recently correlated with bacterial tolerance to U. Additionally, a plethora of oxygenase genes were also identified in the isolate, potentially involved in the breakdown of organic compounds facilitating the strain's successful colonization and survival in the SRS co-contaminated soils. The WGS project of <em>Burkholderia</em> sp. strain SRS-W-2-2016 is available at DDBJ/ENA/GenBank under the accession #MSDV00000000.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 62-68"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.02.011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34884039","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":"RNA-seq analysis of mangosteen (Garcinia mangostana L.) fruit ripening","authors":"Azhani Abdul-Rahman,&nbsp;Hoe-Han Goh,&nbsp;Kok-Keong Loke,&nbsp;Normah Mohd Noor,&nbsp;Wan Mohd Aizat","doi":"10.1016/j.gdata.2017.05.013","DOIUrl":"10.1016/j.gdata.2017.05.013","url":null,"abstract":"<div><p>Mangosteen (<em>Garcinia mangostana</em> L.) is known for its delectable taste and contains high amount of xanthones which have been reported to possess anti-cancer, anti-inflammatory and other bioactive properties. However, stage-specific regulation of mangosteen fruit ripening has never been studied in detail. We have performed a comparative transcriptomic analysis of three ripening stages (Stage 0, 2 and 6) of mangosteen. We have obtained a raw data from six libraries through Illumina HiSeq 4000. A total of ~<!--> <!-->40<!--> <!-->Gb of raw data were generated. Clean reads of 650,887,650 (bp) were obtained from 656,913,570 (bp) raw reads. The raw transcriptome data were deposited to SRA database, with the BioProject accession number of PRJNA339916. These data will be beneficial for transcriptome profiling in order to study the regulation of mangosteen fruit ripening. The lack of a complete sequence database from this species impedes protein identification. These data sets provide a reference data for the exploration of novel genes or proteins to understand mangosteen fruit ripening behaviour.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 159-160"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.05.013","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35040867","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":"Intraspecies comparative genomics of three strains of Orientia tsutsugamushi with different antibiotic sensitivity","authors":"Hsiao-Mei Liao ,&nbsp;Chien-Chung Chao ,&nbsp;Haiyan Lei ,&nbsp;Bingjie Li ,&nbsp;Shien Tsai ,&nbsp;Guo-Chiuan Hung ,&nbsp;Wei-Mei Ching ,&nbsp;Shyh-Ching Lo","doi":"10.1016/j.gdata.2017.03.012","DOIUrl":"10.1016/j.gdata.2017.03.012","url":null,"abstract":"<div><p>We recently reported the genome of <em>Orientia tsutsugamushi</em> (OT) strain Karp (GenBank Accession #: NZ_LYMA00000000.2, <span>https://www.ncbi.nlm.nih.gov/nuccore/NZ_LYMA00000000.2</span><svg><path></path></svg>) with &gt;<!--> <!-->2<!--> <!-->Mb in size through clone-based sequencing and high throughput genomic shotgun sequencing (HTS). The genomes of OT strains AFSC4 and AFSC7 were similarly sequenced by HTS Since strains AFSC4 (GenBank Accession #: NZ_LYMT00000000.1, <span>https://www.ncbi.nlm.nih.gov/nuccore/1035784408</span><svg><path></path></svg>) and AFSC7 (GenBank Accession #: NZ_LYMB00000000.1, <span>https://www.ncbi.nlm.nih.gov/nuccore/1035854767</span><svg><path></path></svg>) were more resistant to antibiotics than strain Karp, we conducted comparative analysis of the three draft genomes annotated by RAST server aimed to identify possible genetic bases of difference in microbial antibiotic sensitivity. Intraspecies comparative genomics analysis of the three OT strains revealed that two ORFs encoding hypothetical proteins in both strains AFSC4 and AFSC7 are absent in strain Karp.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 84-88"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.03.012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34900561","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":"APMicroDB: A microsatellite database of Acyrthosiphon pisum","authors":"Ritika Bishnoi ,&nbsp;Deepak Singla","doi":"10.1016/j.gdata.2017.03.014","DOIUrl":"10.1016/j.gdata.2017.03.014","url":null,"abstract":"<div><p>Pea aphids represent a complex genetic system that could be used for QTL analysis, genetic diversity and population genetics studies. Here, we described the development of first microsatellite repeat database of the pea aphid (APMicroDB), accessible at “<span>http://deepaklab.com/aphidmicrodb</span><svg><path></path></svg>”. We identified 3,40,233 SSRs using MIcroSAtellite (MISA) tool that was distributed in 14,067 (out of 23,924) scaffold of the pea aphid. We observed 89.53% simple repeats of which 73.41% were mono-nucleotide, followed by di-nucleotide repeats. This database stored information about the repeats kind, GC content, motif type (mono - hexa), genomic location etc. We have also incorporated the primer information derived from Primer3 software of the 250bp flanking region of the identified marker. Blast tool is also provided for searching the user query sequence for identified marker and their primers. This work has an immense use for scientific community working in the field of agricultural pest management, QTL mapping, and host-pathogen interaction analysis.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 111-115"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.03.014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34917033","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 sequence of three Psychrobacter sp. strains with potential applications in bioremediation","authors":"Aide Lasa,&nbsp;Jesús L. Romalde","doi":"10.1016/j.gdata.2017.01.005","DOIUrl":"10.1016/j.gdata.2017.01.005","url":null,"abstract":"<div><p>To date, the genus <em>Psychrobacter</em> consists of 37 recognized species isolated from different sources, however they are more frequently found in cold and other non-polar environments of low water activity. Some strains belonging to the genus have shown different enzymatic activities with potential applications in bioremediation or food industry. In the present study, the whole genome sequences of three <em>Psychrobacter</em>-like strains (C 20.9, Cmf 22.2 and Rd 27.2) isolated from reared clams in Galicia (Spain) are described. The sequenced genomes resulted in an assembly size of 3,143,782<!--> <!-->bp for C 20.9 isolate, 3,168,467<!--> <!-->bp for Cmf 22.2 isolate and 3,028,386<!--> <!-->bp for Rd 27.2 isolate. Among the identified coding sequences of the genomes, mercury detoxification and biogeochemistry genes were found, as well as genes related to heavy metals and antibiotic resistance. Also virulence-related features were identified such as the siderophore vibrioferrin or an aerobactin-like siderophore. The phylogenetic analysis of the 16S rRNA gene suggested that these strains may represent novel species of the <em>Psychrobacter</em> genus. The genome sequences of the <em>Psychrobacter</em> sp. strains have been deposited at DDBJ/EMBL/GenBank under the accession numbers MRYA00000000 (Cmf 22.2), MRYB00000000 (Rd 27.2) and MRYC00000000 (C 20.9), and the sequences could be found at the site <span>https://www.ncbi.nlm.nih.gov/bioproject/PRJNA353858</span><svg><path></path></svg>.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 7-10"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.01.005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34756913","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-wide chromatin accessibility, DNA methylation and gene expression analysis of histone deacetylase inhibition in triple-negative breast cancer","authors":"Matias A. Bustos ,&nbsp;Matthew P. Salomon ,&nbsp;Nellie Nelson ,&nbsp;Sandy C. Hsu ,&nbsp;Maggie L. DiNome ,&nbsp;Dave S.B. Hoon ,&nbsp;Diego M. Marzese","doi":"10.1016/j.gdata.2017.01.002","DOIUrl":"10.1016/j.gdata.2017.01.002","url":null,"abstract":"<div><p>Triple-negative breast cancer (TNBC), especially the subset with a basal phenotype, represents the most aggressive subtype of breast cancer. Unlike other solid tumors, TNBCs harbor a low number of driver mutations. Conversely, we and others have demonstrated a significant impact of epigenetic alterations, including DNA methylation and histone post-translational modifications, affecting TNBCs. Due to the promising results in pre-clinical studies, histone deacetylase inhibitors (HDACi) are currently being tested in several clinical trials for breast cancer and other solid tumors. However, the genome-wide epigenetic and transcriptomic implications of HDAC inhibition are still poorly understood. Here, we provide detailed information about the design of a multi-platform dataset that describes the epigenomic and transcriptomic effects of HDACi. This dataset includes genome-wide chromatin accessibility (assessed by ATAC-Sequencing), DNA methylation (assessed by Illumina HM450K BeadChip) and gene expression (assessed by RNA-Sequencing) analyses before and after HDACi treatment of HCC1806 and MDA-MB-231, two human TNBC cell lines with basal-like phenotype.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 14-16"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.01.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34766522","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":"Topoisomerase I inhibition leads to length-dependent gene expression changes in human primary astrocytes","authors":"Akira Gokoolparsadh ,&nbsp;Zhiming Fang ,&nbsp;Nady Braidy ,&nbsp;Irina Voineagu","doi":"10.1016/j.gdata.2016.12.005","DOIUrl":"10.1016/j.gdata.2016.12.005","url":null,"abstract":"<div><p>Topoisomerase I is required for the proper expression of long genes (&gt;<!--> <!-->100<!--> <!-->kb) in mouse and human cortical neurons, including many candidate genes for autism spectrum disorder (ASD) [1]. Given the important role of astrocytes in brain development [2], we investigated whether long genes, including autism susceptibility genes, also require topoisomerase I expression in human primary astrocytes. We carried genome-wide expression profiling of cultured human primary astrocytes following treatment with the topoisomerase I inhibitor Topotecan, using Illumina microarrays. We identified several thousands of differentially expressed genes and confirmed that topoisomerase I inhibition affects gene expression in human primary astrocytes in a length-dependent manner. We also identified over 20 ASD-associated genes that show topoisomerase-dependent gene expression in human primary astrocytes but have not been previously reported as topoisomerase-I-dependent in neurons. The microarray data have been deposited in NCBI GEO (<span>https://www.ncbi.nlm.nih.gov/geo/</span><svg><path></path></svg>) under accession number GSE90052.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"11 ","pages":"Pages 113-115"},"PeriodicalIF":0.0,"publicationDate":"2017-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2016.12.005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54417320","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 sequence of Sugiyamaella xylanicola UFMG-CM-Y1884T, a xylan-degrading yeast species isolated from rotting wood samples in Brazil","authors":"Thiago M. Batista ,&nbsp;Rennan G. Moreira ,&nbsp;Heron O. Hilário ,&nbsp;Camila G. Morais ,&nbsp;Glória R. Franco ,&nbsp;Luiz H. Rosa ,&nbsp;Carlos A. Rosa","doi":"10.1016/j.gdata.2017.01.006","DOIUrl":"10.1016/j.gdata.2017.01.006","url":null,"abstract":"<div><p>We present the draft genome sequence of the type strain of the yeast <em>Sugiyamaella xylanicola</em> UFMG-CM-Y1884^T (=<!--> <!-->UFMG-CA-32.1^T <!-->=<!--> <!-->CBS 12683^T), a xylan-degrading species capable of fermenting <span>d</span>-xylose to ethanol. The assembled genome has a size of ~<!--> <!-->13.7<!--> <!-->Mb and a GC content of 33.8% and contains 5971 protein-coding genes. We identified 15 genes with significant similarity to the <span>d</span>-xylose reductase gene from several other fungal species. The draft genome assembled from whole-genome shotgun sequencing of the yeast <em>Sugiyamaella xylanicola</em> UFMG-CM-Y1884^T (=<!--> <!-->UFMG-CA-32.1^T <!-->=<!--> <!-->CBS 12683^T) has been deposited at DDBJ/ENA/GenBank under the accession number MQSX00000000 under version MQSX01000000.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"11 ","pages":"Pages 120-121"},"PeriodicalIF":0.0,"publicationDate":"2017-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.01.006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42613561","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}