Genomics Data最新文献

{"title":"Small RNA sequencing for secondary metabolite analysis in Persicaria minor","authors":"Abdul Fatah A. Samad ,&nbsp;Nazaruddin Nazaruddin ,&nbsp;Muhammad Sajad ,&nbsp;Jaeyres Jani ,&nbsp;Abdul Munir Abdul Murad ,&nbsp;Zamri Zainal ,&nbsp;Ismanizan Ismail","doi":"10.1016/j.gdata.2017.05.014","DOIUrl":"10.1016/j.gdata.2017.05.014","url":null,"abstract":"<div><p><em>Persicaria minor</em> (kesum) is an important medicinal plant and commonly found in southeast countries; Malaysia, Thailand, Indonesia, and Vietnam. This plant is enriched with a variety of secondary metabolites (SMs), and among these SMs, terpenoids are in high abundance. Terpenoids are comprised of many valuable biomolecules which have well-established role in agriculture and pharmaceutical industry. In <em>P. minor</em>, for the first time, we have generated small RNAs data sets, which can be used as tool in deciphering their roles in terpenoid biosynthesis pathways. Fungal pathogen, <em>Fusarium oxysporum</em> was used as elicitor to trigger SMs biosynthesis in <em>P. minor.</em> Raw reads and small RNA analysis data have already been deposited at GenBank under the accessions; SRX2645684 (<em>Fusarium</em>-treated), SRX2645685 (<em>Fusarium</em>-treated), SRX2645686 (mock-infected), and SRX2645687 (mock-infected).</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"13 ","pages":"Pages 3-4"},"PeriodicalIF":0.0,"publicationDate":"2017-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.05.014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35040869","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":"Transcriptome of barley under three different heavy metal stress reaction","authors":"Martina Kintlová ,&nbsp;Nicolas Blavet ,&nbsp;Radim Cegan ,&nbsp;Roman Hobza","doi":"10.1016/j.gdata.2017.05.016","DOIUrl":"10.1016/j.gdata.2017.05.016","url":null,"abstract":"<div><p>In the present study, we used Illumina sequencing technology (HiSeq 2000) to sequence the transcriptome of barley (<em>Hordeum vulgare</em> L., cv. Morex) under three different heavy metal stress conditions: copper, zinc and cadmium. For each of those metals, the concentration causing a 50% inhibitory effect for root growth (EC₅₀) was determined. We sequenced the total RNA of both roots and shoots from barley with and without heavy metal treatments in three replicates. Raw reads of the transcriptome project have been deposited in NCBI's BioProject accession number PRJNA382490. The obtained transcriptomic data will be useful for further studies focusing on heavy metal tolerance and comparative transcriptome analysis in barley.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"13 ","pages":"Pages 15-17"},"PeriodicalIF":0.0,"publicationDate":"2017-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.05.016","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35099245","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 detects pharmacological inhibition of Epstein-Barr virus late transcription during spontaneous reactivation","authors":"An T. Phan ,&nbsp;Delsy M. Martinez ,&nbsp;JJ L. Miranda","doi":"10.1016/j.gdata.2017.05.012","DOIUrl":"10.1016/j.gdata.2017.05.012","url":null,"abstract":"<div><p>The stepwise and sequential expression of viral genes underlies progression of the infectious life cycle. The Epstein-Barr virus (EBV) is both a tractable model for elucidating principles of transcription as well as a global health threat. We describe an experimental protocol and bioinformatics pipeline for functional identification of EBV true late genes, the last step of transcription prior to virion packaging and egress. All data have been uploaded to the Gene Expression Omnibus under accession code GSE96689. The key improvement over previous approaches is leveraging the sensitivity of RNA-seq to detect gene expression changes during spontaneous reactivation.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"13 ","pages":"Pages 5-6"},"PeriodicalIF":0.0,"publicationDate":"2017-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.05.012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35040870","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":"Whole-genome shotgun sequence of phenazine-producing endophytic Streptomyces kebangsaanensis SUK12","authors":"Juwairiah Remali ,&nbsp;Kok-Keong Loke ,&nbsp;Chyan Leong Ng ,&nbsp;Wan Mohd Aizat ,&nbsp;John Tiong ,&nbsp;Noraziah Mohamad Zin","doi":"10.1016/j.gdata.2017.05.015","DOIUrl":"10.1016/j.gdata.2017.05.015","url":null,"abstract":"<div><p><em>Streptomyces</em> sp. produces bioactive compounds with a broad spectrum of activities. <em>Streptomyces kebangsaanesis</em> SUK12 has been identified as a novel endophytic bacteria isolated from ethnomedicinal plant <em>Portulaca olerace</em>, and was found to produce the phenazine class of biologically active antimicrobial metabolites. The potential use of the phenazines has led to our research interest in determining the genome sequence of <em>Streptomyces kebangsaanensis</em> SUK12. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number PRJNA269542. The raw sequence data are available [<span>https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP105770</span><svg><path></path></svg>].</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"13 ","pages":"Pages 7-10"},"PeriodicalIF":0.0,"publicationDate":"2017-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.05.015","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35060968","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":"Oviductal transcriptional profiling of a bovine fertility model by next-generation sequencing","authors":"Angela Maria Gonella-Diaza ,&nbsp;Sónia Cristina da Silva Andrade ,&nbsp;Mariana Sponchiado ,&nbsp;Guilherme Pugliesi ,&nbsp;Fernando Silveira Mesquita ,&nbsp;Veerle Van Hoeck ,&nbsp;Ricardo de Francisco Strefezzi ,&nbsp;Gustavo R. Gasparin ,&nbsp;Luiz L. Coutinho ,&nbsp;Mario Binelli","doi":"10.1016/j.gdata.2017.06.004","DOIUrl":"10.1016/j.gdata.2017.06.004","url":null,"abstract":"<div><p>In cattle, the oviduct plays a fundamental role in the reproductive process. Oviductal functions are controlled by the ovarian sex steroids: estradiol and progesterone. Here, we tested the hypothesis that the exposure to contrasting sex steroid milieus differentially impacts the oviductal transcriptional profile. We manipulated growth of the pre-ovulatory follicle to obtain cows that ovulated a larger (LF group) or a smaller (SF group) follicle. The LF group presented greater proestrus/estrus concentrations of estradiol and metaestrus concentrations of progesterone (Gonella-Diaza et al. 2015 [1], Mesquita et al. 2014 [2]). Also, the LF group was associated with greater fertility in timed-artificial insemination programs (Pugliesi et al. 2016 <span>[3]</span>). Cows were slaughtered on day 4 of the estrous cycle and total RNA was extracted from ampulla and isthmus fragments and analyzed by RNAseq. The resulting reads were mapped to the bovine genome (<em>Bos taurus</em> UMD 3.1, NCBI). The differential expression analyses revealed that 325 and 367 genes in ampulla and 274 and 316 genes in the isthmus were up-regulated and down-regulated in LF samples, respectively. To validate the RNAseq results, transcript abundance of 23 genes was assessed by qPCR and expression patterns were consistent between the two techniques. A functional enrichment analysis was performed using Database for Annotation, Visualization and Integrated Discovery (DAVID) software. Processes enriched in the LF group included tissue morphology changes (extracellular matrix remodeling), cellular changes (proliferation), and secretion changes (growth factors, ions and metal transporters). An overview of the gene expression data was deposited in the NCBI's Gene Expression Omnibus (GEO) and is accessible through the accession number <span>GSE65681</span><svg><path></path></svg>. In conclusion, differences in the peri-ovulatory sex steroid milieu modify the oviductal gene expression profiles. Such differences may be associated with the greater fertility of the LF cows. This dataset is useful for further investigations of the oviductal biology and the impact of sex-steroid on the female reproductive tract.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"13 ","pages":"Pages 27-29"},"PeriodicalIF":0.0,"publicationDate":"2017-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.06.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35130956","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":"Cultivar-specific transcriptome prediction and annotation in Ficus carica L.","authors":"Liceth Solorzano Zambrano,&nbsp;Gabriele Usai,&nbsp;Alberto Vangelisti,&nbsp;Flavia Mascagni,&nbsp;Tommaso Giordani,&nbsp;Rodolfo Bernardi,&nbsp;Andrea Cavallini,&nbsp;Riccardo Gucci,&nbsp;Giovanni Caruso,&nbsp;Claudio D'Onofrio,&nbsp;Mike Frank Quartacci,&nbsp;Piero Picciarelli,&nbsp;Barbara Conti,&nbsp;Andrea Lucchi,&nbsp;Lucia Natali","doi":"10.1016/j.gdata.2017.07.005","DOIUrl":"10.1016/j.gdata.2017.07.005","url":null,"abstract":"<div><p>The availability of transcriptomic data sequence is a key step for functional genomics studies. Recently, a repertoire of predicted genes of a Japanese cultivar of fig (<em>Ficus carica</em> L.) was released. Because of the great phenotypic variability that can be found in this species, we decided to study another fig genotype, the Italian cv. Dottato, in order to perform comparative studies between the two cultivars and extend the pan genome of this species. We isolated, sequenced and assembled fig genomic DNA from young fruits of cv. Dottato. Then, putative gene sequences were predicted and annotated. Finally, a comparison was performed between cvs. Dottato and Horaishi predicted transcriptomes. Our data provide a resource (available at the Sequence Read Archive database under SRP109082) to be used for functional genomics of fig, in order to fill the gap of knowledge still existing in this species concerning plant development, defense and adaptation to the environment.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"13 ","pages":"Pages 64-66"},"PeriodicalIF":0.0,"publicationDate":"2017-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.07.005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35192134","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":"Cataloguing the bacterial community of the Great Salt Plains, Oklahoma using 16S rRNA based metagenomics pyrosequencing","authors":"Ahmed H. Gad","doi":"10.1016/j.gdata.2017.03.002","DOIUrl":"10.1016/j.gdata.2017.03.002","url":null,"abstract":"<div><p>The Great Salt Plains of Oklahoma (GSP) is an extreme region, a hypersaline environment from marine origin and a unique area of the Salt National Wild Refuge in the north-central region of Oklahoma. In this study we analyzed the diversity and distribution of bacteria in two habitats; vegetated areas (GAB) and salt flat areas (GAS) in the sediments of GSP using the high-throughput techniques of 16S rRNA gene amplicon (V1-V2 regions) metagenomics-454 pyrosequencing. The filtered sequences resulted to a total of 303,723 paired end reads were generated, assigned into 1646 numbers of OTUs and 56.4% G<!--> <!-->+<!--> <!-->C content for GAB, and a total of 144,496 paired end reads were generated, assigned into 785 numbers of OTUs and 56.7% G<!--> <!-->+ C content for GAS. All the resulting 16S rRNA was of an average length<!--> <!-->~<!--> <!-->187<!--> <!-->bp, assigned to 37 bacterial phyla and candidate divisions. The abundant OTUs were affiliated with Proteobacteria (36.2% in GAB and 31.5% in GAS), Alphaproteobacteria (13.3% in GAB and 8.7% in GAS), Gammaproteobacteria (13% in GAB and 14.2% in GAS), Deltaproteobacteria (6.5% in GAB and 6.1% in GAS), Betaproteobacteria (2.6% in GAB and 1.14% in GAS), Bacteroidetes (16.8% in GAB and 24.3% in GAS), Chloroflexi (8.7% in GAB and 6% in GAS), Actinobacteria (8.5% in GAB and 5.8% in GAS) and Firmicutes (6.5% in GAB and 6.6% in GAS). This is the first study of a high resolution microbial phylogenetic profile of the GSP and the findings stipulate evidence of the bacterial heterogeneity that might be originated by surface and subsurface environments and better understanding of the ecosystem dynamics of GSP. Metagenome sequence data are available at NCBI with accession numbers; LT699840-LT700186.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 54-57"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.03.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34878760","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":"Dynamic regulation of small RNAome during the early stage of cardiac differentiation from pluripotent embryonic stem cells","authors":"Yue Li ,&nbsp;An Zeng ,&nbsp;Ge Li ,&nbsp;Ya-Na Guan ,&nbsp;Huang-Tian Yang ,&nbsp;Bairong Shen ,&nbsp;Qing Jing","doi":"10.1016/j.gdata.2017.05.006","DOIUrl":"10.1016/j.gdata.2017.05.006","url":null,"abstract":"<div><p>Embryonic stem cells (mESCs), having potential to differentiate into three germ-layer cells including cardiomyocytes, shall be a perfect model to help understanding heart development. Here, using small RNA deep sequencing, we studied the small RNAome in the early stage of mouse cardiac differentiation. We found that the expression pattern of most microRNA (miRNA) were highly enriched at the beginning and declined thereafter, some were still insufficiently expressed on day 6, and most miRNAs recovered in the following days. When pluripotent embryonic stem cells are differentiating to cardiomyocytes, targeted genes are concentrated on TGF, WNT and cytoskeletal remodeling pathway. The pathway and network of dynamically changed target genes of the miRNAs at different time points were also investigated. Furthermore, we demonstrated that small rDNA-derived RNAs (srRNAs) were significantly up-regulated during differentiation, especially in stem cells. The pathways of srRNAs targeted genes were also presented. We described the existence and the differential expression of transfer RNA (tRNA), Piwi-interacting RNA (piRNA) and Endogenous siRNAs (<em>endo</em>-siRNAs) in this process. This study reports the genome-wide small RNAome profile, and provides a uniquely comprehensive view of the small RNA regulatory network that governs embryonic stem cell differentiation and cardiac development.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 136-145"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.05.006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35023906","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":"Complete genome sequence of a natural compounds producer, Streptomyces violaceus S21","authors":"Jiafang Fu ,&nbsp;Chuanqing Zhong ,&nbsp;Zhilong Zhao ,&nbsp;Gongli Zong ,&nbsp;Guangxiang Cao","doi":"10.1016/j.gdata.2017.04.002","DOIUrl":"10.1016/j.gdata.2017.04.002","url":null,"abstract":"<div><p>The complete genome sequence of <em>Streptomyces violaceus</em> strain S21, a valuable natural compounds producer isolated from the forest soil, is firstly presented here. The genome comprised 7.91M<!--> <!-->bp, with a G<!--> <!-->+<!--> <!-->C content of 72.65%. A range of genes involved in pathways of secondary product biosynthesis were predicted. The genome sequence is available at DDBJ/EMBL/Genbank under the accession number <span>CP020570</span><svg><path></path></svg>. This genome is annotated with 6856 predicted genes identifying the natural product biosynthetic gene clusters in <em>S. violaceus</em>.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 116-117"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.04.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34984743","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":"Small RNA-seq analysis in response to methyl jasmonate and abscisic acid treatment in Persicaria minor","authors":"Nazaruddin Nazaruddin ,&nbsp;Abdul Fatah A. Samad ,&nbsp;Muhammad Sajad ,&nbsp;Jaeyres Jani ,&nbsp;Zamri Zainal ,&nbsp;Ismanizan Ismail","doi":"10.1016/j.gdata.2017.05.011","DOIUrl":"https://doi.org/10.1016/j.gdata.2017.05.011","url":null,"abstract":"<div><p><em>Persicaria minor</em> (Kesum) is an important medicinal plant with high level of secondary metabolite contents, especially, terpenoids and flavonoids. Previous studies have revealed that application of exogenous phytohormone could increase secondary metabolite contents of the plant. MicroRNAs (miRNAs) are small RNAs that play important regulatory roles in various biological processes. In order to explore the possible role of miRNA in the regulation of these phytohormones signaling pathway and uncovering their potential correlation, we, for the first time, have generated the smallRNA library of Kesum plant. The library was developed in response to methyl jasmonate (MJ) and abscisic acid (ABA) treatment by using next-generation sequencing technology. Raw reads have been deposited to SRA database with the accession numbers, SRX2655642 and SRX2655643 (MJ-treated), SRXSRX2655644 and SRX2655645 (ABA-treated) and SRX2655646and SRX2655647 (Control).</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 157-158"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.05.011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92077599","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}