Genomics Data最新文献

{"title":"DNA shotgun sequencing analysis of Garcinia mangostana L. variety Mesta","authors":"Syuhaidah Abu Bakar ,&nbsp;Suresh Kumar ,&nbsp;Kok-Keong Loke ,&nbsp;Hoe-Han Goh ,&nbsp;Normah Mohd Noor","doi":"10.1016/j.gdata.2017.05.001","DOIUrl":"10.1016/j.gdata.2017.05.001","url":null,"abstract":"<div><p>Mangosteen (<em>Garcinia mangostana</em> Linn.) is an ultra-tropical tree characterized by its unique dark purple fruits with white flesh. The xanthone-rich purple pericarp tissue contains valuable compounds with medicinal properties. Following previously reported genome sequencing of a common variety of mangosteen <span>[1]</span>, we performed another whole genome sequencing of a commercially popular variety of this fruit species (var. Mesta) for comparative analysis of its genome composition. Raw reads of the DNA sequencing project were deposited to SRA database with the accession number SRX2709728.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 118-119"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.05.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35005012","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":"Sequencing and de novo transcriptome assembly of the Chinese giant salamander (Andrias davidianus)","authors":"Yong Huang,&nbsp;Xiao Chan Gao,&nbsp;Jian Li Xiong,&nbsp;Hong Tao Ren,&nbsp;Xi Hong Sun","doi":"10.1016/j.gdata.2017.03.011","DOIUrl":"https://doi.org/10.1016/j.gdata.2017.03.011","url":null,"abstract":"<div><p>Next-generation technologies for determination of genomics and transcriptomics composition have a wide range of applications. <em>Andrias davidianus</em>, has become an endangered amphibian species of salamander endemic in China. However, there is a lack of the molecular information. In this study, we obtained the RNA-Seq data from a pool of <em>A. davidianus</em> tissue including spleen, liver, muscle, kidney, skin, testis, gut and heart using Illumina HiSeq 2500 platform. A total of 15,398,997,600<!--> <!-->bp were obtained, corresponding to 102,659,984 raw reads. A total of 102,659,984 reads were filtered after removing low-quality reads and trimming the adapter sequences. The Trinity program was used to de novo assemble 132,912 unigenes with an average length of 690<!--> <!-->bp and N50 of 1263<!--> <!-->bp. Unigenes were annotated through number of databases. These transcriptomic data of <em>A. davidianus</em> should open the door to molecular evolution studies based on the entire transcriptome or targeted genes of interest to sequence. The raw data in this study can be available in NCBI SRA database with accession number of SRP099564.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 109-110"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.03.011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92030635","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":"SMRT sequencing data for Garcinia mangostana L. variety Mesta","authors":"Mohd Razik Midin ,&nbsp;Kok-Keong Loke ,&nbsp;Maria Madon ,&nbsp;Mohd Shukor Nordin ,&nbsp;Hoe-Han Goh ,&nbsp;Normah Mohd Noor","doi":"10.1016/j.gdata.2017.04.003","DOIUrl":"https://doi.org/10.1016/j.gdata.2017.04.003","url":null,"abstract":"<div><p>The “Queen of Fruits” mangosteen (<em>Garcinia mangostana</em> L.) produces commercially important fruits with desirable taste of flesh and pericarp rich in xanthones with medicinal properties. To date, only limited knowledge is available on the cytogenetics and genome sequences of a common variety of mangosteen (Abu Bakar et al., 2016 <span>[1]</span>). Here, we report the first single-molecule real-time (SMRT) sequencing data from whole genome sequencing of mangosteen of Mesta variety. Raw reads of the SMRT sequencing project can be obtained from SRA database with the accession numbers SRX2718652 until SRX2718659.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 134-135"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.04.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92077598","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":"Novel quorum quenching enzymes identified from draft genome of Roseomonas sp. TAS13","authors":"Eri Nasuno ,&nbsp;Tomohiro Suzuki ,&nbsp;Ryoko Suzuki ,&nbsp;Chigusa Okano ,&nbsp;Takeshi Kurokura ,&nbsp;Ken-ichi Iimura ,&nbsp;Norihiro Kato","doi":"10.1016/j.gdata.2017.02.001","DOIUrl":"10.1016/j.gdata.2017.02.001","url":null,"abstract":"<div><p><em>Roseomonas</em> sp. strain TAS13 isolated from an activated sludge sample degrades <em>N</em>-acylhomoserine lactones (AHLs) that are widely utilized as a signal in bacterial quorum sensing systems. The draft genome of <em>Roseomonas</em> sp. TAS13 contains 816 contigs (total 5,078,941<!--> <!-->bp) which carries 4760 protein-coding genes and 52 tRNA genes (DDBJ/EMBL/GenBank accession numbers BDLP01000001 through BDLP01000816).</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 22-23"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.02.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34796481","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":"Comparative study the expression of calcium cycling genes in Bombay duck (Harpadon nehereus) and beltfish (Trichiurus lepturus) with different swimming activities","authors":"Hui Zhang ,&nbsp;Gilbert Audira ,&nbsp;Yuan Li ,&nbsp;Weiwei Xian ,&nbsp;Muhammed Muhsin Varikkodan ,&nbsp;Chung-Der Hsiao","doi":"10.1016/j.gdata.2017.03.003","DOIUrl":"10.1016/j.gdata.2017.03.003","url":null,"abstract":"<div><p>The contraction and relaxation events of the muscle is mediated by the coordination of many important calcium cycling proteins of ryanodine receptor (RYR), troponin C (TNNC), parvalbumin (PVALB), sarcoendoplasmic reticulum calcium transport ATPase (SERCA) and calsequestrin (CASQ). In higher vertebrates, the expression level of calcium cycling proteins are positively correlated to the muscle contraction/relaxation ability of the cell. In this study, we used RNAseq to explore the expression profile of calcium cycling genes between two marine fish of Bombay duck (<em>Harpadon nehereus</em>) and beltfish (<em>Trichiurus lepturus</em>) with poor and robust swimming activities, respectively. We have studied the hypothesis whether the expression level of calcium cycling proteins are also positive correlated to swimming ability in fish. We used Illumina sequencing technology (NextSeq500) to sequence, assemble and annotate the muscle transcriptome of Bombay duck for the first time. A total of 47,752,240 cleaned reads (deposited in NCBI SRA database with accession number of SRX1706379) were obtained from RNA sequencing and 26,288 unigenes (with N50 of 486<!--> <!-->bp) were obtained after de novo assembling with Trinity software. BLASTX against NR, GO, KEGG and eggNOG databases show 100%, 65%, 26%, 94% and 88% annotation rate, respectively. Comparison of the dominantly expressed unigenes in fish muscle shows calcium cycling gene expression in beltfish (SRX1674471) is 1.4- to 51.6-fold higher than Bombay duck. Among five calcium cycling genes, the fold change results are very significant in CASQ (51.6 fold) and PVALB (9.1 fold) and both of them are responsive for calcium binding to reduce free calcium concentration in the sarcoendoplasmic reticulum and cytoplasm. In conclusion, we confirmed that the high abundant expression rate of calcium cycling genes in robust swimming fish species. The current muscle transcriptome and identified calcium cycling gene data can provide more insights into the muscle physiology of fish.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 58-61"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.03.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34884037","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":"Mannose-Binding Lectin (MBL) gene polymorphisms in susceptibility to pulmonary tuberculosis among the Lur population of Lorestan Province of Iran","authors":"Ali Amiri ,&nbsp;Toomaj Sabooteh ,&nbsp;Farhad Shahsavar ,&nbsp;Khatereh Anbari ,&nbsp;Flora Pouremadi","doi":"10.1016/j.gdata.2017.05.005","DOIUrl":"10.1016/j.gdata.2017.05.005","url":null,"abstract":"<div><h3>Objective</h3><p>Tuberculosis (TB) is caused by infection of Mycobacterium tuberculosis. Host genetic variability is an important determinant of the risk of developing TB in humans. Although the association between <em>MBL</em> polymorphisms and TB has been studied in various populations, the results are controversial. The aim of this study was to investigate mannose-binding lectin (<em>MBL</em>) gene polymorphisms with susceptibility to pulmonary tuberculosis (PTB) in a Lur population of Iran.</p></div><div><h3>Methods</h3><p>In this case-control study, four functional <em>MBL</em> gene polymorphisms (<em>HL</em>, <em>XY</em>, <em>PQ</em> and <em>AB</em>) were genotyped by using PCR Single Strand Conformation Polymorphism (SSCP) technique in a Lur population living in Lorestan Province, consisting of 100 patients with pulmonary tuberculosis (PTB) age and sex matched 100 healthy controls (HCs). Association analyses were performed with the SPSS 21 statistical software.</p></div><div><h3>Results</h3><p>We found that <em>MBL</em> (<em>HH</em>) genotype polymorphism significantly was associated with increased susceptibility to TB (35% in patients vs. 22% in controls, P<!--> <!-->=<!--> <!-->0.0417, OR<!--> <!-->=<!--> <!-->1.909, %95 CI<!--> <!-->=<!--> <!-->1.020–3.573). Additionally, <em>H</em> allele showed a significant association with increased risk of TB (56.5% in patients vs. 46% in controls, P<!--> <!-->=<!--> <!-->0.0357, OR<!--> <!-->=<!--> <!-->1.525, %95 CI<!--> <!-->=<!--> <!-->1.028–2.262). Also, the distribution of <em>L</em> allele in patients was significantly lower frequency in TB patients compared to controls (43.5% vs. 54%, P<!--> <!-->=<!--> <!-->0.0357, OR<!--> <!-->=<!--> <!-->0.656, %95 CI<!--> <!-->=<!--> <!-->0.442–0.973). However, the allelic and genotypic frequencies of <em>AB</em>, <em>XY</em> and <em>PQ</em> polymorphisms were not significantly different between the patients and the controls. We couldn't detect any significant differences between haplotypes among TB patients and healthy controls.</p></div><div><h3>Conclusions</h3><p>Our findings demonstrated that <em>HH</em> genotype and <em>H</em> allele may increase the susceptibility to pulmonary TB in the Lur population of Iran, although <em>L</em> allele may decrease the susceptibility to pulmonary TB in this population. We suggest that it is necessary to further more studies with larger sample size and other ethnic population.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 146-150"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.05.005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35023907","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 draft genome of Corchorus olitorius cv. JRO-524 (Navin)","authors":"Debabrata Sarkar ,&nbsp;Ajay Kumar Mahato ,&nbsp;Pratik Satya ,&nbsp;Avijit Kundu ,&nbsp;Sangeeta Singh ,&nbsp;Pawan Kumar Jayaswal ,&nbsp;Akshay Singh ,&nbsp;Kaushlendra Bahadur ,&nbsp;Sasmita Pattnaik ,&nbsp;Nisha Singh ,&nbsp;Avrajit Chakraborty ,&nbsp;Nur Alam Mandal ,&nbsp;Debajeet Das ,&nbsp;Tista Basu ,&nbsp;Amitha Mithra Sevanthi ,&nbsp;Dipnarayan Saha ,&nbsp;Subhojit Datta ,&nbsp;Chandan Sourav Kar ,&nbsp;Jiban Mitra ,&nbsp;Karabi Datta ,&nbsp;Nagendra Kumar Singh","doi":"10.1016/j.gdata.2017.05.007","DOIUrl":"10.1016/j.gdata.2017.05.007","url":null,"abstract":"<div><p>Here, we present the draft genome (377.3<!--> <!-->Mbp) of <em>Corchorus olitorious</em> cv. JRO-524 (Navin), which is a leading dark jute variety developed from a cross between African (cv. Sudan Green) and indigenous (cv. JRO-632) types. We predicted from the draft genome a total of 57,087 protein-coding genes with annotated functions. We identified a large number of 1765 disease resistance-like and defense response genes in the jute genome. The annotated genes showed the highest sequence similarities with that of <em>Theobroma cacao</em> followed by <em>Gossypium raimondii</em>. Seven chromosome-scale genetically anchored pseudomolecules were constructed with a total size of 8.53<!--> <!-->Mbp and used for synteny analyses with the cocoa and cotton genomes. Like other plant species, <em>gypsy</em> and <em>copia</em> retrotransposons were the most abundant classes of repeat elements in jute. The raw data of our study are available in SRA database of NCBI with accession number SRX1506532. The genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession LLWS00000000, and the version described in this paper will be the first version (LLWS01000000).</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 151-154"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.05.007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35024313","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":"De novo transcriptome assembly and its annotation for the aposematic wood tiger moth (Parasemia plantaginis)","authors":"Galarza Juan A. ,&nbsp;Kishor Dhaygude ,&nbsp;Johanna Mappes","doi":"10.1016/j.gdata.2017.03.008","DOIUrl":"10.1016/j.gdata.2017.03.008","url":null,"abstract":"<div><p>In this paper we report the public availability of transcriptome resources for the aposematic wood tiger moth (<em>Parasemia plantaginis</em>). A comprehensive assembly methods, quality statistics, and annotation are provided. This reference transcriptome may serve as a useful resource for investigating functional gene activity in aposematic Lepidopteran species. All data is freely available at the European Nucleotide Archive (<span>http://www.ebi.ac.uk/ena</span><svg><path></path></svg>) under study accession number: PRJEB14172.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 71-73"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.03.008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34892887","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 Cercospora sojina isolate S9, a fungus causing frogeye leaf spot (FLS) disease of soybean","authors":"Fanchang Zeng ,&nbsp;Chaofan Wang ,&nbsp;Guirong Zhang ,&nbsp;Junmei Wei ,&nbsp;Carl A. Bradley ,&nbsp;Ray Ming","doi":"10.1016/j.gdata.2017.02.014","DOIUrl":"10.1016/j.gdata.2017.02.014","url":null,"abstract":"<div><p>Fungi are the causal agents of many of the world's most serious plant diseases causing disastrous consequences for large-scale agricultural production. Pathogenicity genomic basis is complex in fungi as multicellular eukaryotic pathogens. The fungus <em>Cercospora sojina</em> is a plant pathogen that threatens global soybean supplies. Here, we report the genome sequence of <em>C</em>. <em>sojina</em> strain S9 and detect genome features and predicted genomic elements. The genome sequence of <em>C</em>. <em>sojina</em> is a valuable resource with potential in studying the fungal pathogenicity and soybean host resistance to frogeye leaf spot (FLS), which is caused by <em>C</em>. <em>sojina</em>. The <em>C</em>. <em>sojina</em> genome sequence has been deposited and available at DDBJ/EMBL/GenBank under the project accession number AHPQ00000000.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 79-80"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.02.014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34892890","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":"Hypothalamic transcriptome analysis of congenic-derived F2 mice (chromosome 17:3–45 Mb) exhibiting preferential carbohydrate (versus fat) intake","authors":"Brenda K. Richards,&nbsp;Claudia Kappen,&nbsp;Susan Newman","doi":"10.1016/j.gdata.2017.02.009","DOIUrl":"10.1016/j.gdata.2017.02.009","url":null,"abstract":"","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 24-27"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.02.009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34796482","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}