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Genomics Data

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https://www.readbyqxmd.com/read/28702356/genome-sequence-of-bradyrhizobium-sp-lmtr-3-a-diazotrophic-symbiont-of-lima-bean-phaseolus-lunatus
#1
Ernesto Ormeño-Orrillo, Luis Rey, David Durán, Carlos A Canchaya, Doris Zúñiga-Dávila, Juan Imperial, Esperanza Martínez-Romero, Tomás Ruiz-Argüeso
Bradyrhizobium sp. LMTR 3 is a representative strain of one of the geno(species) of diazotrophic symbionts associated with Lima bean (Phaseolus lunatus) in Peru. Its 7.83 Mb genome was sequenced using the Illumina technology and found to encode a complete set of genes required for nodulation and nitrogen fixation, and additional genes putatively involved in root colonization. Its draft genome sequence and annotation have been deposited at GenBank under the accession number MAXC00000000.
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28702355/whole-genome-sequencing-and-annotation-of-halophilic-salinicoccus-sp-bab-3246-isolated-from-the-coastal-region-of-gujarat
#2
Vishal Mevada, Shradhdha Patel, Jignesh Pandya, Himani Joshi, Rajesh Patel
Salinicoccus sp. BAB 3246 is a halophilic bacterium isolated from a marine water sample collected from the coastal region of Gujarat, India, from a surface water stream. Based on 16sRNA sequencing, the organism was identified as Salinicoccus sp. BAB 3246 (Genebank ID: KF889285). The present work was performed to determine the whole genome sequence of the organism using Ion Torrent PGM platform followed by assembly using the CLC genomics workbench and genome annotation using RAST, BASys and MaGe. The complete genome sequence was 713,204 bp identified by with second largest size for Salinicoccus sp...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28664146/oviductal-transcriptional-profiling-of-a-bovine-fertility-model-by-next-generation-sequencing
#3
Angela Maria Gonella-Diaza, Sónia Cristina da Silva Andrade, Mariana Sponchiado, Guilherme Pugliesi, Fernando Silveira Mesquita, Veerle Van Hoeck, Ricardo de Francisco Strefezzi, Gustavo R Gasparin, Luiz L Coutinho, Mario Binelli
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...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28652975/draft-genome-sequence-of-massilia-sp-kim-isolated-from-south-african-grassland-biome-soils
#4
Surendra Vikram, Nerissa Govender, Mubanga Helen Kabwe, Oliver Bezuidt, Thulani P Makhalanyane
Massilia sp. are aerobic, Gram-negative, rod-shaped bacteria that are found in air, water, and soils. Here we describe the draft genome sequence of Massilia sp. KIM, isolated from the South African grassland soils. The total length of the genome was estimated at 5.73 Mb, comprised of 17 contigs. The draft genome has been deposited in the DDBJ/EMBL/GenBank under the accession MVAD10000000 and is available for download at: https://www.ncbi.nlm.nih.gov/nuccore/MVAD00000000. Additionally, the raw short reads are available in the NCBI SRA database under the accession number: SRR5469241...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28652974/the-draft-genome-sequence-of-hymenobacter-sp-cra2-isolated-from-nama-karoo-shrub-land-soils-from-south-africa
#5
Mubanga H Kabwe, Nerissa Govender, Surendra Vikram, Oliver M Bezuidt, Thulani P Makhalanyane
Here we report the draft genome sequence of Hymenobacter sp. CRA2 isolated from the Nama Karoo shrub land soils of the Northern Cape, South Africa. This genome is approximately 5.88 Mb long and the assembly comprised 45 contigs. The draft genome sequence has been deposited in DDBJ/EMBL/GenBank under the accession number NZ_MVBC00000000 and is available for download at: https://www.ncbi.nlm.nih.gov/nuccore/NZ_MVBC00000000.1.
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28649496/de-novo-transcriptome-assembly-of-loggerhead-sea-turtle-nesting-of-the-colombian-caribbean
#6
Javier Hernández-Fernández, Andrés Pinzón, Leonardo Mariño-Ramírez
Loggerhead sea turtle Caretta caretta is widely distributed in the oceans of tropical and subtropical latitude. This turtle is an endangered species due to anthropic and natural factors that have decreased their population levels. In this study, RNA sequencing and de-novo assembly of genes expressed in blood were performed. The raw FASTQ files have been deposited on NCBI's SRA database with accession number SRX2629512. A total of 5.4 Gb raw sequence data were obtained, corresponding to 48,257,019 raw reads...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28626638/transcriptome-of-barley-under-three-different-heavy-metal-stress-reaction
#7
Martina Kintlová, Nicolas Blavet, Radim Cegan, Roman Hobza
In the present study, we used Illumina sequencing technology (HiSeq 2000) to sequence the transcriptome of barley (Hordeum vulgare 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...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28626637/transcriptome-analysis-of-reproductive-tissue-differentiation-in-jatropha-curcas-linn
#8
Nisha Govender, Siju Senan, Zeti-Azura Mohamed-Hussein, Wickneswari Ratnam
Shoot and inflorescence are central physiological and developmental tissues of plants. Flowering is one of the most important agronomic traits for improvement of crop yield. To analyze the vegetative to reproductive tissue transition in Jatropha curcas, gene expression profiles were generated from shoot and inflorescence tissues. RNA isolated from both tissues was sequenced using the Ilumina HiSeq 2500 platform. Differential gene expression analysis identified key biological processes associated with vegetative to reproductive tissue transition...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28580299/whole-genome-shotgun-sequence-of-phenazine-producing-endophytic-streptomyces-kebangsaanensis-suk12
#9
Juwairiah Remali, Kok-Keong Loke, Chyan Leong Ng, Wan Mohd Aizat, John Tiong, Noraziah Mohamad Zin
Streptomyces sp. produces bioactive compounds with a broad spectrum of activities. Streptomyces kebangsaanesis SUK12 has been identified as a novel endophytic bacteria isolated from ethnomedicinal plant Portulaca olerace, 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 Streptomyces kebangsaanensis SUK12. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number PRJNA269542...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28560170/rna-seq-detects-pharmacological-inhibition-of-epstein-barr-virus-late-transcription-during-spontaneous-reactivation
#10
An T Phan, Delsy M Martinez, Jj L Miranda
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...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28560169/small-rna-sequencing-for-secondary-metabolite-analysis-in-persicaria-minor
#11
Abdul Fatah A Samad, Nazaruddin Nazaruddin, Muhammad Sajad, Jaeyres Jani, Abdul Munir Abdul Murad, Zamri Zainal, Ismanizan Ismail
Persicaria minor (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 P. minor, 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...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28560168/genome-sequence-of-the-oleaginous-yeast-rhodotorula-toruloides-strain-cgmcc-2-1609
#12
Christine Sambles, Sabine Middelhaufe, Darren Soanes, Dagmara Kolak, Thomas Lux, Karen Moore, Petra Matoušková, David Parker, Rob Lee, John Love, Stephen J Aves
Most eukaryotic oleaginous species are yeasts and among them the basidiomycete red yeast, Rhodotorula (Rhodosporidium) toruloides (Pucciniomycotina) is known to produce high quantities of lipids when grown in nitrogen-limiting media, and has potential for biodiesel production. The genome of the CGMCC 2.1609 strain of this oleaginous red yeast was sequenced using a hybrid of Roche 454 and Illumina technology generating 13 × coverage. The de novo assembly was carried out using MIRA and scaffolded using MAQ and BAMBUS...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28560167/rna-seq-analysis-of-mangosteen-garcinia-mangostana-l-fruit-ripening
#13
Azhani Abdul-Rahman, Hoe-Han Goh, Kok-Keong Loke, Normah Mohd Noor, Wan Mohd Aizat
Mangosteen (Garcinia mangostana 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...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28560166/small-rna-seq-analysis-in-response-to-methyl-jasmonate-and-abscisic-acid-treatment-in-persicaria-minor
#14
Nazaruddin Nazaruddin, Abdul Fatah A Samad, Muhammad Sajad, Jaeyres Jani, Zamri Zainal, Ismanizan Ismail
Persicaria minor (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...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28560165/draft-genome-of-the-oomycete-pathogen-phytophthora-cactorum-strain-lv007-isolated-from-european-beech-fagus-sylvatica
#15
Laura J Grenville-Briggs, Sandeep K Kushwaha, Michelle R Cleary, Johanna Witzell, Eugene I Savenkov, Stephen C Whisson, Aakash Chawade, Ramesh R Vetukuri
Phytophthora cactorum is a broad host range phytopathogenic oomycete. P. cactorum strain LV007 was isolated from a diseased European Beech (Fagus sylvatica) in Malmö, Sweden in 2016. The draft genome of P. cactorum strain LV007 is 67.81 Mb. It contains 15,567 contigs and 21,876 predicted protein-coding genes. As reported for other phytopathogenic Phytophthora species, cytoplasmic effector proteins including RxLR and CRN families were identified. The genome sequence has been deposited at DDBJ/ENA/GenBank under the accession NBIJ00000000...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28540183/the-draft-genome-of-corchorus-olitorius-cv-jro-524-navin
#16
Debabrata Sarkar, Ajay Kumar Mahato, Pratik Satya, Avijit Kundu, Sangeeta Singh, Pawan Kumar Jayaswal, Akshay Singh, Kaushlendra Bahadur, Sasmita Pattnaik, Nisha Singh, Avrajit Chakraborty, Nur Alam Mandal, Debajeet Das, Tista Basu, Amitha Mithra Sevanthi, Dipnarayan Saha, Subhojit Datta, Chandan Sourav Kar, Jiban Mitra, Karabi Datta, Pran Gobinda Karmakar, Tilak Raj Sharma, Trilochan Mohapatra, Nagendra Kumar Singh
Here, we present the draft genome (377.3 Mbp) of Corchorus olitorious 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 Theobroma cacao followed by Gossypium raimondii...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28540182/mannose-binding-lectin-mbl-gene-polymorphisms-in-susceptibility-to-pulmonary-tuberculosis-among-the-lur-population-of-lorestan-province-of-iran
#17
Ali Amiri, Toomaj Sabooteh, Farhad Shahsavar, Khatereh Anbari, Flora Pouremadi
OBJECTIVE: 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 MBL polymorphisms and TB has been studied in various populations, the results are controversial. The aim of this study was to investigate mannose-binding lectin (MBL) gene polymorphisms with susceptibility to pulmonary tuberculosis (PTB) in a Lur population of Iran. METHODS: In this case-control study, four functional MBL gene polymorphisms (HL, XY, PQ and AB) 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)...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28540181/dynamic-regulation-of-small-rnaome-during-the-early-stage-of-cardiac-differentiation-from-pluripotent-embryonic-stem-cells
#18
Yue Li, An Zeng, Ge Li, Ya-Na Guan, Huang-Tian Yang, Bairong Shen, Qing Jing
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...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28529883/smrt-sequencing-data-for-garcinia-mangostana-l-variety-mesta
#19
Mohd Razik Midin, Kok-Keong Loke, Maria Madon, Mohd Shukor Nordin, Hoe-Han Goh, Normah Mohd Noor
The "Queen of Fruits" mangosteen (Garcinia mangostana 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 [1]). 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...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28529882/transcriptomic-data-of-arabidopsis-thaliana-hypocotyl-upon-suppression-of-expansin-genes
#20
Iqmal Asyraf Ilias, Othman Babul Airianah, Syarul Nataqain Baharum, Hoe-Han Goh
Expansin is a cell wall loosening protein without hydrolytic activity, which allows cell expansion by influencing cell wall extensibility. Previous studies showed that the suppression of expansin genes (EXPA1, EXPA3, EXPA5 and EXPA10) resulted in defective organ growth and altered cell wall chemical composition [1,2]. However, the molecular mechanism on how the suppression of non-enzymatic expansin expression can result in widespread effects on plant cell wall and organ growth is still unclear. In this study, we performed transcriptomic analysis on the hypocotyls of previously reported transgenic Arabidopsis line [1] to investigate the effects of expansin gene suppression on the global gene expression pattern, particularly on the cell wall related genes...
June 2017: Genomics Data
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