Genome assembly of Chryseobacterium sp. strain IHBB 10212 from glacier top-surface soil in the Indian trans-Himalayas with potential for hydrolytic enzymes
Publication date: Available online 1 July 2017 Source:Genomics Data Author(s): Mohinder Pal, Mohit Kumar Swarnkar, Hena Dhar, Sanjay Chhibber, Arvind Gulati The cold-active esterases are gaining importance due to their catalytic activities finding applications in chemical industry, food processes and detergent industry as additives, and organic synthesis of unstable compounds as catalysts. In the present study, the complete genome sequence of 4,843,645bp with an average 34.08% G+C content and 4,260 protein-coding genes are reported for the low temperature-active esterase-producing novel strain of Chrysobacterium iso...
Source: Genomics Data - July 2, 2017 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of Bradyrhizobium paxllaeri LMTR 21T isolated from Lima bean (Phaseolus lunatus) in Peru
Publication date: Available online 30 June 2017 Source:Genomics Data Author(s): Ernesto Ormeño-Orrillo, Luis Rey, David Durán, Carlos A. Canchaya, Marco A. Rogel, Doris Zúñiga-Dávila, Juan Imperial, Tomás Ruiz-Argüeso, Esperanza Martínez-Romero Bradyrhizobium paxllaeri is a prevalent species in root nodules of the Lima bean (Phaseolus lunatus) in Peru. LMTR 21T is the type strain of the species and was isolated from a root nodule collected in an agricultural field in the Peruvian central coast. Its 8.29Mbp genome encoded 7635 CDS, 71 tRNAs and 3 rRNAs genes. All genes required to stablish a nitrogen-fixi...
Source: Genomics Data - July 1, 2017 Category: Genetics & Stem Cells Source Type: research
Genome sequence of Bradyrhizobium sp. LMTR 3, a diazotrophic symbiont of Lima bean (Phaseolus lunatus)
Publication date: Available online 28 June 2017 Source:Genomics Data Author(s): 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 7.83Mb 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 d...
Source: Genomics Data - June 29, 2017 Category: Genetics & Stem Cells Source Type: research
Whole genome sequencing and annotation of halophilic Salinicoccus sp. BAB 3246 isolated from the coastal region of Gujarat
Publication date: Available online 21 June 2017 Source:Genomics Data Author(s): 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 annota...
Source: Genomics Data - June 22, 2017 Category: Genetics & Stem Cells Source Type: research
Oviductal transcriptional profiling of a bovine fertility model by next-generation sequencing
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. (Source: Genomics Data)
Source: Genomics Data - June 16, 2017 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of Massilia sp. KIM isolated from South African grassland biome soils
Publication date: Available online 10 June 2017 Source:Genomics Data Author(s): 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 5.73Mb, 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.ni...
Source: Genomics Data - June 10, 2017 Category: Genetics & Stem Cells Source Type: research
De novo transcriptome assembly of loggerhead sea turtle nesting of the Colombian Caribbean
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 5.4Gb raw sequence data were obtained, corresponding to 48,257,019 raw reads. Trinity pipeline was used to perform a de-novo assembly, we were able to identify 64,930 transcripts for female loggerhead turtle transcriptome with an N50 of 1131bp. The obtained transcriptome data will be useful for further studies of the physiology, biochemistry and evolution in this species. (Source: Genomics Data)
Source: Genomics Data - June 9, 2017 Category: Genetics & Stem Cells Source Type: research
The draft genome sequence of Hymenobacter sp. CRA2 isolated from Nama Karoo shrub land soils from South Africa
Publication date: Available online 8 June 2017 Source:Genomics Data Author(s): 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 5.88Mb 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. (Source: Genomics Data)
Source: Genomics Data - June 9, 2017 Category: Genetics & Stem Cells Source Type: research
Whole-genome shotgun sequence of phenazine-producing endophytic Streptomyces kebangsaanensis SUK12
Publication date: Available online 24 May 2017 Source:Genomics Data Author(s): Juwairiah Remali, Loke Kok Keong, Chyan Leong Ng, Wan Mohd Aizat, John J.L. 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 ke...
Source: Genomics Data - May 25, 2017 Category: Genetics & Stem Cells Source Type: research
Transcriptome of barley under three different heavy metal stress reaction
Publication date: Available online 22 May 2017 Source:Genomics Data Author(s): 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 tra...
Source: Genomics Data - May 23, 2017 Category: Genetics & Stem Cells Source Type: research
Genome sequence of the oleaginous yeast Rhodotorula toruloides strain CGMCC 2.1609
Publication date: Available online 15 May 2017 Source:Genomics Data Author(s): 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 ...
Source: Genomics Data - May 16, 2017 Category: Genetics & Stem Cells Source Type: research
Transcriptome analysis of reproductive tissue differentiation in Jatropha curcas Linn.
Publication date: Available online 15 May 2017 Source:Genomics Data Author(s): Nisha Govender, Siju Senan, Zeti-Azura Mohamed-Hussein, Wickneswari Ratnam Shoot and inflorescence are central physiological and developmental process 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 b...
Source: Genomics Data - May 16, 2017 Category: Genetics & Stem Cells Source Type: research
RNA-seq detects pharmacological inhibition of Epstein-Barr virus late transcription during spontaneous reactivation
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. (Source: Genomics Data)
Source: Genomics Data - May 13, 2017 Category: Genetics & Stem Cells Source Type: research
Small RNA-seq analysis in response to methyl jasmonate and abscisic acid treatment in Persicaria minor
Publication date: Available online 12 May 2017 Source:Genomics Data Author(s): 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 ...
Source: Genomics Data - May 13, 2017 Category: Genetics & Stem Cells Source Type: research
Draft genome of the oomycete pathogen Phytophthora cactorum strain LV007 isolated from European beech (Fagus sylvatica)
Publication date: Available online 12 May 2017 Source:Genomics Data Author(s): 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 67.81Mb. It contains 15,567 contigs and 21,876 predicted protein-coding genes. As reported for other phytopathogenic Phytophthora species, cytoplasmi...
Source: Genomics Data - May 13, 2017 Category: Genetics & Stem Cells Source Type: research
