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Genomics Data

F Nadiya, N Anjali, Jinu Thomas, A Gangaprasad, K K Sabu
Elettaria cardamomum (L.) Maton, known as 'queen of spices, is a perennial herbaceous monocot of the family Zingiberaceae, native to southern India. Cardamom is an economically valuable spice crop and used widely in culinary and medicinal purposes. In the present study, using Ion Proton RNA sequencing technology, we performed transcriptome sequencing and de novo transcriptome assembly of a wild and five cultivar genotypes of cardamom. RNA-seq generated a total of 22,811,983 (92 base) and 24,889,197 (75 base) raw reads accounting for approximately 8...
March 2017: Genomics Data
Ricky Padilla-Del Valle, Luis R Morales-Vale, Carlos Ríos-Velázquez
In Puerto Rico, the microbial diversity of the thermal spring (ThS) in Coamo has never been studied using metagenomics. The focus of our research was to generate a metagenomic library from the ThS of Coamo, Puerto Rico and explore the microbial and functional diversity. The metagenomic library from the ThS waters was generated using direct DNA isolation. High molecular weight (40 kbp) DNA was end-repaired, electro eluted and ligated into a fosmid vector (pCCFOS1); then transduced into Escherichia coli EPI300-T1R using T1 bacteriophages...
March 2017: Genomics Data
Vitaly V Kadnikov, Andrey V Mardanov, Andrey B Poltaraus, Diyana S Sokolova, Ekaterina M Semenova, Nikolay V Ravin, Tatiyana P Tourova, Tamara N Nazina
The draft genome sequence of Geobacillus sp. strain 1017, a thermophilic aerobic oil-oxidizing bacterium isolated from formation water of the Dagang high-temperature oilfield, China, is presented here. The genome comprised 3.6 Mbp, with the G + C content of 51.74%. The strain had a number of genes responsible for numerous metabolic and transport systems, exopolysaccharide biosynthesis, and decomposition of sugars and aromatic compounds, as well as the genes related to resistance to metals and metalloids...
March 2017: Genomics Data
Jorge-Tonatiuh Ayala-Sumuano, Alexei Licea-Navarro, Enrique Rudiño-Piñera, Estefanía Rodríguez, Claudia Rodríguez-Almazán
Next-generation technologies for determination of genomics and transcriptomics composition have a wide range of applications. Moreover, the development of tools for big data set analysis has allowed the identification of molecules and networks involved in metabolism, evolution or behavior. By natural habitats aquatic organisms have implemented molecular strategies for survival, including the production and secretion of toxic compounds for their predators; therefore these organisms are possible sources of proteins or peptides with potential biotechnological application...
March 2017: Genomics Data
Alejandra Perina, Ana M González-Tizón, Iago F Meilán, Andrés Martínez-Lage
: The shrimp Palaemon serratus is a coastal decapod crustacean with a high commercial value. It is harvested for human consumption. In this study, we used Illumina sequencing technology (HiSeq 2000) to sequence, assemble and annotate the transcriptome of P. serratus. RNA was isolated from muscle of adults individuals and, from a pool of larvae. A total number of 4 cDNA libraries were constructed, using the TruSeq RNA Sample Preparation Kit v2. The raw data in this study was deposited in NCBI SRA database with study accession number of SRP090769...
March 2017: Genomics Data
A V Nedoluzhko, F S Sharko, S V Tsygankova, E S Boulygina, A S Sokolov, S M Rastorguev, V V Kadnikov, A V Mardanov, N V Ravin, A M Mazur, A A Polilov, N M Gruzdeva, E B Prokhortchouk, K G Skryabin
The vast majority of multicellular organisms coexist with bacterial symbionts that may play various roles during their life cycle. Parasitoid wasp Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae) belongs to the smallest known insects whose size is comparable with some bacteria. Using 16S rRNA gene sequencing and Whole Genome Sequencing (WGS), we described microbiota diversity for this arthropod and its potential impact on their lifecycle. Metagenomic sequences were deposited to SRA database which is available at NCBI with accession number SRX2363723 and SRX2363724...
March 2017: Genomics Data
Alexey Afonin, Anton Sulima, Aleksandr Zhernakov, Vladimir Zhukov
Rhizobium leguminosarum bv. viciae RCAM1026 is a strain first isolated in 1964 from nodules of "Ramensky 77" cultivar of garden pea (Pisum sativum L.) now routinely used as a model strain in inoculation experiments on pea. Assembly with SPAdes yielded 133 contigs longer then 200 bp (N50 = 202,321, GC% = 60.84). Resulting annotated genome is 7,248,686 bp encoding 6792 genes.
March 2017: Genomics Data
Samuel Peninal, Janakiraman Subramanian, Alaganatham Elavarasi, Murugaiyan Kalaiselvam
Anguilliformes, also known as "true eels", are an ecologically diverse group of predominantly marine origin whose members were easily recognized by their extremely elongated bodies with reduced cross-sectional areas and universal lack of pelvic fins. The Marine Eels were collected from landing centres of Parangipettai coastal waters and identified based on their morphometric and meristic characters. The newly recorded species were used for the barcoding analysis. Information on molecular taxonomy of marine eels was very meagre and hence, the present study was aimed to study the barcoding of marine eels which were present along the southeast coast of India...
March 2017: Genomics Data
Thomas C Whisenant
CD4 T cell activation is a central component of the mammalian adaptive immune response and is underscored by a dramatic change in the gene expression profile in these cells. The changes in gene expression that occur during T cell activation are regulated in multiple ways including post-transcriptionally by complexes of RNA-binding proteins. Recently, our study explored the role of the RNA-binding protein U2AF2 and its interacting proteins in mediating posttranscriptional changes in constitutive and alternative splicing during T cell activation...
March 2017: Genomics Data
Aleksandr Zhernakov, Björn Rotter, Peter Winter, Alexey Borisov, Igor Tikhonovich, Vladimir Zhukov
Aimed at gene-based markers design, we generated and analyzed transcriptome sequencing datasets for six pea (Pisum sativum L.) genetic lines that have not previously been massively genotyped. Five cDNA libraries obtained from nodules or nodulated roots of genetic lines Finale, Frisson, Sparkle, Sprint-2 and NGB1238 were sequenced using a versatile 3'-RNA-seq protocol called MACE (Massive Analysis of cDNA Ends). MACE delivers a single next-generation sequence from the 3'-end of each individual cDNA molecule that precisely quantifies the respective transcripts...
March 2017: Genomics Data
Juan Henao, Hermes Pérez, Deisy Abril, Katterine Ospina, Adriana Piza, Kelly Botero, Cristhian Rincón, Jhon Donato, Andrea Hurtado, Erika García, Vanessa Otero, Alexander Del Risco, Brenda Guerra, Yina Cifuentes, Alvaro Ordoñez, Daniel Rojas, Karen Suarez, Daniel Osorio, Andrés Pinzón
We announce the draft genome sequence of three Gram-negative bacteria isolated from coral tissues affected with the black band disease (BBD), identified with the NCBI's Assembly Database accession numbers: MBQF, MAYB and MBQE. These genome drafts constitute an useful tool for the characterisation of these bacteria and for the understanding of the relationship between the microbial consortia associated with the disease and the onset and progression of the pathology.
March 2017: Genomics Data
Anjali Singh, Minakshi Prasad, Bina Mishra, Siddappa Manjunath, Amit Ranjan Sahu, G Bhuvana Priya, Sajad Ahmad Wani, Aditya Prasad Sahoo, Amit Kumar, Shweta Balodi, Anupama Deora, Shikha Saxena, Ravi Kumar Gandham
Bluetongue is an economically important infectious, arthropod borne viral disease of domestic and wild ruminants, caused by Bluetongue virus (BTV). Sheep are considered the most susceptible hosts, while cattle, buffalo and goats serve as reservoirs. The viral pathogenesis of BTV resulting in presence or absence of clinical disease among different hosts is not clearly understood. In the present study, transcriptome of sheep and goats peripheral blood mononuclear cells infected with BTV-16 was explored. The differentially expressed genes (DEGs) identified were found to be significantly enriched for immune system processes - NFκB signaling, MAPK signaling, Ras signaling, NOD signaling, RIG signaling, TNF signaling, TLR signaling, JAK-STAT signaling and VEGF signaling pathways...
March 2017: Genomics Data
Alexey V Beletsky, Mikhail A Filyushin, Eugeny V Gruzdev, Alexander M Mazur, Egor B Prokhortchouk, Elena Z Kochieva, Andrey V Mardanov, Nikolai V Ravin, Konstantin G Skryabin
Monotropa hypopitys (pinesap) is a non-photosynthetic obligately mycoheterotrophic plant of the family Ericaceae. It obtains the carbon and other nutrients from the roots of surrounding autotrophic trees through the associated mycorrhizal fungi. In order to understand the evolutionary changes in the plant genome associated with transition to a heterotrophic lifestyle, we performed de novo transcriptomic analysis of M. hypopitys using next-generation sequencing. We obtained the RNA-Seq data from flowers, flower bracts and roots with haustoria using Illumina HiSeq2500 platform...
March 2017: Genomics Data
Salwa H N Al-Rubae'i, Tamara Sami Naji, Kisma M Turki
Common variants among genes coding for enzymes in sex steroid biosynthetic pathways may influence the risk of endometriosis in Iraqi women patients in the last years. Cytochrome P450c17a1 (CYP17), a gene that codes for a key enzyme (cytochrome P450c17a1) in a rate-limiting step of estrogen biosynthesis has attracted considerable attention as an important gene for endometriosis. To evaluate the relationship between common genetic variations in CYP17 and endometriosis risk and determine the main effects of those variations on the gene expression...
March 2017: Genomics Data
Tatiana A Semashko, Alexander A Arzamasov, Gleb Y Fisunov, Vadim M Govorun
Mycoplasma gallisepticum belongs to class Mollicutes and causes chronic respiratory disease in birds. It has a reduced genome, lack of cell wall and many metabolic pathways, and also easy to culture and non-pathogenic to humans. Aforementioned made it is a convenient model for studying of systems biology of minimal cell. Studying the transcriptomic level of M. gallisepticum is interesting for both understanding of common principles of transcription regulation of minimal cell and response to definite influence for pathogen bacteria...
March 2017: Genomics Data
S S S De S Jagoda, Karim Honein, Appudurai Arulkanthan, Hideki Ushio, Shuichi Asakawa
Here we report the draft genome sequence and annotation of A. veronii strain Ae52 isolated from the kidney of a morbund, septicaemic gold fish (Carassius auratus) in Sri Lanka. This clinical isolate showed resistance to multiple antimicrobials; amoxicillin, neomycin, trimethoprim-sulphonamide, chloramphenicol, tetracycline, enrofloxacin, erythromycin and nitrofurantoin. The size of the draft genome is 4.56 Mbp with 58.66% of G + C content consisting 4328 coding sequences. It harbors a repertoire of putative antibiotic resistant determinants that explains the genetic basis of its resistance to various classes of antibiotics...
March 2017: Genomics Data
Bernard J Pope, Khalid Mahmood, Chol-Hee Jung, Peter Georgeson, Daniel J Park
Constitutional biological processes involve the generation of DNA double-strand breaks (DSBs). The production of such breaks and their subsequent resolution are also highly relevant to neurodegenerative diseases and cancer, in which extensive DNA fragmentation has been described Stephens et al. (2011), Blondet et al. (2001). Tchurikov et al. Tchurikov et al. (2011, 2013) have reported previously that frequent sites of DSBs occur in chromosomal domains involved in the co-ordinated expression of genes. This group report that hot spots of DSBs in human HEK293T cells often coincide with H3K4me3 marks, associated with active transcription Kravatsky et al...
March 2017: Genomics Data
Anwesha Ghosh, Punyasloke Bhadury
Next generation sequencing using platforms such as Illumina MiSeq provides a deeper insight into the structure and function of bacterioplankton communities in coastal ecosystems compared to traditional molecular techniques such as clone library approach which incorporates Sanger sequencing. In this study, structure of bacterioplankton communities was investigated from two stations of Sundarbans mangrove ecoregion using both Sanger and Illumina MiSeq sequencing approaches. The Illumina MiSeq data is available under the BioProject ID PRJNA35180 and Sanger sequencing data under accession numbers KX014101-KX014140 (Stn1) and KX014372-KX014410 (Stn3)...
March 2017: Genomics Data
Zara Ghodsi, Xu Huang, Hossein Hassani
In developmental studies, inferring regulatory interactions of segmentation genetic network play a vital role in unveiling the mechanism of pattern formation. As such, there exists an opportune demand for theoretical developments and new mathematical models which can result in a more accurate illustration of this genetic network. Accordingly, this paper seeks to extract the meaningful regulatory role of the maternal effect genes using a variety of causality detection techniques and to explore whether these methods can suggest a new analytical view to the gene regulatory networks...
March 2017: Genomics Data
Tommaso Giordani, Alberto Vangelisti, Giuseppe Conte, Andrea Serra, Lucia Natali, Annamaria Ranieri, Marcello Mele, Andrea Cavallini
The identification of genes regulating milk secretion by mammary glands is a key-step for exploiting changes in milk composition induced by different diet regimens. Linseed supplementation is a reliable feeding strategy to enhance polyunsaturated fatty acid content in milk fat from sheep, increasing milk quality and nutraceutical value. To investigate the molecular bases of diet induced differences in milk composition, we collected milk from dairy ewes at 90 day of lactation and after 3 weeks of diet supplementation with extruded linseed...
March 2017: Genomics Data
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