Metagenomic analysis of microbial community of a parasitoid wasp Megaphragma amalphitanum
Publication date: Available online 21 December 2016 Source:Genomics Data Author(s): Artem Nedoluzhko 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...
Source: Genomics Data - December 20, 2016 Category: Genetics & Stem Cells Source Type: research
Genome sequencing of three bacteria associated to black band disease from a Colombian reef-building coral
Publication date: Available online 15 December 2016 Source:Genomics Data Author(s): 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 ...
Source: Genomics Data - December 14, 2016 Category: Genetics & Stem Cells Source Type: research
Draft genome of the strain RCAM1026 Rhizobium leguminosarum bv. viciae
Publication date: Available online 14 December 2016 Source:Genomics Data Author(s): 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 = 202321, GC% = 60.84). Resulting annotated genome is 7248686 bp encoding 6792 genes. (Source: Genomics Data)
Source: Genomics Data - December 13, 2016 Category: Genetics & Stem Cells Source Type: research
Gene expression profiling of U2AF2 dependent RNA-protein interactions during CD4+ T cell activation
Publication date: Available online 14 December 2016 Source:Genomics Data Author(s): 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...
Source: Genomics Data - December 13, 2016 Category: Genetics & Stem Cells Source Type: research
Massive Analysis of cDNA Ends (MACE) for transcript-based marker design in pea (Pisum sativum L.)
Publication date: Available online 12 December 2016 Source:Genomics Data Author(s): 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 singl...
Source: Genomics Data - December 12, 2016 Category: Genetics & Stem Cells Source Type: research
Genetic Identification of Marine Eels through DNA Barcoding from Parangipettai Coastal Waters
Publication date: Available online 9 December 2016 Source:Genomics Data Author(s): Samuel Peninal, Janakiraman Subramanian, 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. Inform...
Source: Genomics Data - December 8, 2016 Category: Genetics & Stem Cells Source Type: research
Transcriptome analysis reveals common differential and global gene expression profiles in bluetongue virus serotype 16 (BTV-16) infected peripheral blood mononuclear cells (PBMCs) in sheep and goats
Publication date: Available online 9 December 2016 Source:Genomics Data Author(s): 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 c...
Source: Genomics Data - December 8, 2016 Category: Genetics & Stem Cells Source Type: research
Sequencing and de novo transcriptome assembly of Anthopleura dowii Verrill (1869), from Mexico
Publication date: Available online 5 December 2016 Source:Genomics Data Author(s): Claudia Rodríguez 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 pep...
Source: Genomics Data - December 4, 2016 Category: Genetics & Stem Cells Source Type: research
Common variation of the CYP17 gene in Iraqi women with endometriosis disease
Publication date: March 2017 Source:Genomics Data, Volume 11 Author(s): 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 mai...
Source: Genomics Data - December 2, 2016 Category: Genetics & Stem Cells Source Type: research
De novo transcriptome assembly of the mycoheterotrophic plant Monotropa hypopitys
Publication date: Available online 30 November 2016 Source:Genomics Data Author(s): 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 heter...
Source: Genomics Data - November 30, 2016 Category: Genetics & Stem Cells Source Type: research
Common variation of the CYP17gene in Iraqi women with endometriosis disease
Publication date: Available online 29 November 2016 Source:Genomics Data Author(s): Salwa Hameed Naser, Tamara S Naji, Kismat M Turki Common variants among genes coding for enzymesin sex steroid biosynthetic pathways may influence the riskof endometriosis in Iraqi women patients in the last years. Cytochrome P450c17a1 (CYP17), a gene that codesfor a key enzyme (cytochrome P450c17a1) in a rate-limitingstep of estrogen biosynthesis has attracted considerableattention as an important gene for endometriosis.To evaluate the relationship between common genetic variations in CYP17 and endometriosis riskand determine the main...
Source: Genomics Data - November 29, 2016 Category: Genetics & Stem Cells Source Type: research
Transcription profiling data set of different states of Mycoplasma gallisepticum
Publication date: Available online 29 November 2016 Source:Genomics Data Author(s): 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 regulati...
Source: Genomics Data - November 29, 2016 Category: Genetics & Stem Cells Source Type: research
Insights into bacterioplankton community structure from Sundarbans mangrove ecoregion using Sanger and Illumina MiSeq sequencing approaches: A comparative analysis
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). Proteobacteria-, Firmicutes- and Bacteroidetes-like sequences retrieved from both approaches appeared to be abundant in the studied ecosystem. The Illumina MiSeq data (2.1GB) provided a deeper insight into the structure of bacterioplankton communities and revealed th...
Source: Genomics Data - November 24, 2016 Category: Genetics & Stem Cells Source Type: research
Causality analysis detects the regulatory role of maternal effect genes in the early Drosophila embryo
Publication date: Available online 22 November 2016 Source:Genomics Data Author(s): 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 whet...
Source: Genomics Data - November 21, 2016 Category: Genetics & Stem Cells Source Type: research
Complete genome sequence of the biofilm-forming Microbacterium sp. strain BH-3-3-3, isolated from conventional field-grown lettuce (Lactuca sativa) in Norway
Publication date: Available online 19 November 2016 Source:Genomics Data Author(s): Merete Wiken Dees, May Bente Brurberg, Erik Lysøe The genus Microbacterium contains bacteria that are ubiquitously distributed in various environments and includes plant-associated bacteria that are able to colonize tissue of agricultural crop plants. Here, we report the 3,508,491bp complete genome sequence of Microbacterium sp. strain BH-3-3-3, isolated from conventionally grown lettuce (Lactuca sativa) from a field in Vestfold, Norway. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession CP01767...
Source: Genomics Data - November 19, 2016 Category: Genetics & Stem Cells Source Type: research
