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Genomics Data

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https://www.readbyqxmd.com/read/28413782/apmicrodb-a-microsatellite-database-of-acyrthosiphon-pisum
#1
Ritika Bishnoi, Deepak Singla
Pea aphids represent a complex genetic system that could be used for QTL analysis, genetic diversity and population genetics studies. Here, we described the development of first microsatellite repeat database of the pea aphid (APMicroDB), accessible at "http://deepaklab.com/aphidmicrodb". We identified 3,40,233 SSRs using MIcroSAtellite (MISA) tool that was distributed in 14,067 (out of 23,924) scaffold of the pea aphid. We observed 89.53% simple repeats of which 73.41% were mono-nucleotide, followed by di-nucleotide repeats...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28413781/sequencing-and-de-novo-transcriptome-assembly-of-the-chinese-giant-salamander-andrias-davidianus
#2
Yong Huang, Xiao Chan Gao, Jian Li Xiong, Hong Tao Ren, Xi Hong Sun
Next-generation technologies for determination of genomics and transcriptomics composition have a wide range of applications. Andrias davidianus, 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 A. davidianus 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...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28409117/searching-for-active-mobile-genetic-elements-in-dsrna-fraction-of-pinus-sylvestris-having-witches-broom-abnormalities
#3
A A Pochtovyy, O Yu Baranov, I E Rubel', O A Razumova, V E Padutov, A V Khromov, A V Makhotenko, A P Tkachuk, V V Makarov, V A Gushchin
The most common type of coniferous mobile genetic elements are retrotransposons. Despite of their early positive impact on evolution of modern coniferous species they can have a significant negative impact for Forestry and breeding. Breaking genomic structural integrity mobile elements can cause phenotypic defects of plants. In this regard, the study of the diversity of coniferous mobile genetic elements is particularly interesting. In the present paper, we describe mobile genetic elements in dsRNA fraction of Pinus sylvestris having witches broom abnormalities...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28409116/prepare_taxa_charts-py-a-python-program-to-automate-generation-of-publication-ready-taxonomic-pie-chart-images-from-qiime
#4
Vijay Lakhujani, Chandan Badapanda
QIIME (Quantitative Insights Into Microbial Ecology) is one of the most popular open-source bioinformatics suite for performing metagenome, 16S rRNA amplicon and Internal Transcribed Spacer (ITS) data analysis. Although, it is very comprehensive and powerful tool, it lacks a method to provide publication ready taxonomic pie charts. The script plot_taxa_summary.py bundled with QIIME generate a html file and a folder containing taxonomic pie chart and legend as separate images. The images have randomly generated alphanumeric names...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28409115/a-metagenomic-approach-to-decipher-the-indigenous-microbial-communities-of-arsenic-contaminated-groundwater-of-assam
#5
Saurav Das, Sudipta Sankar Bora, R N S Yadav, Madhumita Barooah
Metagenomic approach was used to understand the structural and functional diversity present in arsenic contaminated groundwater of the Ganges Brahmaputra Delta aquifer system. A metagene dataset (coded as TTGW1) of 89,171 sequences (totaling 125,449,864 base pairs) with an average length of 1406 bps was annotated. About 74,478 sequences containing 101,948 predicted protein coding regions passed the quality control. Taxonomical classification revealed abundance of bacteria that accounted for 98.3% of the microbial population of the metagenome...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28393016/intraspecies-comparative-genomics-of-three-strains-of-orientia-tsutsugamushi-with-different-antibiotic-sensitivity
#6
Hsiao-Mei Liao, Chien-Chung Chao, Haiyan Lei, Bingjie Li, Shien Tsai, Guo-Chiuan Hung, Wei-Mei Ching, Shyh-Ching Lo
We recently reported the genome of Orientia tsutsugamushi (OT) strain Karp (GenBank Accession #: NZ_LYMA00000000.2, https://www.ncbi.nlm.nih.gov/nuccore/NZ_LYMA00000000.2) with > 2 Mb in size through clone-based sequencing and high throughput genomic shotgun sequencing (HTS). The genomes of OT strains AFSC4 and AFSC7 were similarly sequenced by HTS Since strains AFSC4 (GenBank Accession #: NZ_LYMT00000000.1, https://www.ncbi.nlm.nih.gov/nuccore/1035784408) and AFSC7 (GenBank Accession #: NZ_LYMB00000000...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28386532/the-draft-genome-sequence-of-the-plant-growth-promoting-rhizospheric-bacterium-enterobacter-cloacae-sbp-8
#7
Rajnish Prakash Singh, Shrayansh Nalwaya, Prabhat Nath Jha
Here, we report the draft genome sequence and annotation of plant growth promoting rhizobacterium Enterobacter cloacae SBP-8 isolated from the rhizosphere of Sorghum bicolor L. growing in desert region of Rajasthan, India. From the genome sequences, we identified the genes encoding plant growth promoting properties such as 1-aminocyclopropane-1-carboxylate deaminase (AcdS), phosphate solubilisation, siderophore, and IAA (indole acetic acid) production. The genes encoding different functions required for colonization including motility, chemotaxis, adherence, and secretion system (I, II, IV, VI) were also identified...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28386531/draft-genome-sequence-of-cercospora-sojina-isolate-s9-a-fungus-causing-frogeye-leaf-spot-fls-disease-of-soybean
#8
Fanchang Zeng, Chaofan Wang, Guirong Zhang, Junmei Wei, Carl A Bradley, Ray Ming
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 Cercospora sojina is a plant pathogen that threatens global soybean supplies. Here, we report the genome sequence of C. sojina strain S9 and detect genome features and predicted genomic elements. The genome sequence of C. sojina is a valuable resource with potential in studying the fungal pathogenicity and soybean host resistance to frogeye leaf spot (FLS), which is caused by C...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28386530/draft-genome-sequence-of-bacillus-oleronius-dsm-9356-isolated-from-the-termite-reticulitermes-santonensis
#9
Rodney Owusu-Darko, Mushal Allam, Senzo Mtshali, Arshad Ismail, Elna Maria Buys
Bacillus oleronius strain DSM 9356 isolated from the termite Reticulitermes santonensis was sequenced to gain insights in relation to its closest phylogenetic neighbor Bacillus sporothermodurans. The draft genome of strain DSM 9356 contains 5,083,966 bp with an estimated G + C content of 35%, 4899 protein-coding genes, 116 tRNAs and 18 rRNAs. The RAST annotation assigned these genes into 462 subsystems, with the maximum number of genes associated with amino acids and derivatives metabolism (14.84%), followed by carbohydrates (13...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28386529/gene-expression-in-rat-striatum-following-carbon-monoxide-poisoning
#10
Shuichi Hara, Masamune Kobayash, Fumi Kuriiwa, Kunihiko Kurosaki, Hajime Mizukami
Carbon monoxide (CO) poisoning causes brain damage, which is attenuated by treatment with hydrogen [1], [2], a scavenger selective to hydroxyl radical (•OH) [3]. This suggests a role of •OH in brain damage due to CO poisoning. Studies have shown strong enhancement of •OH production in rat striatum by severe CO poisoning with a blood carboxyhemoglobin (COHb) level > 70% due to 3000 ppm CO, but not less severe CO poisoning with a blood COHb level at approximately 50% due to 1000 ppm CO [4]. Interestingly, 5% O2 causes hypoxia comparable with that by 3000 ppm CO and produces much less (•)OH than 3000 ppm CO does [4]...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28386528/de-novo-transcriptome-assembly-and-its-annotation-for-the-aposematic-wood-tiger-moth-parasemia-plantaginis
#11
Juan A Galarza, Kishor Dhaygude, Johanna Mappes
In this paper we report the public availability of transcriptome resources for the aposematic wood tiger moth (Parasemia plantaginis). 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 (http://www.ebi.ac.uk/ena) under study accession number: PRJEB14172.
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28377885/draft-genome-of-bordetella-pseudohinzii-bh370-isolated-from-trachea-and-lung-tissues-of-a-laboratory-mouse
#12
Shih Keng Loong, Kim-Kee Tan, Syuhaida Sulaiman, Pooi Fong Wong, Sazaly AbuBakar
In this study, we present the draft genome sequence of B. pseudohinzii BH370 recovered from the trachea and lung tissues of an ICR mouse in Malaysia. The genome consists of 4,474,040 bp with a GC content of 66.4%. Annotation using RAST algorithm displayed 5119 protein encoding and 52 RNA genes. The CRISPR-cas genomic sequences previously reported in B. pseudohinzii were identified. The nucleotide sequences of BH370 was deposited into the European Nucleotide Archive under the genome assembly accession number FPJN01000000...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28373958/genome-centric-evaluation-of-burkholderia-sp-strain-srs-w-2-2016-resistant-to-high-concentrations-of-uranium-and-nickel-isolated-from-the-savannah-river-site-srs-usa
#13
Ashish Pathak, Ashvini Chauhan, Paul Stothard, Stefan Green, Mark Maienschein-Cline, Rajneesh Jaswal, John Seaman
Savannah River Site (SRS), an approximately 800-km(2) former nuclear weapons production facility located near Aiken, SC remains co-contaminated by heavy metals and radionuclides. To gain a better understanding on microbially-mediated bioremediation mechanisms, several bacterial strains resistant to high concentrations of Uranium (U) and Nickel (Ni) were isolated from the Steeds Pond soils located within the SRS site. One of the isolated strains, designated as strain SRS-W-2-2016, grew robustly on both U and Ni...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28373957/comparative-study-the-expression-of-calcium-cycling-genes-in-bombay-duck-harpadon-nehereus-and-beltfish-trichiurus-lepturus-with-different-swimming-activities
#14
Hui Zhang, Gilbert Audira, Yuan Li, Weiwei Xian, Muhammed Muhsin Varikkodan, Chung-Der Hsiao
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 (Harpadon nehereus) and beltfish (Trichiurus lepturus) with poor and robust swimming activities, respectively...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28367406/cataloguing-the-bacterial-community-of-the-great-salt-plains-oklahoma-using-16s-rrna-based-metagenomics-pyrosequencing
#15
Ahmed H Gad
The Great Salt Plains of Oklahoma (GSP) is an extreme region, a hypersaline environment from marine origin and a unique area of the Salt National Wild Refuge in the north-central region of Oklahoma. In this study we analyzed the diversity and distribution of bacteria in two habitats; vegetated areas (GAB) and salt flat areas (GAS) in the sediments of GSP using the high-throughput techniques of 16S rRNA gene amplicon (V1-V2 regions) metagenomics-454 pyrosequencing. The filtered sequences resulted to a total of 303,723 paired end reads were generated, assigned into 1646 numbers of OTUs and 56...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28367405/synaptic-vesicles-isolated-from-the-electric-organ-of-torpedo-californica-and-from-the-central-nervous-system-of-mus-musculus-contain-small-ribonucleic-acids-srnas
#16
Huinan Li, Cheng Wu, Rodolfo Aramayo, Matthew S Sachs, Mark L Harlow
Synaptic vesicles (SVs) are presynaptic organelles that load and release small molecule neurotransmitters at chemical synapses. In addition to classic neurotransmitters, we have demonstrated that SVs isolated from the Peripheral Nervous Systems (PNS) of the electric organ of Torpedo californica, a model cholinergic synapse, and SVs isolated from the Central Nervous System (CNS) of Mus musculus (mouse) contain small ribonucleic acids (sRNAs; ≤ 50 nucleotides) (Scientific Reports, 5:1-14(14918) Li et al. (2015) [1])...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28337413/draft-genome-sequence-of-thermoanaerobacterium-sp-strain-psu-2-isolated-from-thermophilic-hydrogen-producing-reactor
#17
Sompong O-Thong, Peerawat Khongkliang, Chonticha Mamimin, Apinya Singkhala, Poonsuk Prasertsan, Nils-Kåre Birkeland
Thermoanaerobacterium sp. strain PSU-2 was isolated from thermophilic hydrogen producing reactor and subjected to draft genome sequencing on 454 pyrosequencing and annotated on RAST. The draft genome sequence of strain PSU-2 contains 2,552,497 bases with an estimated G + C content of 35.2%, 2555 CDS, 8 rRNAs and 57 tRNAs. The strain had a number of genes responsible for carbohydrates metabolic, amino acids and derivatives, and protein metabolism of 17.7%, 14.39% and 9.81%, respectively. Strain PSU-2 also had gene responsible for hydrogen biosynthesis as well as the genes related to Ni-Fe hydrogenase...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28316932/bacterial-fauna-associating-with-chironomid-larvae-from-lakes-of-bengaluru-city-india-a-16s-rrna-gene-based-identification
#18
Ramprasad Kuncham, Thiyagarajan Sivaprakasam, R Puneeth Kumar, P Sreenath, Ravi Nayak, Tha Thayumanavan, Gopireddy V Subba Reddy
Chironomid larvae that inhabit in aquatic sediments play an important role as vector for bacterial pathogens. Its life cycle consists of four stages i.e. eggs, larvae, pupae and adult. In the present study we identified bacterial species associated with whole larvae of chironomids from 11 lake sediments of Bangalore region using 16s rRNA gene Sanger sequencing. We found that larvae from all lake sediments associated with bacterial species which include key pathogens. Totally we identified 65 bacterial isolates and obtained GenBank accession numbers (KX980423 - KX980487)...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28289604/metagenome-analysis-of-the-root-endophytic-microbial-community-of-indian-rice-o-sativa-l
#19
Subhadipa Sengupta, Sayak Ganguli, Pankaj K Singh
This study reports the root endophytic microbial community profile in rice (Oryza sativa L.), the largest food crop of Asia, using 16S rRNA gene amplicon sequencing. Metagenome of OS01 and OS04 consisted of 11,17,900 sequences with 300 Mbp size and average 55.6% G + C content. Data of this study are available at NCBI Bioproject (PRJNA360379). The taxonomic analysis of 843 OTU's showed that the sequences belonged to four major phyla revealing dominance of Proteobacteria, Firmicutes, Cyanobacteria and Actinobacteria...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28289603/impact-of-aspirin-on-the-transcriptome-of-streptococcus-pneumoniae-d39
#20
Muhammad Afzal, Sulman Shafeeq
Aspirin or acetylsalicylic acid (ASA) is a medicine used to treat pain, fever, and inflammation. Here, we for the very first time reported the genome-wide transcriptional profiling of aspirin-regulated genes in Streptococcus pneumoniae in the presence of 5 mM aspirin in chemically-defined medium (CDM) using microarray analysis. Our results showed that expression of several genes was differentially expressed in the presence of aspirin. These genes were further grouped into COG (Clusters of Orthologous Groups) functional categories based on the putative functions of the corresponding proteins...
June 2017: Genomics Data
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