APMicroDB: A microsatellite database of Acyrthosiphon pisum
Publication date: Available online 30 March 2017 Source:Genomics Data Author(s): 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 3,81,806 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...
Source: Genomics Data - March 31, 2017 Category: Genetics & Stem Cells Source Type: research
prepare_taxa_charts.py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIME
Publication date: Available online 29 March 2017 Source:Genomics Data Author(s): 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 gene...
Source: Genomics Data - March 30, 2017 Category: Genetics & Stem Cells Source Type: research
Sequencing and de novo transcriptome assembly of the Chinese giant salamander (Andrias davidianus)
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 15,398,997,600bp were obtained, corresponding to 102,659,984 raw reads. A total of 102,659,984 reads were filtered after removing low-quality reads and trimming the adapter sequences. The Trinity program was used to de novo assemble 132,912 unigenes with an average length of 690bp and N50 of 1263bp. Unigenes were annotated through number of databases. These transcriptomic data of A. davidianus should open the door to molecular evo...
Source: Genomics Data - March 29, 2017 Category: Genetics & Stem Cells Source Type: research
Intraspecies comparative genomics of three strains of Orientia tsutsugamushi with different antibiotic sensitivity
Publication date: Available online 28 March 2017 Source:Genomics Data Author(s): 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 >2Mb 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:...
Source: Genomics Data - March 29, 2017 Category: Genetics & Stem Cells Source Type: research
Searching for active mobile genetic elements in dsRNA fraction of P ícea ábies having witches broom abnormalities
Publication date: Available online 28 March 2017 Source:Genomics Data Author(s): A.A. Pochtovyy, O.Yu. Baranov, I.E. Rubel', O.A. Razumova, V.E. Padutov, A.V. Chromov, A.V. Machotenko, 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 ...
Source: Genomics Data - March 29, 2017 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of Bacillus oleronius DSM 9356 isolated from the termite Reticulitermes santonensis
Publication date: Available online 24 March 2017 Source:Genomics Data Author(s): 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 5,083,966bp 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 aci...
Source: Genomics Data - March 24, 2017 Category: Genetics & Stem Cells Source Type: research
The draft genome sequence of the plant growth promoting rhizospheric bacterium Enterobacter cloacae SBP-8
Publication date: Available online 23 March 2017 Source:Genomics Data Author(s): Rajnish Prakash Singh, Shreyansh 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...
Source: Genomics Data - March 23, 2017 Category: Genetics & Stem Cells Source Type: research
Draft genome of Bordetella pseudohinzii BH370 isolated from trachea and lung tissues of a laboratory mouse
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 4,474,040bp 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. (Source: Genomics Data)
Source: Genomics Data - March 22, 2017 Category: Genetics & Stem Cells Source Type: research
De novo transcriptome assembly and its annotation for the aposematic wood tiger moth (Parasemia plantaginis)
Publication date: Available online 21 March 2017 Source:Genomics Data Author(s): Juan A. Galarza, Dhaygude Kishor, Mappes Johanna 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. (Source: Genomics Data)
Source: Genomics Data - March 22, 2017 Category: Genetics & Stem Cells Source Type: research
Gene expression in rat striatum following carbon monoxide poisoning
Publication date: Available online 22 March 2017 Source:Genomics Data Author(s): 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 3000ppm CO, but not less severe CO poisoning with a blood COHb level at approxima...
Source: Genomics Data - March 22, 2017 Category: Genetics & Stem Cells Source Type: research
Comparative study the expression of calcium cycling genes in Bombay duck (Harpadon nehereus) and beltfish (Trichiurus lepturus) with different swimming activities
In conclusion, we confirmed that the high abundant expression rate of calcium cycling genes in robust swimming fish species. The current muscle transcriptome and identified calcium cycling gene data can provide more insights into the muscle physiology of fish. (Source: Genomics Data)
Source: Genomics Data - March 20, 2017 Category: Genetics & Stem Cells Source Type: research
Cataloguing the bacterial community of the Great Salt Plains, Oklahoma using 16S rRNA based metagenomics pyrosequencing
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 56.4% G+C content for GAB, and a total of 144,496 paired end reads were generated, assigned into 785 numbers of OTUs and 56.7% G+ C content for GAS. All the resulting 16S rRNA was of an average length~187bp, assigned to 37 bacterial p...
Source: Genomics Data - March 20, 2017 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of Cercospora sojina isolate S9, a fungus causing frogeye leaf spot (FLS) disease of soybean
Publication date: Available online 15 March 2017 Source:Genomics Data Author(s): 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 se...
Source: Genomics Data - March 15, 2017 Category: Genetics & Stem Cells Source Type: research
Synaptic vesicles isolated from the electric organ of Torpedo californica and from the central nervous system of Mus musculus contain small ribonucleic acids (sRNAs)
Publication date: Available online 8 March 2017 Source:Genomics Data Author(s): 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) (Scienti...
Source: Genomics Data - March 8, 2017 Category: Genetics & Stem Cells Source Type: research
Cataloguing the bacterial community of the Great Salt Plains, Oklahoma using 16s-rRNA based metagenomics pyrosequencing
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 ends reads were generated and assigned into 1646 numbers of OTUs, and 56.4% G+C content for GAB, and a total of 144,496 paired ends were generated, assigned into 785 numbers of OTUs and 56.7% G+ C content for GAS. All the resulting 16S rRNA was of an average length~187bp, assigned to 37 bacterial ...
Source: Genomics Data - March 8, 2017 Category: Genetics & Stem Cells Source Type: research
