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Genomics Data

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https://www.readbyqxmd.com/read/28540183/the-draft-genome-of-corchorus-olitorius-cv-jro-524-navin
#1
Debabrata Sarkar, Ajay Kumar Mahato, Pratik Satya, Avijit Kundu, Sangeeta Singh, Pawan Kumar Jayaswal, Akshay Singh, Kaushlendra Bahadur, Sasmita Pattnaik, Nisha Singh, Avrajit Chakraborty, Nur Alam Mandal, Debajeet Das, Tista Basu, Amitha Mithra Sevanthi, Dipnarayan Saha, Subhojit Datta, Chandan Sourav Kar, Jiban Mitra, Karabi Datta, Pran Gobinda Karmakar, Tilak Raj Sharma, Trilochan Mohapatra, Nagendra Kumar Singh
Here, we present the draft genome (377.3 Mbp) of Corchorus olitorious cv. JRO-524 (Navin), which is a leading dark jute variety developed from a cross between African (cv. Sudan Green) and indigenous (cv. JRO-632) types. We predicted from the draft genome a total of 57,087 protein-coding genes with annotated functions. We identified a large number of 1765 disease resistance-like and defense response genes in the jute genome. The annotated genes showed the highest sequence similarities with that of Theobroma cacao followed by Gossypium raimondii...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28540182/mannose-binding-lectin-mbl-gene-polymorphisms-in-susceptibility-to-pulmonary-tuberculosis-among-the-lur-population-of-lorestan-province-of-iran
#2
Ali Amiri, Toomaj Sabooteh, Farhad Shahsavar, Khatereh Anbari, Flora Pouremadi
OBJECTIVE: Tuberculosis (TB) is caused by infection of Mycobacterium tuberculosis. Host genetic variability is an important determinant of the risk of developing TB in humans. Although the association between MBL polymorphisms and TB has been studied in various populations, the results are controversial. The aim of this study was to investigate mannose-binding lectin (MBL) gene polymorphisms with susceptibility to pulmonary tuberculosis (PTB) in a Lur population of Iran. METHODS: In this case-control study, four functional MBL gene polymorphisms (HL, XY, PQ and AB) were genotyped by using PCR Single Strand Conformation Polymorphism (SSCP) technique in a Lur population living in Lorestan Province, consisting of 100 patients with pulmonary tuberculosis (PTB) age and sex matched 100 healthy controls (HCs)...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28540181/dynamic-regulation-of-small-rnaome-during-the-early-stage-of-cardiac-differentiation-from-pluripotent-embryonic-stem-cells
#3
Yue Li, An Zeng, Ge Li, Ya-Na Guan, Huang-Tian Yang, Bairong Shen, Qing Jing
Embryonic stem cells (mESCs), having potential to differentiate into three germ-layer cells including cardiomyocytes, shall be a perfect model to help understanding heart development. Here, using small RNA deep sequencing, we studied the small RNAome in the early stage of mouse cardiac differentiation. We found that the expression pattern of most microRNA (miRNA) were highly enriched at the beginning and declined thereafter, some were still insufficiently expressed on day 6, and most miRNAs recovered in the following days...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28529883/smrt-sequencing-data-for-garcinia-mangostana-l-variety-mesta
#4
Mohd Razik Midin, Kok-Keong Loke, Maria Madon, Mohd Shukor Nordin, Hoe-Han Goh, Normah Mohd Noor
The "Queen of Fruits" mangosteen (Garcinia mangostana L.) produces commercially important fruits with desirable taste of flesh and pericarp rich in xanthones with medicinal properties. To date, only limited knowledge is available on the cytogenetics and genome sequences of a common variety of mangosteen (Abu Bakar et al., 2016 [1]). Here, we report the first single-molecule real-time (SMRT) sequencing data from whole genome sequencing of mangosteen of Mesta variety. Raw reads of the SMRT sequencing project can be obtained from SRA database with the accession numbers SRX2718652 until SRX2718659...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28529882/transcriptomic-data-of-arabidopsis-thaliana-hypocotyl-upon-suppression-of-expansin-genes
#5
Iqmal Asyraf Ilias, Othman Babul Airianah, Syarul Nataqain Baharum, Hoe-Han Goh
Expansin is a cell wall loosening protein without hydrolytic activity, which allows cell expansion by influencing cell wall extensibility. Previous studies showed that the suppression of expansin genes (EXPA1, EXPA3, EXPA5 and EXPA10) resulted in defective organ growth and altered cell wall chemical composition [1,2]. However, the molecular mechanism on how the suppression of non-enzymatic expansin expression can result in widespread effects on plant cell wall and organ growth is still unclear. In this study, we performed transcriptomic analysis on the hypocotyls of previously reported transgenic Arabidopsis line [1] to investigate the effects of expansin gene suppression on the global gene expression pattern, particularly on the cell wall related genes...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28529881/iso-seq-analysis-of-nepenthes-ampullaria-nepenthes-rafflesiana-and-nepenthes%C3%A2-%C3%A3-%C3%A2-hookeriana-for-hybridisation-study-in-pitcher-plants
#6
Muhammad Mu'izzuddin Zulkapli, Muhammad Aqil Fitri Rosli, Faris Imadi Mohd Salleh, Normah Mohd Noor, Wan Mohd Aizat, Hoe-Han Goh
Tropical pitcher plants in the species-rich Nepenthaceae family of carnivorous plants possess unique pitcher organs. Hybridisation, natural or artificial, in this family is extensive resulting in pitchers with diverse features. The pitcher functions as a passive insect trap with digestive fluid for nutrient acquisition in nitrogen-poor habitats. This organ shows specialisation according to the dietary habit of different Nepenthes species. In this study, we performed the first single-molecule real-time isoform sequencing (Iso-Seq) analysis of full-length cDNA from Nepenthes ampullaria which can feed on leaf litter, compared to carnivorous Nepenthes rafflesiana, and their carnivorous hybrid Nepenthes × hookeriana...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28516036/transcriptome-analysis-of-carica-papaya-embryogenic-callus-upon-de-etiolated-1-det1-gene-suppression
#7
Diyana Jamaluddin, Normah Mohd Noor, Hoe-Han Goh
Papaya is considered to be one of the most nutritional fruits. It is rich in vitamins, carotenoids, flavonoids and other phytonutrient which function as antioxidant in our body [1]. Previous studies revealed that the suppression of a negative regulator gene in photomorphogenesis, De-etiolated 1 (DET1) can improve the phytonutrient in tomato and canola without affecting the fruit quality [2], [3]. This report contains the experimental data on high-throughput 3' mRNA sequencing of transformed papaya callus upon DET1 gene suppression...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28516035/dna-shotgun-sequencing-analysis-of-garcinia-mangostana-l-variety-mesta
#8
Syuhaidah Abu Bakar, Suresh Kumar, Kok-Keong Loke, Hoe-Han Goh, Normah Mohd Noor
Mangosteen (Garcinia mangostana Linn.) is an ultra-tropical tree characterized by its unique dark purple fruits with white flesh. The xanthone-rich purple pericarp tissue contains valuable compounds with medicinal properties. Following previously reported genome sequencing of a common variety of mangosteen [1], we performed another whole genome sequencing of a commercially popular variety of this fruit species (var. Mesta) for comparative analysis of its genome composition. Raw reads of the DNA sequencing project were deposited to SRA database with the accession number SRX2709728...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28507897/comparative-analysis-of-microbial-diversity-in-two-hot-springs-of-bakreshwar-west-bengal-india
#9
Biswadeep Chaudhuri, Trinath Chowdhury, Brajadulal Chattopadhyay
Various aspects of hot springs at Bakreshwar (Lat. 23°52'48″N; Long. 87°22'40″E) in West Bengal, India have been investigated since the middle of 20th century, but comprehending the complete diversity and the complexity of the microbial population therein has been in the continuing process. Some of these microorganisms are found to have immense industrial importance. Microbes generally exist in milieus of varying complexities and diversities. Attempting the usually employed cultivation-based techniques in experimentation with those microbes had confronted various limitations...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28491497/complete-genome-sequence-of-a-natural-compounds-producer-streptomyces-violaceus-s21
#10
Jiafang Fu, Chuanqing Zhong, Zhilong Zhao, Gongli Zong, Guangxiang Cao
The complete genome sequence of Streptomyces violaceus strain S21, a valuable natural compounds producer isolated from the forest soil, is firstly presented here. The genome comprised 7.91M bp, with a G + C content of 72.65%. A range of genes involved in pathways of secondary product biosynthesis were predicted. The genome sequence is available at DDBJ/EMBL/Genbank under the accession number CP020570. This genome is annotated with 6856 predicted genes identifying the natural product biosynthetic gene clusters in S...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28413782/apmicrodb-a-microsatellite-database-of-acyrthosiphon-pisum
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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