keyword
MENU ▼
Read by QxMD icon Read
search

Genome annotation

keyword
https://www.readbyqxmd.com/read/29684575/draft-genome-sequence-of-field-isolate-brucella-melitensis-strain-2007bm-1-from-india
#1
D K Singh, Bablu Kumar, Garima Shrinet, R P Singh, Aparajita Das, B G Mantur, Abhishek, Aruna Pandey, Piyali Mondal, B K Sajjanar, Soni Doimari, Vijayata Singh, Reena Kumari, A K Tiwari, Gandham Ravikumar
OBJECTIVES: Brucellosis, is among one of the most widespread important global zoonotic diseases which is endemic in many parts of India. Brucella melitensis is supposed to be the most pathogenic species for humans. Here, we report draft genome sequence of B. melitensis strain 2007BM/1 isolated from human in India. METHODS: Genomic DNA was extracted from Brucella culture and was sequenced using an Illumina MiSeq platform. The generated reads were assembled using three de novo assemblers and the draft genome was annotated...
April 20, 2018: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29684010/a-machine-learning-based-framework-to-identify-and-classify-long-terminal-repeat-retrotransposons
#2
Leander Schietgat, Celine Vens, Ricardo Cerri, Carlos N Fischer, Eduardo Costa, Jan Ramon, Claudia M A Carareto, Hendrik Blockeel
Transposable elements (TEs) are repetitive nucleotide sequences that make up a large portion of eukaryotic genomes. They can move and duplicate within a genome, increasing genome size and contributing to genetic diversity within and across species. Accurate identification and classification of TEs present in a genome is an important step towards understanding their effects on genes and their role in genome evolution. We introduce TE-Learner, a framework based on machine learning that automatically identifies TEs in a given genome and assigns a classification to them...
April 23, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29683450/targeted-next-generation-sequencing-and-bioinformatics-pipeline-to-evaluate-genetic-determinants-of-constitutional-disease
#3
Allison A Dilliott, Sali M K Farhan, Mahdi Ghani, Christine Sato, Eric Liang, Ming Zhang, Adam D McIntyre, Henian Cao, Lemuel Racacho, John F Robinson, Michael J Strong, Mario Masellis, Dennis E Bulman, Ekaterina Rogaeva, Anthony Lang, Carmela Tartaglia, Elizabeth Finger, Lorne Zinman, John Turnbull, Morris Freedman, Rick Swartz, Sandra E Black, Robert A Hegele
Next-generation sequencing (NGS) is quickly revolutionizing how research into the genetic determinants of constitutional disease is performed. The technique is highly efficient with millions of sequencing reads being produced in a short time span and at relatively low cost. Specifically, targeted NGS is able to focus investigations to genomic regions of particular interest based on the disease of study. Not only does this further reduce costs and increase the speed of the process, but it lessens the computational burden that often accompanies NGS...
April 4, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29682428/non-dispersive-phloem-protein-bodies-npbs-of-populus-trichocarpa-consist-of-a-seor-protein-and-do-not-respond-to-cell-wounding-and-ca-2
#4
Daniel L Mullendore, Timothy Ross-Elliott, Yan Liu, Hanjo H Hellmann, Eric H Roalson, Winfried S Peters, Michael Knoblauch
Differentiating sieve elements in the phloem of angiosperms produce abundant phloem-specific proteins before their protein synthesis machinery is degraded. These P-proteins initially form dense bodies, which disperse into individual filaments when the sieve element matures. In some cases, however, the dense protein agglomerations remain intact and are visible in functional sieve tubes as non-dispersive P-protein bodies, or NPBs. Species exhibiting NPBs are distributed across the entire angiosperm clade. We found that NPBs in the model tree, Populus trichocarpa , resemble the protein bodies described from other species of the order Malpighiales as they all consist of coaligned tubular fibrils bundled in hexagonal symmetry...
2018: PeerJ
https://www.readbyqxmd.com/read/29682169/draft-genome-sequence-of-fermentimonas-caenicola-strain-sit8-isolated-from-the-human-gut
#5
Mamadou Beye, Sofiane Bakour, Sory Ibrahima Traore, Jaishriram Rathored, Noémie Labas, Didier Raoult, Pierre-Edouard Fournier
We report the properties of a draft genome sequence of the bacterium Fermentimonas caenicola strain SIT8 (= CSUR P1560). This strain, whose genome is described here, was isolated from the fecal flora of a healthy 28-month-old Senegalese boy. Strain SIT8 is a facultatively anaerobic Gram-negative bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,824,451-bp long (1 chromosome but no plasmid) contains 2354 protein-coding and 46 RNA genes, including four rRNA genes...
2018: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29682168/genome-sequence-of-planktotalea-frisia-type-strain-sh6-1-t-a-representative-of-the-roseobacter-group-isolated-from-the-north-sea-during-a-phytoplankton-bloom
#6
Insa Bakenhus, Sonja Voget, Anja Poehlein, Thorsten Brinkhoff, Rolf Daniel, Meinhard Simon
Planktotalea frisia SH6-1T Hahnke et al. (Int J Syst Evol Microbiol 62:1619-24, 2012) is a planktonic marine bacterium isolated during a phytoplankton bloom from the southern North Sea. It belongs to the Roseobacter group within the alphaproteobacterial family Rhodobacteraceae . Here we describe the draft genome sequence and annotation of the type strain SH6-1T . The genome comprises 4,106,736 bp and contains 4128 protein-coding and 38 RNA genes. The draft genome sequence provides evidence for at least three extrachromosomal elements, encodes genes for DMSP utilization, quorum sensing, photoheterotrophy and a type IV secretion system...
2018: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29682127/de-novo-sequencing-of-a-sparassis-latifolia-genome-and-its-associated-comparative-analyses
#7
Donglai Xiao, Lu Ma, Chi Yang, Zhenghe Ying, Xiaoling Jiang, Yan-Quan Lin
Known to be rich in β- glucan, Sparassis latifolia ( S. latifolia ) is a valuable edible fungus cultivated in East Asia. A few studies have suggested that S. latifolia is effective on antidiabetic, antihypertension, antitumor, and antiallergen medications. However, it is still unclear genetically why the fungus has these medical effects, which has become a key bottleneck for its further applications. To provide a better understanding of this fungus, we sequenced its whole genome, which has a total size of 48...
2018: Canadian Journal of Infectious Diseases & Medical Microbiology
https://www.readbyqxmd.com/read/29681136/chromosome-scale-pseudomolecules-refined-by-optical-physical-and-genetic-maps-in-flax
#8
Frank M You, Jin Xiao, Pingchuan Li, Zhen Yao, Gaofeng Jia, Liqiang He, Tingting Zhu, Ming-Cheng Luo, Xiue Wang, Michael K Deyholos, Sylvie Cloutier
Genomes of varying sizes have been sequenced with next generation sequencing platforms. However, most reference sequences include draft unordered scaffolds containing chimera caused by mis-scaffolding. A BioNano genome (BNG) optical map was constructed to improve the previously sequenced flax genome (Linum usitatissimum L., 2n=30, ~373 Mb), which consisted of 3,852 scaffolds larger than 1 kb and totalling 300.6 Mb. The high resolution BNG map of cv. CDC Bethune totalled 317 Mb and consisted of 251 BNG contigs with an N50 of 2...
April 22, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29679119/the-role-of-iron-competition-in-the-antagonistic-action-of-the-rice-endophyte-streptomyces-sporocinereus-osish-2-against-the-pathogen-magnaporthe-oryzae
#9
Jiarui Zeng, Ting Xu, Lidan Cao, Chunyi Tong, Xuan Zhang, Dingyi Luo, Shuping Han, Pei Pang, Weibin Fu, Jindong Yan, Xuanming Liu, Yonghua Zhu
Rice blast caused by Magnaporthe oryzae severely impacts global rice yield stability. The rice endophyte Streptomyces sporocinereus OsiSh-2, with strong antagonistic activity towards M. oryzae, has been reported in our previous study. To decipher the model of the antagonistic action of OsiSh-2 towards M. oryzae, we compared the iron-capturing abilities of these two strains. The cultivation of OsiSh-2 and a M. oryzae strain under iron-rich and iron-starved conditions showed that M. oryzae depended more on iron supplementation for growth and development than did OsiSh-2...
April 20, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/29679055/towards-annotating-the-plant-epigenome-the-arabidopsis-thaliana-small-rna-locus-map
#10
Thomas J Hardcastle, Sebastian Y Müller, David C Baulcombe
Based on 98 public and internal small RNA high throughput sequencing libraries, we mapped small RNAs to the genome of the model organism Arabidopsis thaliana and defined loci based on their expression using an empirical Bayesian approach. The resulting loci were subsequently classified based on their genetic and epigenetic context as well as their expression properties. We present the results of this classification, which broadly conforms to previously reported divisions between transcriptional and post-transcriptional gene silencing small RNAs, and to PolIV and PolV dependencies...
April 20, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29679020/comparative-genomics-provides-insights-into-the-lifestyle-and-reveals-functional-heterogeneity-of-dark-septate-endophytic-fungi
#11
Dániel G Knapp, Julianna B Németh, Kerrie Barry, Matthieu Hainaut, Bernard Henrissat, Jenifer Johnson, Alan Kuo, Joanne Hui Ping Lim, Anna Lipzen, Matt Nolan, Robin A Ohm, László Tamás, Igor V Grigoriev, Joseph W Spatafora, László G Nagy, Gábor M Kovács
Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations...
April 20, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29678919/investigating-the-central-metabolism-of-clostridium-thermosuccinogenes
#12
Jeroen Girwar Koendjbiharie, Kilian Wiersma, Richard van Kranenburg
Clostridium thermosuccinogenes is a thermophilic anaerobic bacterium able to convert various carbohydrates to succinate and acetate as main fermentation products. Genomes of the four publicly available strains have been sequenced and the genome of the type-strain has been closed. The annotated genomes were used to reconstruct the central metabolism, and enzyme assays were used to validate annotations and to determine co-factor specificity. Genes for the pathways to all fermentation products were identified, as well as for the Embden-Meyerhof-Parnas pathway, and the pentose phosphate pathway...
April 20, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29678234/antibodies-to-in-silico-selected-gpi-anchored-theileria-parva-proteins-neutralize-sporozoite-infection-in-vitro
#13
James Nyagwange, Vishvanath Nene, Stephen Mwalimu, Sonal Henson, Lucilla Steinaa, Benjamin Nzau, Edwin Tijhaar, Roger Pelle
East Coast fever (ECF) caused by Theileria parva kills cattle in East, Central and Southern Africa leading to significant economic losses. Vaccination is used as a control strategy against ECF and is presently dependent on deliberate infection with live sporozoites and simultaneous treatment with a long-acting oxytetracycline. Although effective, this method has serious limitations; the immunity is parasite strain specific and immunized cattle can become life-long asymptomatic carriers of the parasite, posing risk for the spread of the disease...
May 2018: Veterinary Immunology and Immunopathology
https://www.readbyqxmd.com/read/29675032/fspp-a-tool-for-genome-wide-prediction-of-smorf-encoded-peptides-and-their-functions
#14
Hui Li, Li Xiao, Lili Zhang, Jiarui Wu, Bin Wei, Ninghui Sun, Yi Zhao
smORFs are small open reading frames of less than 100 codons. Recent low throughput experiments showed a lot of smORF-encoded peptides (SEPs) played crucial rule in processes such as regulation of transcription or translation, transportation through membranes and the antimicrobial activity. In order to gather more functional SEPs, it is necessary to have access to genome-wide prediction tools to give profound directions for low throughput experiments. In this study, we put forward a functional smORF-encoded peptides predictor (FSPP) which tended to predict authentic SEPs and their functions in a high throughput method...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29674702/identification-of-qtl-controlling-domestication-related-traits-in-cowpea-vigna-unguiculata-l-walp
#15
Sassoum Lo, María Muñoz-Amatriaín, Ousmane Boukar, Ira Herniter, Ndiaga Cisse, Yi-Ning Guo, Philip A Roberts, Shizhong Xu, Christian Fatokun, Timothy J Close
Cowpea (Vigna unguiculata L. Walp) is a warm-season legume with a genetically diverse gene-pool composed of wild and cultivated forms. Cowpea domestication involved considerable phenotypic changes from the wild progenitor, including reduction of pod shattering, increased organ size, and changes in flowering time. Little is known about the genetic basis underlying these changes. In this study, 215 recombinant inbred lines derived from a cross between a cultivated and a wild cowpea accession were used to evaluate nine domestication-related traits (pod shattering, peduncle length, flower color, days to flowering, 100-seed weight, pod length, leaf length, leaf width and seed number per pod)...
April 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29674560/complete-genome-sequence-of-a-natural-escherichia-coli-o145-h11-isolate-that-belongs-to-phylogroup-a
#16
Michelle Qiu Carter, Antares Pham
Escherichia coli O145:H11 strain RM14721 was originally isolated from wildlife feces near a leafy greens-growing region in Yuma, AZ. This strain was initially positive for stx 1 ; however, in subsequent cultures, stx 1 was not detected by PCR. Here, we report the complete genome sequence and annotation of RM14721.
April 19, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29673330/modular-assembly-of-transposable-element-arrays-by-microsatellite-targeting-in-the-guayule-and-rice-genomes
#17
José A Valdes Franco, Yi Wang, Naxin Huo, Grisel Ponciano, Howard A Colvin, Colleen M McMahan, Yong Q Gu, William R Belknap
BACKGROUND: Guayule (Parthenium argentatum A. Gray) is a rubber-producing desert shrub native to Mexico and the United States. Guayule represents an alternative to Hevea brasiliensis as a source for commercial natural rubber. The efficient application of modern molecular/genetic tools to guayule improvement requires characterization of its genome. RESULTS: The 1.6 Gb guayule genome was sequenced, assembled and annotated. The final 1.5 Gb assembly, while fragmented (N50  = 22 kb), maps > 95% of the shotgun reads and is essentially complete...
April 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29673315/inter-genome-comparison-of-the-quorn-fungus-fusarium-venenatum-and-the-closely-related-plant-infecting-pathogen-fusarium-graminearum
#18
Robert King, Neil Andrew Brown, Martin Urban, Kim E Hammond-Kosack
BACKGROUND: The soil dwelling saprotrophic non-pathogenic fungus Fusarium venenatum, routinely used in the commercial fermentation industry, is phylogenetically closely related to the globally important cereal and non-cereal infecting pathogen F. graminearum. This study aimed to sequence, assemble and annotate the F. venenatum (strain A3/5) genome, and compare this genome with F. graminearum. RESULTS: Using shotgun sequencing, a 38,660,329 bp F. venenatum genome was assembled into four chromosomes, and a 78,618 bp mitochondrial genome...
April 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29673008/a-gwas-meta-analysis-from-5-population-based-cohorts-implicates-ion-channel-genes-in-the-pathogenesis-of-irritable-bowel-syndrome
#19
F Bonfiglio, M Henström, A Nag, F Hadizadeh, T Zheng, M C Cenit, E Tigchelaar, F Williams, A Reznichenko, W E Ek, N V Rivera, G Homuth, A A Aghdassi, T Kacprowski, M Männikkö, V Karhunen, L Bujanda, J Rafter, C Wijmenga, J Ronkainen, P Hysi, A Zhernakova, M D'Amato
BACKGROUND: Irritable bowel syndrome (IBS) shows genetic predisposition, however, large-scale, powered gene mapping studies are lacking. We sought to exploit existing genetic (genotype) and epidemiological (questionnaire) data from a series of population-based cohorts for IBS genome-wide association studies (GWAS) and their meta-analysis. METHODS: Based on questionnaire data compatible with Rome III Criteria, we identified a total of 1335 IBS cases and 9768 asymptomatic individuals from 5 independent European genotyped cohorts...
April 19, 2018: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
https://www.readbyqxmd.com/read/29671916/assembly-and-annotation-of-a-draft-genome-sequence-for-glycine-latifolia-a-perennial-wild-relative-of-soybean
#20
Qiong Liu, Sungyul Chang, Glen L Hartman, Leslie L Domier
Glycine latifolia (Benth.) Newell & Hymowitz (2n=40), one of the 27 wild perennial relatives of soybean, possesses genetic diversity and agronomically favorable traits that are lacking in soybean. Here, we report the 939-Mb draft genome assembly of G. latifolia (PI 559298) using exclusively linked-reads sequenced from a single Chromium library. We organized scaffolds into 20 chromosome-scale pseudomolecules utilizing two genetic maps and the Glycine max (L.) Merr. genome sequence. High copy numbers of putative 91-bp centromere-specific tandem repeats were observed in consecutive blocks within predicted pericentromeric regions on several pseudomolecules...
April 19, 2018: Plant Journal: for Cell and Molecular Biology
keyword
keyword
83321
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"