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https://www.readbyqxmd.com/read/28929370/a-termite-symbiotic-mushroom-maximizing-sexual-activity-at-growing-tips-of-vegetative-hyphae
#1
Huei-Mei Hsieh, Mei-Chu Chung, Pao-Yang Chen, Fei-Man Hsu, Wen-Wei Liao, Ai-Ning Sung, Chun-Ru Lin, Chung-Ju Rachel Wang, Yu-Hsin Kao, Mei-Jane Fang, Chi-Yung Lai, Chieh-Chen Huang, Jyh-Ching Chou, Wen-Neng Chou, Bill Chia-Han Chang, Yu-Ming Ju
BACKGROUND: Termitomyces mushrooms are mutualistically associated with fungus-growing termites, which are widely considered to cultivate a monogenotypic Termitomyces symbiont within a colony. Termitomyces cultures isolated directly from termite colonies are heterokaryotic, likely through mating between compatible homokaryons. RESULTS: After pairing homokaryons carrying different haplotypes at marker gene loci MIP and RCB from a Termitomyces fruiting body associated with Odontotermes formosanus, we observed nuclear fusion and division, which greatly resembled meiosis, during each hyphal cell division and conidial formation in the resulting heterokaryons...
September 19, 2017: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/28887485/direct-comparison-of-performance-of-single-nucleotide-variant-calling-in-human-genome-with-alignment-based-and-assembly-based-approaches
#2
Leihong Wu, Gokhan Yavas, Huixiao Hong, Weida Tong, Wenming Xiao
Complementary to reference-based variant detection, recent studies revealed that many novel variants could be detected with de novo assembled genomes. To evaluate the effect of reads coverage and the accuracy of assembly-based variant calling, we simulated short reads containing more than 3 million of single nucleotide variants (SNVs) from the whole human genome and compared the efficiency of SNV calling between the assembly-based and alignment-based calling approaches. We assessed the quality of the assembled contig and found that a minimum of 30X coverage of short reads was needed to ensure reliable SNV calling and to generate assembled contigs with a good coverage of genome and genes...
September 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28886064/sexcmd-development-and-validation-of-sex-marker-sequences-for-whole-exome-genome-and-rna-sequencing
#3
Seongmun Jeong, Jiwoong Kim, Won Park, Hongmin Jeon, Namshin Kim
Over the last decade, a large number of nucleotide sequences have been generated by next-generation sequencing technologies and deposited to public databases. However, most of these datasets do not specify the sex of individuals sampled because researchers typically ignore or hide this information. Male and female genomes in many species have distinctive sex chromosomes, XX/XY and ZW/ZZ, and expression levels of many sex-related genes differ between the sexes. Herein, we describe how to develop sex marker sequences from syntenic regions of sex chromosomes and use them to quickly identify the sex of individuals being analyzed...
2017: PloS One
https://www.readbyqxmd.com/read/28879444/comparative-study-on-whole-genome-sequences-of-aspergillus-terreus-soil-fungus-and-diaporthe-ampelina-endophytic-fungus-with-reference-to-lovastatin-production
#4
S D Bhargavi, V K Praveen, M Anil Kumar, J Savitha
Lovastatin is a competitive inhibitor of the enzyme hydroxymethyl glutaryl coenzyme A reductase (HMGR) in cholesterol biosynthetic pathway and hence used in the treatment of hyperlipidemia. In a previous study, we report a tropical soil isolate, Aspergillus terreus (KM017963), which produces ample amount of lovastatin than its counterpart that are endophytic in origin. Bioinformatic analysis of whole genome sequence of A. terreus (AH007774.1), a soil isolate revealed the presence of gene cluster (AF141924.1 & AF141925...
September 6, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28878799/integration-of-physical-genetic-and-cytogenetic-mapping-data-for-cellulose-synthase-cesa-genes-in-flax-linum-usitatissimum-l
#5
Olga Y Yurkevich, Ilya V Kirov, Nadezhda L Bolsheva, Olga A Rachinskaya, Zoya E Grushetskaya, Svyatoslav A Zoschuk, Tatiana E Samatadze, Marina V Bogdanova, Valentina A Lemesh, Alexandra V Amosova, Olga V Muravenko
Flax, Linum usitatissimum L., is a valuable multi-purpose plant, and currently, its genome is being extensively investigated. Nevertheless, mapping of genes in flax genome is still remaining a challenging task. The cellulose synthase (CesA) multigene family involving in the process of cellulose synthesis is especially important for metabolism of this fiber crop. For the first time, fluorescent in situ hybridization (FISH)-based chromosomal localization of the CesA conserved fragment (KF011584.1), 5S, and 26S rRNA genes was performed in landrace, oilseed, and fiber varieties of L...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28869567/using-next-generation-sequencing-to-identify-and-quantify-the-genetic-composition-of-resistance-breaking-commercial-isolates-of-cydia-pomonella-granulovirus
#6
Gianpiero Gueli Alletti, Annette J Sauer, Birgit Weihrauch, Eva Fritsch, Karin Undorf-Spahn, Jörg T Wennmann, Johannes A Jehle
The use of Cydia pomonella granulovirus (CpGV) isolates as biological control agents of codling moth (CM) larvae is important in organic and integrated pome fruit production worldwide. The commercially available isolates CpGV-0006, CpGV-R5, and CpGV-V15 have been selected for the control of CpGV resistant CM populations in Europe. In infection experiments, CpGV-0006 and CpGV-R5 were able to break type I resistance and to a lower extent also type III resistance, whereas CpGV-V15 overcame type I and the rarely occurring type II and type III resistance...
September 4, 2017: Viruses
https://www.readbyqxmd.com/read/28867604/characterization-and-genomic-localization-of-a-smad4-processed-pseudogene
#7
Christopher M Watson, Nick Camm, Laura A Crinnion, Agne Antanaviciute, Julian Adlard, Alexander F Markham, Ian M Carr, Ruth Charlton, David T Bonthron
Like many clinical diagnostic laboratories, we undertake routine investigation of cancer-predisposed individuals by high-throughput sequencing of patient DNA that has been target-enriched for genes associated with hereditary cancer. Accurate diagnosis using such reagents requires alertness against rare nonpathogenic variants that may interfere with variant calling. In a cohort of 2042 such cases, we identified five that initially appeared to be carriers of a 95-bp deletion of SMAD4 intron 6. More detailed analysis indicated that these individuals all carried one copy of a SMAD4 processed gene...
August 31, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28863142/assessing-the-accuracy-of-blood-rna-profiles-to-identify-patients-with-post-concussion-syndrome-a-pilot-study-in-a-military-patient-population
#8
Jimmaline J Hardy, Scott R Mooney, Andrea N Pearson, Dawn McGuire, Daniel J Correa, Roger P Simon, Robert Meller
Mild traumatic brain injury (mTBI) is a complex, neurophysiological condition that can have detrimental outcomes. Yet, to date, no objective method of diagnosis exists. Physical damage to the blood-brain-barrier and normal waste clearance via the lymphatic system may enable the detection of biomarkers of mTBI in peripheral circulation. Here we evaluate the accuracy of whole transcriptome analysis of blood to predict the clinical diagnosis of post-concussion syndrome (PCS) in a military cohort. Sixty patients with clinically diagnosed chronic concussion and controls (no history of concussion) were recruited (retrospective study design)...
2017: PloS One
https://www.readbyqxmd.com/read/28855980/pseudomonas-endocarditis-with-an-unstable-phenotype-the-challenges-of-isolate-characterization-and-carbapenem-stewardship-with-a-partial-review-of-the-literature
#9
Emil Lesho, Erik Snesrud, Yoon Kwak, Ana Ong, Rosslyn Maybank, Maryrose Laguio-Vila, Ann R Falsey, Mary Hinkle
BACKGROUND: Pseudomonas endocarditis is exceedingly rare, especially in patients without predisposing risks. We present such a case that included unexpected switches in antibacterial resistance profiles in two Pseudomonas aeruginosa (PA) strains with the same whole-genome sequence. The case also involved diagnostic and treatment challenges, such as issues with automated testing platforms, choosing the optimal aminoglycoside, minimizing unnecessary carbapenem exposure, and the need for faster, more informative laboratory tests...
2017: Antimicrobial Resistance and Infection Control
https://www.readbyqxmd.com/read/28855620/phylogeny-and-expression-pattern-analysis-of-tcp-transcription-factors-in-cassava-seedlings-exposed-to-cold-and-or-drought-stress
#10
Ning Lei, Xiang Yu, Shuxia Li, Changying Zeng, Liangping Zou, Wenbin Liao, Ming Peng
The TCP transcription factors usually act as integrators of multiple growth regulatory and environmental stimuli. However, little is known about this gene family in the important tropical crop cassava (Manihot esculenta). In this study, 36 TCP genes were identified and renamed based on cassava whole-genome sequence and their sequence similarity with Arabidopsis TCPs. Typical TCP domains were detected in these proteins by multiple sequence alignment analysis. Evolutionary analysis indicated that MeTCPs could be divided into 8 subgroups, which was further supported by gene structure and conserved motif analyses...
August 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28841720/whole-genome-sequencing-reveals-mutational-landscape-underlying-phenotypic-differences-between-two-widespread-chinese-cattle-breeds
#11
Yao Xu, Yu Jiang, Tao Shi, Hanfang Cai, Xianyong Lan, Xin Zhao, Martin Plath, Hong Chen
Whole-genome sequencing provides a powerful tool to obtain more genetic variability that could produce a range of benefits for cattle breeding industry. Nanyang (Bos indicus) and Qinchuan (Bos taurus) are two important Chinese indigenous cattle breeds with distinct phenotypes. To identify the genetic characteristics responsible for variation in phenotypes between the two breeds, in the present study, we for the first time sequenced the genomes of four Nanyang and four Qinchuan cattle with 10 to 12 fold on average of 97...
2017: PloS One
https://www.readbyqxmd.com/read/28832569/swegen-a-whole-genome-data-resource-of-genetic-variability-in-a-cross-section-of-the-swedish-population
#12
Adam Ameur, Johan Dahlberg, Pall Olason, Francesco Vezzi, Robert Karlsson, Marcel Martin, Johan Viklund, Andreas Kusalananda Kähäri, Pär Lundin, Huiwen Che, Jessada Thutkawkorapin, Jesper Eisfeldt, Samuel Lampa, Mats Dahlberg, Jonas Hagberg, Niclas Jareborg, Ulrika Liljedahl, Inger Jonasson, Åsa Johansson, Lars Feuk, Joakim Lundeberg, Ann-Christine Syvänen, Sverker Lundin, Daniel Nilsson, Björn Nystedt, Patrik Ke Magnusson, Ulf Gyllensten
Here we describe the SweGen data set, a comprehensive map of genetic variation in the Swedish population. These data represent a basic resource for clinical genetics laboratories as well as for sequencing-based association studies by providing information on genetic variant frequencies in a cohort that is well matched to national patient cohorts. To select samples for this study, we first examined the genetic structure of the Swedish population using high-density SNP-array data from a nation-wide cohort of over 10 000 Swedish-born individuals included in the Swedish Twin Registry...
August 23, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28830129/genome-re-sequencing-to-identify-snp-markers-for-muscle-color-traits-in-broiler-chickens
#13
Hyeonmin R Kong, Nicholas B Anthony, Kaylee C Rowland, Bhuwan Khatri, Byungwhi C Kong
Objective: Meat quality including muscle color in chickens is an important trait and continuous selective pressures for fast growth and high yield have negatively impacted this trait. This study was conducted to investigate genetic variations responsible for regulating muscle color. Methods: Whole genome re-sequencing analysis using Illumina HiSeq paired end read method was performed with pooled DNA samples isolated from two broiler chicken lines divergently selected for muscle color [high muscle color (HMC) and low muscle color (LMC)] along with their random bred control line (RAN)...
August 22, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28821255/the-whole-genomic-analysis-of-orf-virus-strain-hn3-12-isolated-from-henan-province-central-china
#14
Huiqin Chen, Wei Li, Zhenzhan Kuang, Daxiang Chen, Xiaoqing Liao, Ming Li, Shuhong Luo, Wenbo Hao
BACKGROUND: The Orf virus (ORFV) is the causative agent of orf, a globally-occurring, acute, pustular, contagious disease affecting sheep, goats and humans with a worldwide distribution. Currently, the genomic analysis of four ORFV strains from the Fujian province in southern China and a NA1/11 strain isolated from the Jilin province in northeast China have been reported. However, little is known about the genomic information of ORFV strains from central China. RESULTS: From a recent outbreak in a sheep herd in the Henan province of central China, a novel ORFV strain (HN3/12) was isolated and cultured in ovine fetal turbinate (OFTu) cells...
August 18, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28810845/a-bioinformatics-approach-for-identifying-transgene-insertion-sites-using-whole-genome-sequencing-data
#15
Doori Park, Su-Hyun Park, Yong Wook Ban, Youn Shic Kim, Kyoung-Cheul Park, Nam-Soo Kim, Ju-Kon Kim, Ik-Young Choi
BACKGROUND: Genetically modified crops (GM crops) have been developed to improve the agricultural traits of modern crop cultivars. Safety assessments of GM crops are of paramount importance in research at developmental stages and before releasing transgenic plants into the marketplace. Sequencing technology is developing rapidly, with higher output and labor efficiencies, and will eventually replace existing methods for the molecular characterization of genetically modified organisms...
August 15, 2017: BMC Biotechnology
https://www.readbyqxmd.com/read/28808018/a-genome-tree-of-life-for-the-fungi-kingdom
#16
JaeJin Choi, Sung-Hou Kim
Fungi belong to one of the largest and most diverse kingdoms of living organisms. The evolutionary kinship within a fungal population has so far been inferred mostly from the gene-information-based trees ("gene trees"), constructed commonly based on the degree of differences of proteins or DNA sequences of a small number of highly conserved genes common among the population by a multiple sequence alignment (MSA) method. Since each gene evolves under different evolutionary pressure and time scale, it has been known that one gene tree for a population may differ from other gene trees for the same population depending on the subjective selection of the genes...
August 29, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28807002/high-resolution-measurement-of-duf1220-domain-copy-number-from-whole-genome-sequence-data
#17
David P Astling, Ilea E Heft, Kenneth L Jones, James M Sikela
BACKGROUND: DUF1220 protein domains found primarily in Neuroblastoma BreakPoint Family (NBPF) genes show the greatest human lineage-specific increase in copy number of any coding region in the genome. There are 302 haploid copies of DUF1220 in hg38 (~160 of which are human-specific) and the majority of these can be divided into 6 different subtypes (referred to as clades). Copy number changes of specific DUF1220 clades have been associated in a dose-dependent manner with brain size variation (both evolutionarily and within the human population), cognitive aptitude, autism severity, and schizophrenia severity...
August 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28794860/minion-analysis-and-reference-consortium-phase-2-data-release-and-analysis-of-r9-0-chemistry
#18
Miten Jain, John R Tyson, Matthew Loose, Camilla L C Ip, David A Eccles, Justin O'Grady, Sunir Malla, Richard M Leggett, Ola Wallerman, Hans J Jansen, Vadim Zalunin, Ewan Birney, Bonnie L Brown, Terrance P Snutch, Hugh E Olsen
BACKGROUND: Long-read sequencing is rapidly evolving and reshaping the suite of opportunities for genomic analysis. For the MinION in particular, as both the platform and chemistry develop, the user community requires reference data to set performance expectations and maximally exploit third-generation sequencing. We performed an analysis of MinION data derived from whole genome sequencing of Escherichiacoli K-12 using the R9.0 chemistry, comparing the results with the older R7.3 chemistry...
2017: F1000Research
https://www.readbyqxmd.com/read/28771695/challenges-for-visualizing-three-dimensional-data-in-genomic-browsers
#19
REVIEW
Mike Goodstadt, Marc A Marti-Renom
Genomic interactions reveal the spatial organization of genomes and genomic domains, which is known to play key roles in cell function. Physical proximity can be represented as two-dimensional heat maps or matrices. From these, three-dimensional (3D) conformations of chromatin can be computed revealing coherent structures that highlight the importance of nonsequential relationships across genomic features. Mainstream genomic browsers have been classically developed to display compact, stacked tracks based on a linear, sequential, per-chromosome coordinate system...
August 3, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28771119/silvanigrella-aquatica-gen-nov-sp-nov-isolated-from-a-freshwater-lake-description-of-silvanigrellaceae-fam-nov-and-silvanigrellales-ord-nov-reclassification-of-the-order-bdellovibrionales-in-the-class-oligoflexia-reclassification-of-the-families-bacteriovoracaceae
#20
Martin W Hahn, Johanna Schmidt, Ulrike Koll, Manfred Rohde, Susanne Verbarg, Alexandra Pitt, Ryosuke Nakai, Takeshi Naganuma, Elke Lang
The unusual chemo-organoheterotrophic proteobacterial strain MWH-Nonnen-W8redT was isolated from a lake located in the Black Forest (Schwarzwald), Germany, by using the filtration-acclimatization method. Phylogenetic analyses based on the 16S rRNA gene sequence of the strain could not provide clear hints on classification of the strain in one of the current classes of the phylum Proteobacteria. Whole-genome sequencing resulted in a genome size of 3.5 Mbp and revealed a quite low DNA G+C content of 32.6 mol%...
August 2017: International Journal of Systematic and Evolutionary Microbiology
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