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https://www.readbyqxmd.com/read/29452952/phasevarions-of-bacterial-pathogens-methylomics-sheds-new-light-on-old-enemies
#1
REVIEW
John M Atack, Aimee Tan, Lauren O Bakaletz, Michael P Jennings, Kate L Seib
A wide variety of bacterial pathogens express phase-variable DNA methyltransferases that control expression of multiple genes via epigenetic mechanisms. These randomly switching regulons - phasevarions - regulate genes involved in pathogenesis, host adaptation, and antibiotic resistance. Individual phase-variable genes can be identified in silico as they contain easily recognized features such as simple sequence repeats (SSRs) or inverted repeats (IRs) that mediate the random switching of expression. Conversely, phasevarion-controlled genes do not contain any easily identifiable features...
February 13, 2018: Trends in Microbiology
https://www.readbyqxmd.com/read/29444255/identification-of-the-dna-methyltransferases-establishing-the-methylome-of-the-cyanobacterium-synechocystis-sp-pcc-6803
#2
Martin Hagemann, Katrin Gärtner, Matthias Scharnagl, Paul Bolay, Steffen C Lott, Janina Fuss, Bruno Huettel, Richard Reinhardt, Stephan Klähn, Wolfgang R Hess
DNA methylation in bacteria is important for defense against foreign DNA, but is also involved in DNA repair, replication, chromosome partitioning, and regulatory processes. Thus, characterization of the underlying DNA methyltransferases in genetically tractable bacteria is of paramount importance. Here, we characterized the methylome and orphan methyltransferases in the model cyanobacterium Synechocystis sp. PCC 6803. Single molecule real-time (SMRT) sequencing revealed four DNA methylation recognition sequences in addition to the previously known motif m5CGATCG, which is recognized by M...
February 12, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29427433/highly-sensitive-detection-of-mutations-in-cho-cell-recombinant-dna-using-multi-parallel-single-molecule-real-time-dna-sequencing
#3
Joseph F Cartwright, Karin Anderson, Joseph Longworth, Philip Lobb, David C James
High-fidelity replication of biologic-encoding recombinant DNA sequences by engineered mammalian cell cultures is an essential pre-requisite for the development of stable cell lines for the production of biotherapeutics. However, immortalized mammalian cells characteristically exhibit an increased point mutation frequency compared to mammalian cells in vivo, both across their genomes and at specific loci (hotspots). Thus unforeseen mutations in recombinant DNA sequences can arise and be maintained within producer cell populations...
February 10, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29417994/bacterial-diversity-and-community-structure-in-chongqing-radish-paocai-brines-revealed-using-pacbio-smrt-sequencing-technology
#4
Jixia Yang, Jialu Cao, Haiyan Xu, Qiangchuan Hou, Zhongjie Yu, Heping Zhang, Zhihong Sun
BACKGROUND: Traditional Chongqing radish paocai fermented with aged brine is considered to have the most intense flavor and authentic taste. Eight "Yanzhi" (red, RRPB group) and "Chunbulao" (white, WRPB) radish paocai brine samples were collected from Chongqing peasant households, and the diversity and community structures of bacteria present in these brines were determined using PacBio SMRT sequencing of their full-length 16S rRNA genes. RESULTS: In total, 30 phyla, 218 genera and 306 species were identified from the RRPB group, with 20 phyla, 261 genera and 420 species present in the WRPB group...
February 8, 2018: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/29401301/single-molecule-real-time-smrt-sequencing-comes-of-age-applications-and-utilities-for-medical-diagnostics
#5
Simon Ardui, Adam Ameur, Joris R Vermeesch, Matthew S Hestand
Short read massive parallel sequencing has emerged as a standard diagnostic tool in the medical setting. However, short read technologies have inherent limitations such as GC bias, difficulties mapping to repetitive elements, trouble discriminating paralogous sequences, and difficulties in phasing alleles. Long read single molecule sequencers resolve these obstacles. Moreover, they offer higher consensus accuracies and can detect epigenetic modifications from native DNA. The first commercially available long read single molecule platform was the RS system based on PacBio's single molecule real-time (SMRT) sequencing technology, which has since evolved into their RSII and Sequel systems...
February 1, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29396453/smrt-sequencing-of-full-length-transcriptome-of-flea-beetle-agasicles-hygrophila-selman-and-vogt
#6
Dong Jia, Yuanxin Wang, Yanhong Liu, Jun Hu, Yanqiong Guo, Lingling Gao, Ruiyan Ma
This study was aimed at generating the full-length transcriptome of flea beetle Agasicles hygrophila (Selman and Vogt) using single-molecule real-time (SMRT) sequencing. Four developmental stages of A. hygrophila, including eggs, larvae, pupae, and adults were harvested for isolating total RNA. The mixed samples were used for SMRT sequencing to generate the full-length transcriptome. Based on the obtained transcriptome data, alternative splicing event, simple sequence repeat (SSR) analysis, coding sequence prediction, transcript functional annotation, and lncRNA prediction were performed...
February 2, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29396409/sensitive-detection-of-mitochondrial-dna-variants-for-analysis-of-mitochondrial-dna-enriched-extracts-from-frozen-tumor-tissue
#7
M J A Weerts, E C Timmermans, R H A M Vossen, D van Strijp, M C G N Van den Hout-van Vroonhoven, W F J van IJcken, P J van der Zaag, S Y Anvar, S Sleijfer, J W M Martens
Large variation exists in mitochondrial DNA (mtDNA) not only between but also within individuals. Also in human cancer, tumor-specific mtDNA variation exists. In this work, we describe the comparison of four methods to extract mtDNA as pure as possible from frozen tumor tissue. Also, three state-of-the-art methods for sensitive detection of mtDNA variants were evaluated. The main aim was to develop a procedure to detect low-frequent single-nucleotide mtDNA-specific variants in frozen tumor tissue. We show that of the methods evaluated, DNA extracted from cytosol fractions following exonuclease treatment results in highest mtDNA yield and purity from frozen tumor tissue (270-fold mtDNA enrichment)...
February 2, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29375672/complete-genome-sequence-of-lactobacillus-pentosus-slc13-isolated-from-mustard-pickles-a-potential-probiotic-strain-with-antimicrobial-activity-against-foodborne-pathogenic-microorganisms
#8
Min-Lang Huang, Jing-Yao Huang, Cheng-Yen Kao, Tony J Fang
Background: Lactobacillus pentosus SLC13 is a high exopolysaccharide (EPS)-producing strain with broad-spectrum antimicrobial activity and the ability to grow in simulated gastrointestinal conditions. SLC13 was isolated from mustard pickles in Taiwan for potential probiotic applications. To better understand the molecular base for its antimicrobial activity and high EPS production, entire genome of SLC13 was determined by PacBio SMRT sequencing. Results: L. pentosus SLC13 contains a genome with a 3,520,510-bp chromosome and a 62,498-bp plasmid...
2018: Gut Pathogens
https://www.readbyqxmd.com/read/29371344/whole-genome-sequence-of-mycoplasma-bovis-strain-ningxia-1
#9
Peng Sun, Haifeng Luo, Xin Zhang, Jingyi Xu, Yanan Guo, Shenghu He
A genome sequence of the Mycoplasma bovis Ningxia-1 strain was tested by Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing technology. The strain was isolated from a lesioned calf lung in 2013 in Pengyang, Ningxia, China. The single circular chromosome of 1,033,629 bp shows differences between complete Mycoplasma bovis genome in insertion-like sequences (ISs), integrative conjugative elements (ICEs), lipoproteins (LPs), variable surface lipoproteins (VSPs), pathogenicity islands (PAIs), etc...
January 25, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29367880/cytogenomic-identification-and-long-read-single-molecule-real-time-smrt-sequencing-of-a-bardet-biedl-syndrome-9-bbs9-deletion
#10
Jennifer Reiner, Laura Pisani, Wanqiong Qiao, Ram Singh, Yao Yang, Lisong Shi, Wahab A Khan, Robert Sebra, Ninette Cohen, Arvind Babu, Lisa Edelmann, Ethylin Wang Jabs, Stuart A Scott
Bardet-Biedl syndrome (BBS) is a recessive disorder characterized by heterogeneous clinical manifestations, including truncal obesity, rod-cone dystrophy, renal anomalies, postaxial polydactyly, and variable developmental delays. At least 20 genes have been implicated in BBS, and all are involved in primary cilia function. We report a 1-year-old male child from Guyana with obesity, postaxial polydactyly on his right foot, hypotonia, ophthalmologic abnormalities, and developmental delay, which together indicated a clinical diagnosis of BBS...
2018: NPJ Genomic Medicine
https://www.readbyqxmd.com/read/29352165/construction-of-full-length-japanese-reference-panel-of-class-i-hla-genes-with-single-molecule-real-time-sequencing
#11
Takahiro Mimori, Jun Yasuda, Yoko Kuroki, Tomoko F Shibata, Fumiki Katsuoka, Sakae Saito, Naoki Nariai, Akira Ono, Naomi Nakai-Inagaki, Kazuharu Misawa, Keiko Tateno, Yosuke Kawai, Nobuo Fuse, Atsushi Hozawa, Shinichi Kuriyama, Junichi Sugawara, Naoko Minegishi, Kichiya Suzuki, Kengo Kinoshita, Masao Nagasaki, Masayuki Yamamoto
Human leukocyte antigen (HLA) is a gene complex known for its exceptional diversity across populations, importance in organ and blood stem cell transplantation, and associations of specific alleles with various diseases. We constructed a Japanese reference panel of class I HLA genes (ToMMo HLA panel), comprising a distinct set of HLA-A, HLA-B, HLA-C, and HLA-H alleles, by single-molecule, real-time (SMRT) sequencing of 208 individuals included in the 1070 whole-genome Japanese reference panel (1KJPN). For high-quality allele reconstruction, we developed a novel pipeline, Primer-Separation Assembly and Refinement Pipeline (PSARP), in which the SMRT sequencing and additional short-read data were used...
January 19, 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29346292/isoform-sequencing-and-state-of-art-applications-for-unravelling-complexity-of-plant-transcriptomes
#12
REVIEW
Dong An, Hieu X Cao, Changsheng Li, Klaus Humbeck, Wenqin Wang
Single-molecule real-time (SMRT) sequencing developed by PacBio, also called third-generation sequencing (TGS), offers longer reads than the second-generation sequencing (SGS). Given its ability to obtain full-length transcripts without assembly, isoform sequencing (Iso-Seq) of transcriptomes by PacBio is advantageous for genome annotation, identification of novel genes and isoforms, as well as the discovery of long non-coding RNA (lncRNA). In addition, Iso-Seq gives access to the direct detection of alternative splicing, alternative polyadenylation (APA), gene fusion, and DNA modifications...
January 18, 2018: Genes
https://www.readbyqxmd.com/read/29321642/profiling-of-metabolome-and-bacterial-community-dynamics-in-ensiled-medicago-sativa-inoculated-without-or-with-lactobacillus-plantarum-or-lactobacillus-buchneri
#13
X S Guo, W C Ke, W R Ding, L M Ding, D M Xu, W W Wang, P Zhang, F Y Yang
Using gas chromatography mass spectrometry and the PacBio single molecule with real-time sequencing technology (SMRT), we analyzed the detailed metabolomic profiles and microbial community dynamics involved in ensiled Medicago sativa (alfalfa) inoculated without or with the homofermenter Lactobacillus plantarum or heterofermenter Lactobacillus buchneri. Our results revealed that 280 substances and 102 different metabolites were present in ensiled alfalfa. Inoculation of L. buchneri led to remarkable up-accumulation in concentrations of 4-aminobutyric acid, some free amino acids, and polyols in ensiled alfalfa, whereas considerable down-accumulation in cadaverine and succinic acid were observed in L...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29258419/hisea-hierarchical-seed-aligner-for-pacbio-data
#14
Nilesh Khiste, Lucian Ilie
BACKGROUND: The next generation sequencing (NGS) techniques have been around for over a decade. Many of their fundamental applications rely on the ability to compute good genome assemblies. As the technology evolves, the assembly algorithms and tools have to continuously adjust and improve. The currently dominant technology of Illumina produces reads that are too short to bridge many repeats, setting limits on what can be successfully assembled. The emerging SMRT (Single Molecule, Real-Time) sequencing technique from Pacific Biosciences produces uniform coverage and long reads of length up to sixty thousand base pairs, enabling significantly better genome assemblies...
December 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29234337/community-profiling-of-fusarium-in-combination-with-other-plant-associated-fungi-in-different-crop-species-using-smrt-sequencing
#15
Florian Walder, Klaus Schlaeppi, Raphaël Wittwer, Alain Y Held, Susanne Vogelgsang, Marcel G A van der Heijden
Fusarium head blight, caused by fungi from the genus Fusarium, is one of the most harmful cereal diseases, resulting not only in severe yield losses but also in mycotoxin contaminated and health-threatening grains. Fusarium head blight is caused by a diverse set of species that have different host ranges, mycotoxin profiles and responses to agricultural practices. Thus, understanding the composition of Fusarium communities in the field is crucial for estimating their impact and also for the development of effective control measures...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29229636/topical-antibiotic-use-co-selects-for-the-carriage-of-mobile-genetic-elements-conferring-resistance-to-unrelated-antimicrobials-in-staphylococcus-aureus
#16
Glen P Carter, Mark B Schultz, Sarah L Baines, Anders Goncalves da Silva, Helen Heffernan, Audrey Tiong, Peter H Pham, Ian R Monk, Timothy P Stinear, Benjamin P Howden, Deborah A Williamson
Topical antibiotics such as mupirocin and fusidic acid are commonly used in the prevention and treatment of skin infections, particularly those caused by staphylococci. However, widespread use of these agents is associated with increased resistance to these agents, potentially limiting their efficacy. Of particular concern is the observation that resistance to topical antibiotics is often associated with multidrug resistance, suggesting that topical antibiotics may play a role in the emergence of multidrug-resistant (MDR) strains...
December 11, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29188195/comparative-genomic-analysis-of-two-clonally-related-multidrug-resistant-mycobacterium-tuberculosis-by-single-molecule-real-time-sequencing
#17
Kenneth Siu-Sing Leung, Gilman Kit-Hang Siu, Kingsley King-Gee Tam, Sabrina Wai-Chi To, Rahim Rajwani, Pak-Leung Ho, Samson Sai-Yin Wong, Wei W Zhao, Oliver Chiu-Kit Ma, Wing-Cheong Yam
Background: Multidrug-resistant tuberculosis (MDR-TB) is posing a major threat to global TB control. In this study, we focused on two consecutive MDR-TB isolated from the same patient before and after the initiation of anti-TB treatment. To better understand the genomic characteristics of MDR-TB, Single Molecule Real-Time (SMRT) Sequencing and comparative genomic analyses was performed to identify mutations that contributed to the stepwise development of drug resistance and growth fitness in MDR-TB under in vivo challenge of anti-TB drugs...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29186486/long-read-sequence-assembly-of-the-firefly-pyrocoelia-pectoralis-genome
#18
Xinhua Fu, Jingjing Li, Yu Tian, Weipeng Quan, Shu Zhang, Qian Liu, Fan Liang, Xinlei Zhu, Liangsheng Zhang, Depeng Wang, Jiang Hu
Findings: Here, we developed a highly reliable genome resource for the terrestrial firefly Pyrocoelia pectoralis (E. Oliv., 1883) (Coleoptera: Lampyridae) using single molecule real time (SMRT) sequencing on the PacBio Sequel platform. In total, 57.8Gb long reads were generated and assembled into a 760.4Mb genome, which is close to the estimated genome size and covered 98.7% complete and 0.7% partial insect BUSCOs. The k-mer analysis showed this genome is highly heterozygous. However, our long-read assembly demonstrates continuousness with a contig N50 length of 3...
November 24, 2017: GigaScience
https://www.readbyqxmd.com/read/29184138/centromere-evolution-and-cpg-methylation-during-vertebrate-speciation
#19
Kazuki Ichikawa, Shingo Tomioka, Yuta Suzuki, Ryohei Nakamura, Koichiro Doi, Jun Yoshimura, Masahiko Kumagai, Yusuke Inoue, Yui Uchida, Naoki Irie, Hiroyuki Takeda, Shinich Morishita
Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here, we perform de novo long-read genome assembly of three inbred medaka strains that are derived from geographically isolated subpopulations and undergo speciation. Using single-molecule real-time (SMRT) sequencing, we obtain three chromosome-mapped genomes of length ~734, ~678, and ~744Mbp with a resource of twenty-two centromeric regions of length 20-345kbp. Centromeres are positionally conserved among the three strains and even between four pairs of chromosomes that were duplicated by the teleost-specific whole-genome duplication 320-350 million years ago...
November 28, 2017: Nature Communications
https://www.readbyqxmd.com/read/29178836/chromosome-level-assembly-and-secondary-metabolite-potential-of-the-parasitic-fungus-cordyceps-militaris
#20
Glenna J Kramer, Justin R Nodwell
BACKGROUND: Cordyceps militaris is an insect pathogenic fungus that is prized for its use in traditional medicine. This and other entomopathogenic fungi are understudied sources for the discovery of new bioactive molecules. In this study, PacBio SMRT long read sequencing technology was used to sequence the genome of C. militaris with a focus on the genetic potential for secondary metabolite production in the genome assembly of this fungus. RESULTS: This is first chromosome level assembly of a species in the Cordyceps genera...
November 25, 2017: BMC Genomics
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