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https://www.readbyqxmd.com/read/28529883/smrt-sequencing-data-for-garcinia-mangostana-l-variety-mesta
#1
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/28528545/discovery-and-biosynthesis-of-gladiolin-a-burkholderia-gladioli-antibiotic-with-promising-activity-against-mycobacterium-tuberculosis
#2
Lijiang Song, Matthew Jenner, Joleen Masschelein, Cerith Jones, Matthew J Bull, Simon R Harris, Ruben C Hartkoorn, Anthony Vocat, Isolda Romero-Canelón, Paul Coupland, Gordon Webster, Matthew Dunn, Rebecca Weiser, Christopher Paisey, Stewart T Cole, Julian Parkhill, Eshwar Mahenthiralingam, Gregory L Challis
An antimicrobial activity screen of Burkholderia gladioli BCC0238, a clinical isolate from a cystic fibrosis patient, led to the discovery of gladiolin, a novel macrolide antibiotic with potent activity against Mycobacterium tuberculosis H37Rv. Gladiolin is structurally-related to etnangien, a highly unstable antibiotic from Sorangium cellulosum that is also active against Mycobacteria. Like etnangien, gladiolin was found to inhibit RNA polymerase, a validated drug target in M. tuberculosis. However, gladiolin lacks the highly labile hexaene moiety of etnangien and was thus found to possess significantly increased chemical stability...
May 22, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28464822/a-high-quality-assembly-of-the-nile-tilapia-oreochromis-niloticus-genome-reveals-the-structure-of-two-sex-determination-regions
#3
Matthew A Conte, William J Gammerdinger, Kerry L Bartie, David J Penman, Thomas D Kocher
BACKGROUND: Tilapias are the second most farmed fishes in the world and a sustainable source of food. Like many other fish, tilapias are sexually dimorphic and sex is a commercially important trait in these fish. In this study, we developed a significantly improved assembly of the tilapia genome using the latest genome sequencing methods and show how it improves the characterization of two sex determination regions in two tilapia species. RESULTS: A homozygous clonal XX female Nile tilapia (Oreochromis niloticus) was sequenced to 44X coverage using Pacific Biosciences (PacBio) SMRT sequencing...
May 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28455781/reduction-in-fecal-microbiota-diversity-and-short-chain-fatty-acid-producers-in-methicillin-resistant-staphylococcus-aureus-infected-individuals-as-revealed-by-pacbio-single-molecule-real-time-sequencing-technology
#4
J Zhao, L Nian, L Y Kwok, T Sun, J Zhao
Methicillin-resistant Staphylococcus aureus (MRSA) may cause potentially lethal infections. Increasing evidence suggests that the gut microbiota is associated with human health. Yet, whether patients with MRSA infections carry specific signatures in their fecal microbiota composition has not been determined. Thus, this study aimed to compare the fecal microbiota profile of MRSA-positive patients (n=15) with individuals without MRSA infection (n=15) by using the PacBio single molecule, real-time (SMRT) DNA sequencing system and real-time quantitative polymerase chain reaction (qPCR)...
April 28, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/28438580/first-complete-genome-sequence-of-bacillus-glycinifermentans-b-27
#5
Kai Bernd Stadermann, Jochen Blom, Claudia Borgmeier, Natalie Sciberras, Sandra Herbold, Maike Kipker, Guido Meurer, Stella Molck, Daniel Petri, Stefan Pelzer, Jessica Schneider
The first complete genome sequence of Bacillus glycinifermentans B-27 was determined by SMRT sequencing generating a genome sequence with a total length of 4,607,442 bases. Based on this sequence 4738 protein-coding sequences were predicted and used to identify gene clusters that are related to the production of secondary metabolites such as Lichenysin, Bacillibactin and Bacitracin. This genomic potential combined with the ability of B. glycinifermentans B-27 to grown in bile containing media might contribute to a future application of this strain as probiotic in productive livestock potentially inhibiting competing and pathogenic organisms...
April 21, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28430818/comparative-genomics-of-burkholderia-multivorans-a-ubiquitous-pathogen-with-a-highly-conserved-genomic-structure
#6
Charlotte Peeters, Vaughn S Cooper, Philip J Hatcher, Bart Verheyde, Aurélien Carlier, Peter Vandamme
The natural environment serves as a reservoir of opportunistic pathogens. A well-established method for studying the epidemiology of such opportunists is multilocus sequence typing, which in many cases has defined strains predisposed to causing infection. Burkholderia multivorans is an important pathogen in people with cystic fibrosis (CF) and its epidemiology suggests that strains are acquired from non-human sources such as the natural environment. This raises the central question of whether the isolation source (CF or environment) or the multilocus sequence type (ST) of B...
2017: PloS One
https://www.readbyqxmd.com/read/28424528/elucidation-of-quantitative-structural-diversity-of-remarkable-rearrangement-regions-shufflons-in-inci2-plasmids
#7
Tsuyoshi Sekizuka, Michiko Kawanishi, Mamoru Ohnishi, Ayaka Shima, Kengo Kato, Akifumi Yamashita, Mari Matsui, Satowa Suzuki, Makoto Kuroda
A multiple DNA inversion system, the shufflon, exists in incompatibility (Inc) I1 and I2 plasmids. The shufflon generates variants of the PilV protein, a minor component of the thin pilus. The shufflon is one of the most difficult regions for de novo genome assembly because of its structural diversity even in an isolated bacterial clone. We determined complete genome sequences, including those of IncI2 plasmids carrying mcr-1, of three Escherichia coli strains using single-molecule, real-time (SMRT) sequencing and Illumina sequencing...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28415976/smrt-genome-assembly-corrects-reference-errors-resolving-the-genetic-basis-of-virulence-in-mycobacterium-tuberculosis
#8
Afif Elghraoui, Samuel J Modlin, Faramarz Valafar
BACKGROUND: The genetic basis of virulence in Mycobacterium tuberculosis has been investigated through genome comparisons of virulent (H37Rv) and attenuated (H37Ra) sister strains. Such analysis, however, relies heavily on the accuracy of the sequences. While the H37Rv reference genome has had several corrections to date, that of H37Ra is unmodified since its original publication. RESULTS: Here, we report the assembly and finishing of the H37Ra genome from single-molecule, real-time (SMRT) sequencing...
April 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28400415/recombination-dependent-replication-and-gene-conversion-homogenize-repeat-sequences-and-diversify-plastid-genome-structure
#9
Tracey A Ruhlman, Jin Zhang, John C Blazier, Jamal S M Sabir, Robert K Jansen
PREMISE OF THE STUDY: There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact, more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements...
April 11, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28381259/halc-high-throughput-algorithm-for-long-read-error-correction
#10
Ergude Bao, Lingxiao Lan
BACKGROUND: The third generation PacBio SMRT long reads can effectively address the read length issue of the second generation sequencing technology, but contain approximately 15% sequencing errors. Several error correction algorithms have been designed to efficiently reduce the error rate to 1%, but they discard large amounts of uncorrected bases and thus lead to low throughput. This loss of bases could limit the completeness of downstream assemblies and the accuracy of analysis. RESULTS: Here, we introduce HALC, a high throughput algorithm for long read error correction...
April 5, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28369806/identification-of-microbial-profile-of-koji-using-single-molecule-real-time-sequencing-technology
#11
Wenyan Hui, Qiangchuan Hou, Chenxia Cao, Haiyan Xu, Yi Zhen, Lai-Yu Kwok, Tiansong Sun, Heping Zhang, Wenyi Zhang
Koji is a kind of Japanese traditional fermented starter that has been used for centuries. Many fermented foods are made from koji, such as sake, miso, and soy sauce. This study used the single molecule real-time sequencing technology (SMRT) to investigate the bacterial and fungal microbiota of 3 Japanese koji samples. After SMRT analysis, a total of 39121 high-quality sequences were generated, including 14354 bacterial and 24767 fungal sequence reads. The high-quality gene sequences were assigned to 5 bacterial and 2 fungal plyla, dominated by Proteobacteria and Ascomycota, respectively...
May 2017: Journal of Food Science
https://www.readbyqxmd.com/read/28364362/advantages-of-genome-sequencing-by-long-read-sequencer-using-smrt-technology-in-medical-area
#12
REVIEW
Kazuma Nakano, Akino Shiroma, Makiko Shimoji, Hinako Tamotsu, Noriko Ashimine, Shun Ohki, Misuzu Shinzato, Maiko Minami, Tetsuhiro Nakanishi, Kuniko Teruya, Kazuhito Satou, Takashi Hirano
PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions...
March 31, 2017: Human Cell
https://www.readbyqxmd.com/read/28361880/genomic-structure-of-the-horse-major-histocompatibility-complex-class-ii-region-resolved-using-pacbio-long-read-sequencing-technology
#13
Agnese Viļuma, Sofia Mikko, Daniela Hahn, Loren Skow, Göran Andersson, Tomas F Bergström
The mammalian Major Histocompatibility Complex (MHC) region contains several gene families characterized by highly polymorphic loci with extensive nucleotide diversity, copy number variation of paralogous genes, and long repetitive sequences. This structural complexity has made it difficult to construct a reliable reference sequence of the horse MHC region. In this study, we used long-read single molecule, real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio) to sequence eight Bacterial Artificial Chromosome (BAC) clones spanning the horse MHC class II region...
March 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28348836/evolution-of-a-zoonotic-pathogen-investigating-prophage-diversity-in-enterohaemorrhagic-escherichia-coli-o157-by-long-read-sequencing
#14
Sharif Shaaban, Lauren A Cowley, Sean P McAteer, Claire Jenkins, Timothy J Dallman, James L Bono, David L Gally
Enterohaemorrhagic Escherichia coli (EHEC) O157 is a zoonotic pathogen for which colonization of cattle and virulence in humans is associated with multiple horizontally acquired genes, the majority present in active or cryptic prophages. Our understanding of the evolution and phylogeny of EHEC O157 continues to develop primarily based on core genome analyses; however, such short-read sequences have limited value for the analysis of prophage content and its chromosomal location. In this study, we applied Single Molecule Real Time (SMRT) sequencing, using the Pacific Biosciences long-read sequencing platform, to isolates selected from the main sub-clusters of this clonal group...
December 2016: Microbial Genomics
https://www.readbyqxmd.com/read/28336599/complete-genome-sequence-and-methylome-analysis-of-acinetobacter-calcoaceticus-65
#15
Alexey Fomenkov, Tamas Vincze, Sergey K Degtyarev, Richard J Roberts
Acinetobacter calcoaceticus 65 is the original source strain for the restriction enzyme Acc65I. Its complete sequence and full methylome were determined using single-molecule real-time (SMRT) sequencing.
March 23, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28334874/efficient-cnv-breakpoint-analysis-reveals-unexpected-structural-complexity-and-correlation-of-dosage-sensitive-genes-with-clinical-severity-in-genomic-disorders
#16
Ling Zhang, Jingmin Wang, Cheng Zhang, Dongxiao Li, Claudia M B Carvalho, Haoran Ji, Jianqiu Xiao, Ye Wu, Weichen Zhou, Hongyan Wang, Li Jin, Yang Luo, Xiru Wu, James R Lupski, Feng Zhang, Yuwu Jiang
Genomic disorders are the clinical conditions manifested by submicroscopic genomic rearrangements including copy number variants (CNVs). The CNVs can be identified by array-based comparative genomic hybridization (aCGH), the most commonly used technology for molecular diagnostics of genomic disorders. However, clinical aCGH only informs CNVs in the probe-interrogated regions. Neither orientational information nor the resulting genomic rearrangement structure is provided, which is a key to uncovering mutational and pathogenic mechanisms underlying genomic disorders...
May 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28272530/hybrid-sequencing-and-map-finding-hysemafi-optional-strategies-for-extensively-deciphering-gene-splicing-and-expression-in-organisms-without-reference-genome
#17
Guogui Ning, Xu Cheng, Ping Luo, Fan Liang, Zhen Wang, Guoliang Yu, Xin Li, Depeng Wang, Manzhu Bao
Using second-generation sequencing (SGS) RNA-Seq strategies, extensive alterative splicing prediction is impractical and high variability of isoforms expression quantification is inevitable in organisms without true reference dataset. we report the development of a novel analysis method, termed hybrid sequencing and map finding (HySeMaFi) which combines the specific strengths of third-generation sequencing (TGS) (PacBio SMRT sequencing) and SGS (Illumina Hi-Seq/MiSeq sequencing) to effectively decipher gene splicing and to reliably estimate the isoforms abundance...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28265515/genomic-analysis-of-st88-community-acquired-methicillin-resistant-staphylococcus-aureus-in-ghana
#18
Grace Kpeli, Andrew H Buultjens, Stefano Giulieri, Evelyn Owusu-Mireku, Samuel Y Aboagye, Sarah L Baines, Torsten Seemann, Dieter Bulach, Anders Gonçalves da Silva, Ian R Monk, Benjamin P Howden, Gerd Pluschke, Dorothy Yeboah-Manu, Timothy Stinear
BACKGROUND: The emergence and evolution of community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strains in Africa is poorly understood. However, one particular MRSA lineage called ST88, appears to be rapidly establishing itself as an "African" CA-MRSA clone. In this study, we employed whole genome sequencing to provide more information on the genetic background of ST88 CA-MRSA isolates from Ghana and to describe in detail ST88 CA-MRSA isolates in comparison with other MRSA lineages worldwide...
2017: PeerJ
https://www.readbyqxmd.com/read/28256586/characterization-of-the-dynamic-transcriptome-of-a-herpesvirus-with-long-read-single-molecule-real-time-sequencing
#19
Dóra Tombácz, Zsolt Balázs, Zsolt Csabai, Norbert Moldován, Attila Szűcs, Donald Sharon, Michael Snyder, Zsolt Boldogkői
Herpesvirus gene expression is co-ordinately regulated and sequentially ordered during productive infection. The viral genes can be classified into three distinct kinetic groups: immediate-early, early, and late classes. In this study, a massively parallel sequencing technique that is based on PacBio Single Molecule Real-time sequencing platform, was used for quantifying the poly(A) fraction of the lytic transcriptome of pseudorabies virus (PRV) throughout a 12-hour interval of productive infection on PK-15 cells...
March 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28223461/identification-of-a-pseudomonas-aeruginosa-pao1-dna-methyltransferase-its-targets-and-physiological-roles
#20
Sebastian Doberenz, Denitsa Eckweiler, Olga Reichert, Vanessa Jensen, Boyke Bunk, Cathrin Spröer, Adrian Kordes, Emanuela Frangipani, Khai Luong, Jonas Korlach, Stephan Heeb, Jörg Overmann, Volkhard Kaever, Susanne Häussler
DNA methylation is widespread among prokaryotes, and most DNA methylation reactions are catalyzed by adenine DNA methyltransferases, which are part of restriction-modification (R-M) systems. R-M systems are known for their role in the defense against foreign DNA; however, DNA methyltransferases also play functional roles in gene regulation. In this study, we used single-molecule real-time (SMRT) sequencing to uncover the genome-wide DNA methylation pattern in the opportunistic pathogen Pseudomonas aeruginosa PAO1...
February 21, 2017: MBio
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