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https://www.readbyqxmd.com/read/29677397/two-ancestral-genes-shaped-the-xanthomonas-campestris-tal-effector-gene-repertoire
#1
Nicolas Denancé, Boris Szurek, Erin L Doyle, Emmanuelle Lauber, Lisa Fontaine-Bodin, Sébastien Carrère, Endrick Guy, Ahmed Hajri, Aude Cerutti, Tristan Boureau, Stéphane Poussier, Matthieu Arlat, Adam J Bogdanove, Laurent D Noël
Xanthomonas transcription activator-like effectors (TALEs) are injected inside plant cells to promote host susceptibility by enhancing transcription of host susceptibility genes. TALE-encoding (tal) genes were thought to be absent from Brassicaceae-infecting Xanthomonas campestris (Xc) genomes based on four reference genomic sequences. We discovered tal genes in 26 of 49 Xc strains isolated worldwide and used a combination of single molecule real time (SMRT) and tal amplicon sequencing to yield a near-complete description of the TALEs found in Xc (Xc TALome)...
April 20, 2018: New Phytologist
https://www.readbyqxmd.com/read/29675009/genomic-structural-variations-affecting-virulence-during-clonal-expansion-of-pseudomonas-syringae-pv-actinidiae-biovar-3-in-europe
#2
Giuseppe Firrao, Emanuela Torelli, Cesare Polano, Patrizia Ferrante, Francesca Ferrini, Marta Martini, Simone Marcelletti, Marco Scortichini, Paolo Ermacora
Pseudomonas syringae pv. actinidiae (Psa) biovar 3 caused pandemic bacterial canker of Actinidia chinensis and Actinidia deliciosa since 2008. In Europe, the disease spread rapidly in the kiwifruit cultivation areas from a single introduction. In this study, we investigated the genomic diversity of Psa biovar 3 strains during the primary clonal expansion in Europe using single molecule real-time (SMRT), Illumina and Sanger sequencing technologies. We recorded evidences of frequent mobilization and loss of transposon Tn6212, large chromosome inversions, and ectopic integration of IS sequences (remarkably ISPsy31, ISPsy36, and ISPsy37)...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29665418/a-continuous-genome-assembly-of-the-corkwing-wrasse-symphodus-melops
#3
Morten Mattingsdal, Sissel Jentoft, Ole K Tørresen, Halvor Knutsen, Michael M Hansen, Joana I Robalo, Zuzanna Zagrodzka, Carl André, Enrique Blanco Gonzalez
The wrasses (Labridae) are one of the most successful and species-rich families of the Perciformes order of teleost fish. Its members display great morphological diversity, and occupy distinct trophic levels in coastal waters and coral reefs. The cleaning behaviour displayed by some wrasses, such as corkwing wrasse (Symphodus melops), is of particular interest for the salmon aquaculture industry to combat and control sea lice infestation as an alternative to chemicals and pharmaceuticals. There are still few genome assemblies available within this fish family for comparative and functional studies, despite the rapid increase in genome resources generated during the past years...
April 14, 2018: Genomics
https://www.readbyqxmd.com/read/29660261/the-novel-kir2dl1-allele-kir2dl1-037-defined-in-the-cell-line-spo010-ihw9036
#4
W P Bultitude, A W Gymer, J Robinson, N P Mayor, S G E Marsh
The novel KIR2DL1*037 allele discovered and characterised by Single Molecule Real-Time (SMRT) DNA Sequencing.
April 16, 2018: HLA
https://www.readbyqxmd.com/read/29660070/full-length-transcriptome-sequencing-and-modular-organization-analysis-of-naringin-neoeriocitrin-related-gene-expression-pattern-in-drynaria-roosii
#5
Mei-Yu Sun, Jing-Yi Li, Dong Li, Feng-Jie Huang, Di Wang, Hui Li, Quan Xing, Hui-Bin Zhu, Lei Shi
Drynaria roosii (Nakaike) is a traditional Chinese medicinal fern, known as 'GuSuiBu'. The corresponding effective components of naringin/neoeriocitrin share highly similar chemical structure and medicinal function. Our HPLC-MS/MS results showed that the accumulation of naringin/neoeriocitrin depended on specific tissues or ages. However, little was known about the expression patterns of naringin/neoeriocitrin related genes involved in their regulatory pathways. For lack of the basic genetic information, we applied a combination of SMRT sequencing and SGS to generate the complete and full-length transcriptome of D...
April 12, 2018: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29653034/kir2dl1-allele-sequence-extensions-and-discovery-of-2dl1-0010102-and-2dl1-0010103-alleles-by-dna-sequencing
#6
W P Bultitude, A W Gymer, J Robinson, N P Mayor, S G E Marsh
Full length KIR2DL1 allele sequence extensions characterised by Single Molecule Real-Time (SMRT) DNA Sequencing.
April 13, 2018: HLA
https://www.readbyqxmd.com/read/29627853/insect-symbionts-as-valuable-grist-for-the-biotechnological-mill-an-alkaliphilic-silkworm-gut-bacterium-for-efficient-lactic-acid-production
#7
Xili Liang, Chao Sun, Bosheng Chen, Kaiqian Du, Ting Yu, Vijitra Luang-In, Xingmeng Lu, Yongqi Shao
Insects constitute the most abundant and diverse animal class and act as hosts to an extraordinary variety of symbiotic microorganisms. These microbes living inside the insects play critical roles in host biology and are also valuable bioresources. Enterococcus mundtii EMB156, isolated from the larval gut (gut pH >10) of the model organism Bombyx mori (Lepidoptera: Bombycidae), efficiently produces lactic acid, an important metabolite for industrial production of bioplastic materials. E. mundtii EMB156 grows well under alkaline conditions and stably converts various carbon sources into lactic acid, offering advantages in downstream fermentative processes...
April 7, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29580219/a-sequel-to-sanger-amplicon-sequencing-that-scales
#8
Paul D N Hebert, Thomas W A Braukmann, Sean W J Prosser, Sujeevan Ratnasingham, Jeremy R deWaard, Natalia V Ivanova, Daniel H Janzen, Winnie Hallwachs, Suresh Naik, Jayme E Sones, Evgeny V Zakharov
BACKGROUND: Although high-throughput sequencers (HTS) have largely displaced their Sanger counterparts, the short read lengths and high error rates of most platforms constrain their utility for amplicon sequencing. The present study tests the capacity of single molecule, real-time (SMRT) sequencing implemented on the SEQUEL platform to overcome these limitations, employing 658 bp amplicons of the mitochondrial cytochrome c oxidase I gene as a model system. RESULTS: By examining templates from more than 5000 species and 20,000 specimens, the performance of SMRT sequencing was tested with amplicons showing wide variation in GC composition and varied sequence attributes...
March 27, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29568283/comparative-genomics-of-the-baltic-sea-toxic-cyanobacteria-nodularia-spumigena-uhcc-0039-and-its-response-to-varying-salinity
#9
Jonna E Teikari, Shengwei Hou, Matti Wahlsten, Wolfgang R Hess, Kaarina Sivonen
Salinity is an important abiotic factor controlling the distribution and abundance of Nodularia spumigena , the dominating diazotrophic and toxic phototroph, in the brackish water cyanobacterial blooms of the Baltic Sea. To expand the available genomic information for brackish water cyanobacteria, we sequenced the isolate Nodularia spumigena UHCC 0039 using an Illumina-SMRT hybrid sequencing approach, revealing a chromosome of 5,294,286 base pairs (bp) and a single plasmid of 92,326 bp. Comparative genomics in Nostocales showed pronounced genetic similarity among Nodularia spumigena strains evidencing their short evolutionary history...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29554297/limited-reverse-transcriptase-activity-of-phi29-dna-polymerase
#10
Tomasz Krzywkowski, Malte Kühnemund, Di Wu, Mats Nilsson
Phi29 (Φ29) DNA polymerase is an enzyme commonly used in DNA amplification methods such as rolling circle amplification (RCA) and multiple strand displacement amplification (MDA), as well as in DNA sequencing methods such as single molecule real time (SMRT) sequencing. Here, we report the ability of phi29 DNA polymerase to amplify RNA-containing circular substrates during RCA. We found that circular substrates with single RNA substitutions are amplified at a similar amplification rate as non-chimeric DNA substrates, and that consecutive RNA pyrimidines were generally preferred over purines...
March 15, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29551728/complete-and-assembled-genome-sequence-of-an-ndm-9-and-ctx-m-15-producing-klebsiella-pneumoniae-sequence-type-147-wastewater-isolate-from-switzerland
#11
Magdalena Nüesch-Inderbinen, Katrin Zurfluh, Marc J A Stevens, Roger Stephan
OBJECTIVES: Carbapenem-resistant Klebsiella pneumoniae (CRKP) have emerged worldwide and represent a major threat to human health. Here, we report the genome sequence of K. pneumoniae 002SK2, an NDM-9 and CTX-M-15 producing strain isolated from wastewater in Switzerland and belonging to the international high-risk clone ST147. METHODS: Whole genome sequencing of K. pneumoniae 002SK2 was performed using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) technology RS2 reads (C4/P6 chemistry)...
March 15, 2018: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29546998/unexpected-diversity-in-the-mobilome-of-a-pseudomonas-aeruginosa-strain-isolated-from-a-dental-unit-waterline-revealed-by-smrt-sequencing
#12
Antony T Vincent, Steve J Charette, Jean Barbeau
The Gram-negative bacterium Pseudomonas aeruginosa is found in several habitats, both natural and human-made, and is particularly known for its recurrent presence as a pathogen in the lungs of patients suffering from cystic fibrosis, a genetic disease. Given its clinical importance, several major studies have investigated the genomic adaptation of P. aeruginosa in lungs and its transition as acute infections become chronic. However, our knowledge about the diversity and adaptation of the P. aeruginosa genome to non-clinical environments is still fragmentary, in part due to the lack of accurate reference genomes of strains from the numerous environments colonized by the bacterium...
March 16, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29545792/coupling-of-single-molecule-long-read-sequencing-with-imgt-highv-quest-analysis-expedites-identification-of-siv-gp140-specific-antibodies-from-scfv-phage-display-libraries
#13
Seung Yub Han, Alesia Antoine, David Howard, Bryant Chang, Woo Sung Chang, Matthew Slein, Gintaras Deikus, Sofia Kossida, Patrice Duroux, Marie-Paule Lefranc, Robert P Sebra, Melissa L Smith, Ismael Ben F Fofana
The simian immunodeficiency virus (SIV)/macaque model of human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome pathogenesis is critical for furthering our understanding of the role of antibody responses in the prevention of HIV infection, and will only increase in importance as macaque immunoglobulin (IG) gene databases are expanded. We have previously reported the construction of a phage display library from a SIV-infected rhesus macaque ( Macaca mulatta ) using oligonucleotide primers based on human IG gene sequences...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29545612/resolving-the-complete-genome-of-kuenenia-stuttgartiensis-from-a-membrane-bioreactor-enrichment-using-single-molecule-real-time-sequencing
#14
Jeroen Frank, Sebastian Lücker, Rolf H A M Vossen, Mike S M Jetten, Richard J Hall, Huub J M Op den Camp, Seyed Yahya Anvar
Anaerobic ammonium-oxidizing (anammox) bacteria are a group of strictly anaerobic chemolithoautotrophic microorganisms. They are capable of oxidizing ammonium to nitrogen gas using nitrite as a terminal electron acceptor, thereby facilitating the release of fixed nitrogen into the atmosphere. The anammox process is thought to exert a profound impact on the global nitrogen cycle and has been harnessed as an environment-friendly method for nitrogen removal from wastewater. In this study, we present the first closed genome sequence of an anammox bacterium, Kuenenia stuttgartiensis MBR1...
March 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29531310/ncor-smrt-co-repressors-cooperate-with-c-myc-to-create-an-epigenetic-barrier-to-somatic-cell-reprogramming
#15
Qiang Zhuang, Wenjuan Li, Christina Benda, Zhijian Huang, Tanveer Ahmed, Ping Liu, Xiangpeng Guo, David P Ibañez, Zhiwei Luo, Meng Zhang, Mazid Md Abdul, Zhongzhou Yang, Jiayin Yang, Yinghua Huang, Hui Zhang, Dehao Huang, Jianguo Zhou, Xiaofen Zhong, Xihua Zhu, Xiuling Fu, Wenxia Fan, Yulin Liu, Yan Xu, Carl Ward, Muhammad Jadoon Khan, Shahzina Kanwal, Bushra Mirza, Micky D Tortorella, Hung-Fat Tse, Jiayu Chen, Baoming Qin, Xichen Bao, Shaorong Gao, Andrew P Hutchins, Miguel A Esteban
Somatic cell reprogramming by exogenous factors requires cooperation with transcriptional co-activators and co-repressors to effectively remodel the epigenetic environment. How this interplay is regulated remains poorly understood. Here, we demonstrate that NCoR/SMRT co-repressors bind to pluripotency loci to create a barrier to reprogramming with the four Yamanaka factors (OCT4, SOX2, KLF4 and c-MYC), and consequently, suppressing NCoR/SMRT significantly enhances reprogramming efficiency and kinetics. The core epigenetic subunit of the NCoR/SMRT complex, histone deacetylase 3 (HDAC3), contributes to the effects of NCoR/SMRT by inducing histone deacetylation at pluripotency loci...
March 12, 2018: Nature Cell Biology
https://www.readbyqxmd.com/read/29520014/single-molecule-real-time-sequencing-in-adtkd-muc1-allows-complete-assembly-of-the-vntr-and-exact-positioning-of-causative-mutations
#16
Andrea Wenzel, Janine Altmueller, Arif B Ekici, Bernt Popp, Kurt Stueber, Holger Thiele, Alois Pannes, Simon Staubach, Eduardo Salido, Peter Nuernberg, Richard Reinhardt, André Reis, Patrick Rump, Franz-Georg Hanisch, Matthias T F Wolf, Michael Wiesener, Bruno Huettel, Bodo B Beck
Recently, the Mucin-1 (MUC1) gene has been identified as a causal gene of autosomal dominant tubulointerstitial kidney disease (ADTKD). Most causative mutations are buried within a GC-rich 60 basepair variable number of tandem repeat (VNTR), which escapes identification by massive parallel sequencing methods due to the complexity of the VNTR. We established long read single molecule real time sequencing (SMRT) targeted to the MUC1-VNTR as an alternative strategy to the snapshot assay. Our approach allows complete VNTR assembly, thereby enabling the detection of all variants residing within the VNTR and simultaneous determination of VNTR length...
March 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29495964/improving-eukaryotic-genome-annotation-using-single-molecule-mrna-sequencing
#17
Vincent Magrini, Xin Gao, Bruce A Rosa, Sean McGrath, Xu Zhang, Kymberlie Hallsworth-Pepin, John Martin, John Hawdon, Richard K Wilson, Makedonka Mitreva
BACKGROUND: The advantages of Pacific Biosciences (PacBio) single-molecule real-time (SMRT) technology include long reads, low systematic bias, and high consensus read accuracy. Here we use these attributes to improve on the genome annotation of the parasitic hookworm Ancylostoma ceylanicum using PacBio RNA-Seq. RESULTS: We sequenced 192,888 circular consensus sequences (CCS) derived from cDNAs generated using the CloneTech SMARTer system. These SMARTer-SMRT libraries were normalized and size-selected providing a robust population of expressed structural genes for subsequent genome annotation...
March 1, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29495512/characterizing-the-dna-methyltransferases-of-haloferax-volcanii-via-bioinformatics-gene-deletion-and-smrt-sequencing
#18
Matthew Ouellette, J Peter Gogarten, Jessica Lajoie, Andrea M Makkay, R Thane Papke
DNA methyltransferases (MTases), which catalyze the methylation of adenine and cytosine bases in DNA, can occur in bacteria and archaea alongside cognate restriction endonucleases (REases) in restriction-modification (RM) systems or independently as orphan MTases. Although DNA methylation and MTases have been well-characterized in bacteria, research into archaeal MTases has been limited. A previous study examined the genomic DNA methylation patterns (methylome) of the halophilic archaeon Haloferax volcanii , a model archaeal system which can be easily manipulated in laboratory settings, via single-molecule real-time (SMRT) sequencing and deletion of a putative MTase gene ( HVO_A0006 )...
February 27, 2018: Genes
https://www.readbyqxmd.com/read/29474523/progressive-approach-for-snp-calling-and-haplotype-assembly-using-single-molecular-sequencing-data
#19
Fei Guo, Dan Wang, Lusheng Wang
Motivation: Haplotype information is essential to the complete description and interpretation of genomes, genetic diversity and genetic ancestry. The new technologies can provide Single Molecular Sequencing (SMS) data that cover about 90% of positions over chromosomes. However, the SMS data has a higher error rate comparing to 1% error rate for short reads. Thus, it becomes very difficult for SNP calling and haplotype assembly using SMS reads. Most existing technologies do not work properly for the SMS data...
February 19, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29472906/the-dna-methylome-of-the-hyperthermoacidophilic-crenarchaeon-sulfolobus-acidocaldarius
#20
Mohea Couturier, Ann-Christin Lindås
DNA methylation is the most common epigenetic modification observed in the genomic DNA (gDNA) of prokaryotes and eukaryotes. Methylated nucleobases, N6 -methyl-adenine (m6A), N4 -methyl-cytosine (m4C), and 5-methyl-cytosine (m5C), detected on gDNA represent the discrimination mark between self and non-self DNA when they are part of restriction-modification systems in prokaryotes (Bacteria and Archaea). In addition, m5C in Eukaryotes and m6A in Bacteria play an important role in the regulation of key cellular processes...
2018: Frontiers in Microbiology
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