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https://www.readbyqxmd.com/read/28210248/coexistence-of-blaoxa-48-and-truncated-blandm-1-on-different-plasmids-in-a-klebsiella-pneumoniae-isolate-in-china
#1
Lianyan Xie, Yi Dou, Kaixin Zhou, Yue Chen, Lizhong Han, Xiaokui Guo, Jingyong Sun
Objectives: To describe the genetic environment, transferability, and antibiotic susceptibility of one clinical Klebsiella pneumoniae isolate harboring both blaOXA-48 and blaNDM-1 on different plasmids from a Chinese hospital. Methods: The isolate was subjected to antimicrobial susceptibility testing and multilocus sequence typing using Etest and PCR. The plasmids harboring blaOXA-48 and blaNDM-1 were analyzed through conjugation experiments, S1-nuclease pulsed-field gel electrophoresis, and hybridization with specific probes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28209832/complete-genome-sequences-of-three-multidrug-resistant-clinical-isolates-of-streptococcus-pneumoniae-serotype-19a-with-different-susceptibilities-to-the-myxobacterial-metabolite-carolacton
#2
Jannik Donner, Boyke Bunk, Isabel Schober, Cathrin Spröer, Simone Bergmann, Michael Jarek, Jörg Overmann, Irene Wagner-Döbler
The full-genome sequences of three drug- and multidrug-resistant Streptococcus pneumoniae clinical isolates of serotype 19A were determined by PacBio single-molecule real-time sequencing, in combination with Illumina MiSeq sequencing. A comparison to the genomes of other pneumococci indicates a high nucleotide sequence identity to strains Hungary19A-6 and TCH8431/19A.
February 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28209827/first-complete-genome-sequence-of-marinilactibacilluspiezotolerans-strain-15r-a-marine-lactobacillus-isolated-from-coal-bearing-sediment-2-0-kilometers-below-the-seafloor-determined-by-pacbio-single-molecule-real-time-technology
#3
Yuli Wei, Junwei Cao, Jiasong Fang, Chiaki Kato, Weicheng Cui
Marinilactibacillus piezotolerans strain 15R is a facultatively anaerobic heterotrophic lactobacillus isolated from deep marine subsurface sediment nearly 2 km below the seafloor in the northwestern Pacific. We report here the first whole-genome sequence of strain 15R. The identified genome sequence has 2,767,908 bp, 35.4% G+C content, and predicted 2,552 candidate protein-coding sequences, with no identified plasmids.
February 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28209817/genome-sequence-of-a-unique-magnaporthe-oryzae-rmg-dl-isolate-from-india-that-causes-blast-disease-in-diverse-cereal-crops-obtained-using-pacbio-single-molecule-and-illumina-hiseq2500-sequencing
#4
Aundy Kumar, Neelam Sheoran, Ganesan Prakash, Arpita Ghosh, Surendra K Chikara, Hosahatti Rajashekara, Uday Dhari Singh, Rashmi Aggarwal, Rakesh Kumar Jain
The whole-genome assembly of a unique rice isolate from India, Magnaporthe oryzae RMg-Dl that causes blast disease in diverse cereal crops is presented. Analysis of the 34.82 Mb genome sequence will aid in better understanding the genetic determinants of host range, host jump, survival, pathogenicity, and virulence factors of M. oryzae.
February 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28201990/a-vast-genomic-deletion-in-the-c56bl-6-genome-affects-different-genes-within-the-ifi200-cluster-on-chromosome-1-and-mediates-obesity-and-insulin-resistance
#5
Heike Vogel, Markus Jähnert, Mandy Stadion, Daniela Matzke, Stephan Scherneck, Annette Schürmann
BACKGROUND: Obesity, the excessive accumulation of body fat, is a highly heritable and genetically heterogeneous disorder. The complex, polygenic basis for the disease consisting of a network of different gene variants is still not completely known. RESULTS: In the current study we generated a BAC library of the obese-prone NZO strain to clarify the genomic alteration within the gene cluster Ifi200 on chr.1 including Ifi202b, an obesity gene that is in contrast to NZO not expressed in the lean B6 mouse...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28181326/single-molecule-rna-sequencing-uncovers-trans-splicing-and-improves-annotations-in-anopheles-stephensi
#6
X Jiang, A B Hall, J K Biedler, Z Tu
Single molecule real-time (SMRT) sequencing has recently been used to obtain full-length cDNA sequences that improve genome annotation and reveal RNA isoforms. Here, we used one such method called isoform sequencing from Pacific Biosciences (PacBio) to sequence a cDNA library from the Asian malaria mosquito Anopheles stephensi. More than 600 000 full-length cDNAs, referred to as reads of insert, were identified. Owing to the inherently high error rate of PacBio sequencing, we tested different approaches for error correction...
February 9, 2017: Insect Molecular Biology
https://www.readbyqxmd.com/read/28179027/genome-scaffolding-and-annotation-for-the-pathogen-vector-ixodes-ricinus-by-ultra-long-single-molecule-sequencing
#7
Wibke J Cramaro, Oliver E Hunewald, Lesley Bell-Sakyi, Claude P Muller
BACKGROUND: Global warming and other ecological changes have facilitated the expansion of Ixodes ricinus tick populations. Ixodes ricinus is the most important carrier of vector-borne pathogens in Europe, transmitting viruses, protozoa and bacteria, in particular Borrelia burgdorferi (sensu lato), the causative agent of Lyme borreliosis, the most prevalent vector-borne disease in humans in the Northern hemisphere. To faster control this disease vector, a better understanding of the I...
February 8, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28178315/composition-and-pathogenic-potential-of-a-microbial-bioremediation-product-used-for-crude-oil-degradation
#8
Azam F Tayabali, Gordon Coleman, Jennifer Crosthwait, Kathy C Nguyen, Yan Zhang, Philip Shwed
A microbial bioremediation product (MBP) used for large-scale oil degradation was investigated for microbial constituents and possible pathogenicity. Aerobic growth on various media yielded >108 colonies mL-1. Full-length 16S rDNA sequencing and fatty acid profiling from morphologically distinct colonies revealed ≥13 distinct genera. Full-length 16S rDNA library sequencing, by either Sanger or long-read PacBio technology, suggested that up to 21% of the MBP was composed of Arcobacter. Other high abundance microbial constituents (>6%) included the genera Proteus, Enterococcus, Dysgonomonas and several genera in the order Bacteroidales...
2017: PloS One
https://www.readbyqxmd.com/read/28178259/roche-breaks-with-pacbio-opts-for-genia
#9
(no author information available yet)
No abstract text is available yet for this article.
February 8, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28174040/solid-state-fermentative-production-of-aroma-esters-by-myroides-sp-zb35-and-its-complete-genome-sequence
#10
Zijun Xiao, Wenlong Liang, Xiankun Zhu, Jing-Yi Zhao
Consumers prefer biotechnological food products with high nutritional values and good flavors. Solid-state fermentation is a commonly used technique with a long history. In the present study, Myroides sp. ZB35 was used in solid-state fermentative production of aroma volatiles on a rice medium. Using the headspace solid phase microextraction coupled with gas chromatography-mass spectrometry technique and authentic standards, 22 esters with molecular weight ranging from 102 to 172 were identified. At 192h, the esters reached a total concentration of 1774μg/kg...
February 4, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28159771/improving-and-correcting-the-contiguity-of-long-read-genome-assemblies-of-three-plant-species-using-optical-mapping-and-chromosome-conformation-capture-data
#11
Wen-Biao Jiao, Gonzalo Garcia Accinelli, Benjamin Hartwig, Christiane Kiefer, David Baker, Edouard Severing, Eva-Maria Willing, Mathieu Piednoel, Stefan Woetzel, Eva Madrid-Herrero, Bruno Huettel, Ulrike Hümann, Richard Reinhard, Marcus A Koch, Daniel Swan, Bernardo Clavijo, George Coupland, Korbinian Schneeberger
Long-read sequencing can overcome the weaknesses of short reads in the assembly of eukaryotic genomes, however, at present additional scaffolding is needed to achieve chromosome-level assemblies. We generated PacBio long-read data of the genomes of three relatives of the model plant Arabidopsis thaliana and assembled all three genomes into only a few hundred contigs. To improve the contiguities of these assemblies, we generated BioNano Genomics optical mapping and Dovetail Genomics chromosome conformation capture data for genome scaffolding...
February 3, 2017: Genome Research
https://www.readbyqxmd.com/read/28152050/draft-genome-sequence-of-karnal-bunt-pathogen-tilletia-indica-of-wheat-provides-insights-into-the-pathogenic-mechanisms-of-quarantined-fungus
#12
Anil Kumar, Vishakha Pandey, Manoj Singh, Dinesh Pandey, M S Saharan, Soma S Marla
Karnal bunt disease in wheat is caused by hemibiotrophic fungus, Tilletia indica that has been placed as quarantine pest in more than 70 countries. Despite its economic importance, little knowledge about the molecular components of fungal pathogenesis is known. In this study, first time the genome sequence of T. indica has been deciphered for unraveling the effectors' functions of molecular pathogenesis of Karnal bunt disease. The T. indica genome was sequenced employing hybrid approach of PacBio Single Molecule Real Time (SMRT) and Illumina HiSEQ 2000 sequencing platforms...
2017: PloS One
https://www.readbyqxmd.com/read/28150702/de-novo-hybrid-assembly-of-the-rubber-tree-genome-reveals-evidence-of-paleotetraploidy-in-hevea-species
#13
Wirulda Pootakham, Chutima Sonthirod, Chaiwat Naktang, Panthita Ruang-Areerate, Thippawan Yoocha, Duangjai Sangsrakru, Kanikar Theerawattanasuk, Ratchanee Rattanawong, Napawan Lekawipat, Sithichoke Tangphatsornruang
Para rubber tree (Hevea brasiliensis) is an important economic species as it is the sole commercial producer of high-quality natural rubber. Here, we report a de novo hybrid assembly of BPM24 accession, which exhibits resistance to major fungal pathogens in Southeast Asia. Deep-coverage 454/Illumina short-read and Pacific Biosciences (PacBio) long-read sequence data were acquired to generate a preliminary draft, which was subsequently scaffolded using a long-range "Chicago" technique to obtain a final assembly of 1...
February 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28149688/evolutionary-origins-of-the-emergent-st796-clone-of-vancomycin-resistant-enterococcus-faecium
#14
Andrew H Buultjens, Margaret M C Lam, Susan Ballard, Ian R Monk, Andrew A Mahony, Elizabeth A Grabsch, M Lindsay Grayson, Stanley Pang, Geoffrey W Coombs, J Owen Robinson, Torsten Seemann, Paul D R Johnson, Benjamin P Howden, Timothy P Stinear
From early 2012, a novel clone of vancomycin resistant Enterococcus faecium (assigned the multi locus sequence type ST796) was simultaneously isolated from geographically separate hospitals in south eastern Australia and New Zealand. Here we describe the complete genome sequence of Ef_aus0233, a representative ST796 E. faecium isolate. We used PacBio single molecule real-time sequencing to establish a high quality, fully assembled genome comprising a circular chromosome of 2,888,087 bp and five plasmids. Comparison of Ef_aus0233 to other E...
2017: PeerJ
https://www.readbyqxmd.com/read/28143951/single-molecule-sequencing-of-the-drosophila-serrata-genome
#15
Scott L Allen, Emily K Delaney, Artyom Kopp, Stephen F Chenoweth
Long read sequencing technology promises to greatly enhance de novo assembly of genomes for non-model species. Although the high error rates of long reads have been a stumbling block, sequencing at high coverage permits the self-correction of many errors. Here we sequence and de novo assemble the genome of Drosophila serrata, a species from the montium subgroup that has been well studied for latitudinal clines, sexual selection, and gene expression but which lacks a reference genome. Using 11 PacBio SMRT cells, we generated 12 Gbp of raw sequence data comprising approximately 65x whole genome coverage...
January 30, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28138840/pacbio-for-haplotyping-in-gene-families
#16
Wei Zhang, Joachim Messing
The throughput and read length provided by Pacific Bioscience (PacBio) Single Molecule Real Time (SMRT) sequencing platform makes it feasible to construct contiguous, non-chimeric sequences. This is especially useful for genes with repetitive sequences in their gene bodies in gene families. We illustrate the use of PacBio to sequence and assemble hundreds of transcripts of gluten gene families from different cultivars of wheat using sequence from a single SMRT cell. To this end, we barcoded amplicons from different cultivars, then pooled these into one library for sequencing...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28130360/hybrid-assembly-of-the-large-and-highly-repetitive-genome-of-aegilops-tauschii-a-progenitor-of-bread-wheat-with-the-mega-reads-algorithm
#17
Aleksey V Zimin, Daniela Puiu, Ming-Cheng Luo, Tingting Zhu, Sergey Koren, Guillaume Marcais, James A Yorke, Jan Dvorak, Steven L Salzberg
LLong sequencing reads generated by single-molecule sequencing technology offer the possibility of dramatically improving the contiguity of genome assemblies. The biggest challenge today is that long reads have relatively high error rates, currently around 15%. The high error rates make it difficult to use this data alone, particularly with highly repetitive plant genomes. Errors in the raw data can lead to insertion or deletion errors (indels) in the consensus genome sequence, which in turn create significant problems for downstream analysis; for example, a single indel may shift the reading frame and incorrectly truncate a protein sequence...
January 27, 2017: Genome Research
https://www.readbyqxmd.com/read/28127419/towards-long-read-metagenomics-complete-assembly-of-three-novel-genomes-from-bacteria-dependent-on-a-diazotrophic-cyanobacterium-in-a-freshwater-lake-co-culture
#18
Connor B Driscoll, Timothy G Otten, Nathan M Brown, Theo W Dreher
Here we report three complete bacterial genome assemblies from a PacBio shotgun metagenome of a co-culture from Upper Klamath Lake, OR. Genome annotations and culture conditions indicate these bacteria are dependent on carbon and nitrogen fixation from the cyanobacterium Aphanizomenon flos-aquae, whose genome was assembled to draft-quality. Due to their taxonomic novelty relative to previously sequenced bacteria, we have temporarily designated these bacteria as incertae sedis Hyphomonadaceae strain UKL13-1 (3,501,508 bp and 56...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28100585/fast-and-accurate-de-novo-genome-assembly-from-long-uncorrected-reads
#19
Robert Vaser, Ivan Sovic, Niranjan Nagarajan, Mile Sikic
The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource intensive error correction and consensus generation steps to obtain high quality assemblies. We show that the error correction step can be omitted and high quality consensus sequences can be generated efficiently with a SIMD accelerated, partial order alignment based stand-alone consensus module called Racon. Based on tests with PacBio and Oxford Nanopore datasets we show that Racon coupled with Miniasm enables consensus genomes with similar or better quality than state-of-the-art methods while being an order of magnitude faster...
January 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28100185/an-improved-genome-assembly-uncovers-prolific-tandem-repeats-in-atlantic-cod
#20
Ole K Tørresen, Bastiaan Star, Sissel Jentoft, William B Reinar, Harald Grove, Jason R Miller, Brian P Walenz, James Knight, Jenny M Ekholm, Paul Peluso, Rolf B Edvardsen, Ave Tooming-Klunderud, Morten Skage, Sigbjørn Lien, Kjetill S Jakobsen, Alexander J Nederbragt
BACKGROUND: The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies...
January 18, 2017: BMC Genomics
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