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https://www.readbyqxmd.com/read/28711667/identification-of-three-homologous-latex-clearing-protein-lcp-genes-from-the-genome-of-streptomyces-sp-strain-cfmr-7
#1
Jayaram Nanthini, Su Yean Ong, Kumar Sudesh
Rubber materials have greatly contributed to human civilization. However, being a polymeric material does not decompose easily, it has caused huge environmental problems. On the other hand, only few bacteria are known to degrade rubber, with studies pertaining them being intensively focusing on the mechanism involved in microbial rubber degradation. The Streptomyces sp. strain CFMR 7, which was previously confirmed to possess rubber-degrading ability, was subjected to whole genome sequencing using the single molecule sequencing technology of the PacBio® RS II system...
July 12, 2017: Gene
https://www.readbyqxmd.com/read/28711373/comparative-genomic-and-phylogenetic-analysis-of-a-toxigenic-clinical-isolate-of-corynebacterium-diphtheriae-strain-b-d-16-78-from-malaysia
#2
Kar-Wai Hong, A W Asmah Hani, C A Nurul Aina Murni, R R Pusparani, Chee Kheong Chong, Khebir Verasahib, Wan Noraini W Yusoff, Noorliza M Noordin, Kok Keng Tee, Wai-Fong Yin, Choo Yee Yu, Geik Yong Ang, Kok-Gan Chan
In this study, we report the comparative genomics and phylogenetic analysis of Corynebacterium diphtheriae strain B-D-16-78 that was isolated from a clinical specimen in 2016. The complete genome of C. diphtheriae strain B-D-16-78 was sequenced using PacBio Single Molecule, Real-Time sequencing technology and consists of a 2,474,151-bp circular chromosome with an average GC content of 53.56%. The core genome of C. diphtheriae was also deduced from a total of 74 strains with complete or draft genome sequences and the core genome-based phylogenetic analysis revealed close genetic relationship among strains that shared the same MLST allelic profile...
July 12, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28701704/concatseq-a-method-for-increasing-throughput-of-single-molecule-sequencing-by-concatenating-short-dna-fragments
#3
Ulrich Schlecht, Janine Mok, Carolina Dallett, Jan Berka
Single molecule sequencing (SMS) platforms enable base sequences to be read directly from individual strands of DNA in real-time. Though capable of long read lengths, SMS platforms currently suffer from low throughput compared to competing short-read sequencing technologies. Here, we present a novel strategy for sequencing library preparation, dubbed ConcatSeq, which increases the throughput of SMS platforms by generating long concatenated templates from pools of short DNA molecules. We demonstrate adaptation of this technique to two target enrichment workflows, commonly used for oncology applications, and feasibility using PacBio single molecule real-time (SMRT) technology...
July 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28701143/smrt-gate-a-method-for-validation-of-synthetic-constructs-on-pacific-biosciences-sequencing-platforms
#4
Rosalinda D'Amore, James Johnson, Sam Haldenby, Neil Hall, Margaret Hughes, Ryan Joynson, John G Kenny, Nicola Patron, Christiane Hertz-Fowler, Anthony Hall
Current DNA assembly methods are prone to sequence errors, requiring rigorous quality control (QC) to identify incorrect assemblies or synthesized constructs. Such errors can lead to misinterpretation of phenotypes. Because of this intrinsic problem, routine QC analysis is generally performed on three or more clones using a combination of restriction endonuclease assays, colony PCR, and Sanger sequencing. However, as new automation methods emerge that enable high-throughput assembly, QC using these techniques has become a major bottleneck...
July 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28696923/whole-genome-sequence-of-the-heterozygous-clinical-isolate-candida-krusei-81-b-5
#5
Christina A Cuomo, Terrance Shea, Bo Yang, Reeta Rao, Anja Forche
Candida krusei is a diploid, heterozygous yeast that is an opportunistic fungal pathogen in immunocompromised patients. This species also is utilized for fermenting cocoa beans during chocolate production. One major concern in the clinical setting is the innate resistance of this species to the most commonly used antifungal drug fluconazole. Here we report a high-quality genome sequence and assembly for the first clinical isolate of C. krusei, strain 81-B-5, into 11 scaffolds generated with PacBio sequencing technology...
July 10, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28696422/metagenomic-binning-of-a-marine-sponge-microbiome-reveals-unity-in-defense-but-metabolic-specialization
#6
Beate M Slaby, Thomas Hackl, Hannes Horn, Kristina Bayer, Ute Hentschel
Marine sponges are ancient metazoans that are populated by distinct and highly diverse microbial communities. In order to obtain deeper insights into the functional gene repertoire of the Mediterranean sponge Aplysina aerophoba, we combined Illumina short-read and PacBio long-read sequencing followed by un-targeted metagenomic binning. We identified a total of 37 high-quality bins representing 11 bacterial phyla and two candidate phyla. Statistical comparison of symbiont genomes with selected reference genomes revealed a significant enrichment of genes related to bacterial defense (restriction-modification systems, toxin-antitoxin systems) as well as genes involved in host colonization and extracellular matrix utilization in sponge symbionts...
July 11, 2017: ISME Journal
https://www.readbyqxmd.com/read/28683827/expanding-landscapes-of-the-diversified-mcr-1-bearing-plasmid-reservoirs
#7
Qingjing Wang, Jian Sun, Jun Li, Youfa Ding, Xing-Ping Li, Jingxia Lin, Bachar Hassan, Youjun Feng
BACKGROUND: Polymyxin is a cationic polypeptide antibiotic that can disrupt bacterial cell membrane by interacting with its lipopolysaccharide molecules and is used as a last resort drug against lethal infections by the carbapenem-resistant superbugs (like NDM-1). However, global discovery of the MCR-1 colistin resistance dramatically challenges the newly renewed interest in colistin for clinical use. METHODS: The mcr-1-harboring plasmids were acquired from swine and human Escherichia coli isolated in China, from 2015 to 2016, and subjected to Illumina PacBio RSII and Hi-Seq2000 for full genome sequencing...
July 6, 2017: Microbiome
https://www.readbyqxmd.com/read/28679546/untangling-heteroplasmy-structure-and-evolution-of-an-atypical-mitochondrial-genome-by-pacbio-sequencing
#8
Jean Peccoud, Mohamed Amine Chebbi, Alexandre Cormier, Bouziane Moumen, Clément Gilbert, Isabelle Marcadé, Christopher Chandler, Richard Cordaux
The highly compact mitochondrial genome of terrestrial isopods (Oniscidae) presents two unusual features. First, several loci can individually encode two tRNAs, thanks to single-nucleotide polymorphisms at anticodon sites. Within-individual variation (heteroplasmy) at these loci is thought to have been maintained for millions of years because individuals that do not carry all tRNA genes die, resulting in strong balancing selection. Second, the oniscid mtDNA genome comes in two conformations: a ~14kb linear monomer and a ~28kb circular dimer comprising two monomer units fused in palindrome...
July 5, 2017: Genetics
https://www.readbyqxmd.com/read/28674063/first-report-of-klebsiella-oxytoca-strain-simultaneously-producing-ndm-1-imp-4-and-kpc-2-carbapenemases
#9
Juan Wang, Min Yuan, Hai Chen, Xia Chen, Yuanchun Jia, Xiong Zhu, Li Bai, Xue Bai, Séamus Fanning, Jinxing Lu, Juan Li
The nucleotide sequences of 5 plasmids from one Klebsiella oxytoca isolate were determined using the PacBio RS II system. Plasmid analysis revealed that blaNDM-1 was carried on an IncX3 plasmid. The blaIMP-4 and blaKPC-2 were located on an IncN and an IncP-6 plasmid, respectively. Comparative sequence analysis highlighted the successful spread of carbapenemase-harbouring plasmids among different enterobacterial species. It reports for the first time coproducing NDM-1, KPC-2 and IMP-4 carbapenemases on a K. oxytoca isolate...
July 3, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28663342/comparative-genomics-of-two-sequential-candida-glabrate-clinical-isolates
#10
Luis Vale-Silva, Emmanuel Beaudoing, Van Du T Tran, Dominique Sanglard
Candida glabrate is an important fungal pathogen which develops rapidly antifungal resistance in treated patients. It is known that azole treatments lead to antifungal resistance in this fungal species and that multidrug efflux transporters are involved in this process. Specific mutations in the transcriptional regulator PDR1 result in upregulation of the transporters. In addition, we showed that the PDR1 mutations can contribute to enhance virulence in animal models. We were interested in this study to compare genomes of two specific C...
June 29, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28646867/a-high-quality-annotated-transcriptome-of-swine-peripheral-blood
#11
Haibo Liu, Timothy P L Smith, Dan J Nonneman, Jack C M Dekkers, Christopher K Tuggle
BACKGROUND: High throughput gene expression profiling assays of peripheral blood are widely used in biomedicine, as well as in animal genetics and physiology research. Accurate, comprehensive, and precise interpretation of such high throughput assays relies on well-characterized reference genomes and/or transcriptomes. However, neither the reference genome nor the peripheral blood transcriptome of the pig have been sufficiently assembled and annotated to support such profiling assays in this emerging biomedical model organism...
June 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28642846/decreased-fitness-and-virulence-in-st10-escherichia-coli-harboring-blandm-5-and-mcr-1-against-a-st4981-strain-with-blandm-5
#12
Yawei Zhang, Kang Liao, Hua Gao, Qi Wang, Xiaojuan Wang, Henan Li, Ruobing Wang, Hui Wang
Although coexistence of blaNDM-5 and mcr-1 in Escherichia coli has been reported, little is known about the fitness and virulence of such strains. Three carbapenem-resistant Escherichia coli (GZ1, GZ2, and GZ3) successively isolated from one patient in 2015 were investigated for microbiological fitness and virulence. GZ1 and GZ2 were also resistant to colistin. To verify the association between plasmids and fitness, growth kinetics of the transconjugants were performed. We also analyzed genomic sequences of GZ2 and GZ3 using PacBio sequencing...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28638050/de-novo-yeast-genome-assemblies-from-minion-pacbio-and-miseq-platforms
#13
Francesca Giordano, Louise Aigrain, Michael A Quail, Paul Coupland, James K Bonfield, Robert M Davies, German Tischler, David K Jackson, Thomas M Keane, Jing Li, Jia-Xing Yue, Gianni Liti, Richard Durbin, Zemin Ning
Long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore MinION are capable of producing long sequencing reads with average fragment lengths of over 10,000 base-pairs and maximum lengths reaching 100,000 base- pairs. Compared with short reads, the assemblies obtained from long-read sequencing platforms have much higher contig continuity and genome completeness as long fragments are able to extend paths into problematic or repetitive regions. Many successful assembly applications of the Pacific Biosciences technology have been reported ranging from small bacterial genomes to large plant and animal genomes...
June 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28637205/evolution-and-comparative-genomics-of-paqu-like-conjugative-plasmids-in-vibrio-species
#14
Ruichao Li, Lianwei Ye, Marcus Ho Yin Wong, Zhiwei Zheng, Edward Wai Chi Chan, Sheng Chen
Objectives: To investigate a set of MDR conjugative plasmids found in Vibrio species and characterize the underlying evolution process. Methods: pAQU-type plasmids from Vibrio species were sequenced using both Illumina and PacBio platforms. Bioinformatics tools were utilized to analyse the typical MDR regions and core genes in the plasmids. Results: The nine pAQU-type plasmids ranged from ∼160 to 206 kb in size and were found to harbour as many as 111 core genes encoding conjugative, replication and maintenance functions...
June 20, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28623392/mhc-class-i-diversity-in-chimpanzees-and-bonobos
#15
Vincent Maibach, Jörg B Hans, Christina Hvilsom, Tomas Marques-Bonet, Linda Vigilant
Major histocompatibility complex (MHC) class I genes are critically involved in the defense against intracellular pathogens. MHC diversity comparisons among samples of closely related taxa may reveal traces of past or ongoing selective processes. The bonobo and chimpanzee are the closest living evolutionary relatives of humans and last shared a common ancestor some 1 mya. However, little is known concerning MHC class I diversity in bonobos or in central chimpanzees, the most numerous and genetically diverse chimpanzee subspecies...
June 16, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28606056/comparative-genome-and-transcriptome-analysis-reveals-distinctive-surface-characteristics-and-unique-physiological-potentials-of-pseudomonas-aeruginosa-atcc-27853
#16
Huiluo Cao, Yong Lai, Salim Bougouffa, Zeling Xu, Aixin Yan
BACKGROUND: Pseudomonas aeruginosa ATCC 27853 was isolated from a hospital blood specimen in 1971 and has been widely used as a model strain to survey antibiotics susceptibilities, biofilm development, and metabolic activities of Pseudomonas spp.. Although four draft genomes of P. aeruginosa ATCC 27853 have been sequenced, the complete genome of this strain is still lacking, hindering a comprehensive understanding of its physiology and functional genome. RESULTS: Here we sequenced and assembled the complete genome of P...
June 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28587290/interpreting-microbial-biosynthesis-in-the-genomic-age-biological-and-practical-considerations
#17
REVIEW
Ian J Miller, Marc G Chevrette, Jason C Kwan
Genome mining has become an increasingly powerful, scalable, and economically accessible tool for the study of natural product biosynthesis and drug discovery. However, there remain important biological and practical problems that can complicate or obscure biosynthetic analysis in genomic and metagenomic sequencing projects. Here, we focus on limitations of available technology as well as computational and experimental strategies to overcome them. We review the unique challenges and approaches in the study of symbiotic and uncultured systems, as well as those associated with biosynthetic gene cluster (BGC) assembly and product prediction...
June 6, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28584301/high-resolution-profiling-of-coral-associated-bacterial-communities-using-full-length-16s-rrna-sequence-data-from-pacbio-smrt-sequencing-system
#18
Wirulda Pootakham, Wuttichai Mhuantong, Thippawan Yoocha, Lalita Putchim, Chutima Sonthirod, Chaiwat Naktang, Nalinee Thongtham, Sithichoke Tangphatsornruang
Coral reefs are a complex ecosystem consisting of coral animals and a vast array of associated symbionts including the dinoflagellate Symbiodinium, fungi, viruses and bacteria. Several studies have highlighted the importance of coral-associated bacteria and their fundamental roles in fitness and survival of the host animal. The scleractinian coral Porites lutea is one of the dominant reef-builders in the Indo-West Pacific. Currently, very little is known about the composition and structure of bacterial communities across P...
June 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28580017/complete-genome-sequence-of-vibrio-campbellii-strain-20130629003s01-isolated-from-shrimp-with-acute-hepatopancreatic-necrosis-disease
#19
Xuan Dong, Hailiang Wang, Peizhuo Zou, Jiayuan Chen, Zhen Liu, Xuepeng Wang, Jie Huang
BACKGROUND: Vibrio campbellii is widely distributed in the marine environment and is an important pathogen of aquatic organisms such as shrimp, fish, and mollusks. An isolate of V. campbellii carrying the pirAB(vp) gene, causing acute hepatopancreatic necrosis disease (AHPND), has been reported. There are no previous reports about the complete genome of V. campbellii causing AHPND (VCAHPND). To extend our understanding of the pathogenesis of VCAHPND at the genomic level, the genome of V...
2017: Gut Pathogens
https://www.readbyqxmd.com/read/28572320/complete-genome-sequencing-of-streptomyces-sp-strain-moe7-which-produces-an-extracellular-polysaccharide-with-antioxidant-and-antitumor-activities
#20
Marwa O Elnahas, Kara B De León, Magdy A Amin, Mohamed M D Hussein, Amal E Ali, Judy D Wall
Streptomyces sp. strain MOE7 is a Gram-positive filamentous bacterium isolated from agricultural soil in Columbia, Missouri, USA. Strain MOE7 produces an extracellular polysaccharide with antioxidant and antitumor activities. Through PacBio RSII sequencing, the MOE7 genome was found to be a linear chromosome of 8,399,509 bp with 6,782 protein-coding sequences.
June 1, 2017: Genome Announcements
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