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Sunday, July 7, 2019

Next-generation sequencing-based detection of germline L1-mediated transductions.

While active LINE-1 (L1) elements possess the ability to mobilize flanking sequences to different genomic loci through a process termed transduction influencing genomic content and structure, an approach for detecting polymorphic germline non-reference transductions in massively-parallel sequencing data has been lacking.Here we present the computational approach TIGER (Transduction Inference in GERmline genomes), enabling the discovery of non-reference L1-mediated transductions by combining L1 discovery with detection of unique insertion sequences and detailed characterization of insertion sites. We employed TIGER to characterize polymorphic transductions in fifteen genomes from non-human primate species (chimpanzee, orangutan and rhesus macaque), as well as in a human…

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Sunday, July 7, 2019

Structure of Type IIL restriction-modification enzyme MmeI in complex with DNA has implications for engineering new specificities.

The creation of restriction enzymes with programmable DNA-binding and -cleavage specificities has long been a goal of modern biology. The recently discovered Type IIL MmeI family of restriction-and-modification (RM) enzymes that possess a shared target recognition domain provides a framework for engineering such new specificities. However, a lack of structural information on Type IIL enzymes has limited the repertoire that can be rationally engineered. We report here a crystal structure of MmeI in complex with its DNA substrate and an S-adenosylmethionine analog (Sinefungin). The structure uncovers for the first time the interactions that underlie MmeI-DNA recognition and methylation (5′-TCCRAC-3′; R…

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Sunday, July 7, 2019

Complete genome sequence of a Klebsiella pneumoniae strain carrying blaNDM-1 on a multidrug resistance plasmid

Here, we report the genome sequence of a blaNDM-1-positive Klebsiella pneumoniae AATZP isolate cultured from a perirectal surveillance swab collected upon admission of a patient to the NIH Clinical Center in 2014. Genome sequencing of this isolate revealed three plasmids, including one carrying the blaNDM-1 gene encoding resistance to carbapenems. Copyright © 2016 Conlan et al.

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Sunday, July 7, 2019

Complete genome sequences of two methicillin-sensitive Staphylococcus aureus isolates representing a population subset highly prevalent in human colonization.

Here, we report the high-quality draft genome sequences of two methicillin-susceptible Staphylococcus aureus isolates, 08-02119 and 08-02300. Belonging to sequence type 582 (ST582) and ST7, both isolates are representatives of clonal lineages often associated with asymptomatic colonization of humans. Copyright © 2016 Weber et al.

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Sunday, July 7, 2019

Complete genome sequence of the hyperthermophilic and piezophilic archeon Thermococcus Piezophilus CDGST, able to grow under extreme hydrostatic pressures

We report the genome sequence of Thermococcus superprofundus strain CDGS(T), a new piezophilic and hyperthermophilic member of the order Thermococcales isolated from the world’s deepest hydrothermal vents, at the Mid-Cayman Rise. The genome is consistent with a heterotrophic, anaerobic, and piezophilic lifestyle. Copyright © 2016 Dalmasso et al.

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Sunday, July 7, 2019

Complete genome sequence of Bacillus velezensis CBMB205, a phosphate-solubilizing bacterium isolated from the rhizoplane of rice in the Republic of Korea.

Bacillus velezensis CBMB205 (= KACC 13105(T) = NCCB 100236(T)) was isolated from the rhizoplane of rice (Oryza sativa L. cv. O-dae). According to previous studies, this bacterium has several genes that can promote plant growth, such as the phosphorus-solubilizing protein-coding gene. Here, we present the first complete genome of B. velezensis CBMB205. Copyright © 2016 Hwangbo et al.

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Sunday, July 7, 2019

Complete genome sequence of Psychrobacter alimentarius PAMC 27889, a psychrophile isolated from an Antarctic rock sample.

Psychrobacter alimentarius PAMC 27889, a Gram-negative, psychrophilic bacterium, was isolated from an Antarctic rock sample. Here, we report the complete genome of P. alimentarius PAMC 27889, which has the nonmevalonate methylerythritol phosphate pathway of terpenoid biosynthesis and a complete gene cluster for benzoate degradation. Copyright © 2016 Lee et al.

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Sunday, July 7, 2019

Microsatellite length scoring by Single Molecule Real Time Sequencing – Effects of sequence structure and PCR regime.

Microsatellites are DNA sequences consisting of repeated, short (1-6 bp) sequence motifs that are highly mutable by enzymatic slippage during replication. Due to their high intrinsic variability, microsatellites have important applications in population genetics, forensics, genome mapping, as well as cancer diagnostics and prognosis. The current analytical standard for microsatellites is based on length scoring by high precision electrophoresis, but due to increasing efficiency next-generation sequencing techniques may provide a viable alternative. Here, we evaluated single molecule real time (SMRT) sequencing, implemented in the PacBio series of sequencing apparatuses, as a means of microsatellite length scoring. To this end we…

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Sunday, July 7, 2019

Complete Genome Sequence of Mycobacterium avium, Isolated from Commercial Domestic Pekin Ducks (Anas platyrhynchos domestica), Determined Using PacBio Single-Molecule Real-Time Technology

Mycobacterium avium is an important pathogenic bacterium in birds and has never, to our knowledge, reported to be isolated from domestic ducks. We present here the complete genome sequence of a virulent strain of Mycobacterium avium, isolated from domestic Pekin ducks for the first time, which was determined by PacBio single-molecule real-time technology. Copyright © 2016 Song et al.

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Sunday, July 7, 2019

Complete genome sequence of the fish pathogen Flavobacterium columnare Pf1

Flavobacterium columnare is the etiologic agent of columnaris disease, a devastating fish disease prevailing in worldwide aquaculture industry. Here, we describe the complete genome of F. columnare strain Pf1, a highly virulent strain isolated from yellow catfish (Pelteobagrus fulvidraco) in China. Copyright © 2016 Zhang et al.

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Sunday, July 7, 2019

Complete genome sequence of the D-amino acid catabolism bacterium Phaeobacter sp. strain JL2886, isolated from deep seawater of the South China Sea

Phaeobacter sp. strain JL2886, isolated from deep seawater of the South China Sea, can catabolize d-amino acids. Here, we report the complete genome sequence of Phaeobacter sp. JL2886. It comprises ~4.06 Mbp, with a G+C content of 61.52%. A total of 3,913 protein-coding genes and 10 genes related to d-amino acid catabolism were obtained. Copyright © 2016 Fu et al.

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