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Complete genome sequences of three isolates of Xanthomonas fragariae, the bacterium responsible for angular leaf spots on strawberry plants

Complete genome sequences of three isolates of Xanthomonas fragariae, the bacterium responsible for angular leaf spots on strawberry plants

X anthomonas fragariae is a bacterium under quarantine status in Europe (1) and causes angular leaf spots of strawberry. The first symptoms were observed and described in the United States in 1960 (2), and further spread took place worldwide. A first X. fragariae genome (LMG 25863) was published in 2013 (3), with a draft status of 96 contigs. Recently, two new complete genome sequences of strains (FaP21 and FaP29) originating from California (USA) were published and highlighted the presence of plasmids (4). In this study, three additional strains with different geographic and time origins were sequenced with long-read sequencing technology (PacBio). The strain PD 885, also known as LMG 708, is the type strain, isolated in the United States by B. W. Kennedy in 1962 from Fragaria chiloensis var. ananassa (2). Strains NBC 2815 and PD 5202 were both isolated in The Netherlands from Fragaria ⫻ ananassa in 2011 and 2005, respectively.
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Complete genome sequences of escherichia coli phages vB_EcoM-EP75 and vB_EcoP-EP335

Complete genome sequences of escherichia coli phages vB_EcoM-EP75 and vB_EcoP-EP335

ABSTRACT Phages vB_EcoM-EP75 (EP75) and vB_EcoP-EP335 (EP335) specifically in- fect Shiga toxin (Stx)-producing Escherichia coli (STEC) O157 strains. EP75 has a ge- nome size of 158,143 bp and belongs to the genus Vi1virus. The genome size of EP335 is 76,622 bp, and it belongs to the genus Phieco32virus.

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Complete Genome Sequences of Two Methicillin-Sensitive Staphylococcus aureus Isolates Representing a Population Subset Highly Prevalent in Human Colonization

Complete Genome Sequences of Two Methicillin-Sensitive Staphylococcus aureus Isolates Representing a Population Subset Highly Prevalent in Human Colonization

PacBio sequencing did not indicate the presence of plasmids, which was verified by resolving S1 nuclease-treated genomic DNA via pulsed-field gel electrophoresis (data not shown). The PHAge Search Tool (PHAST [ 8 ]) was applied for the identification and annotation of prophage sequences. In isolate 08-02119, two of three prophage regions were intact (positions 578749 to 657660 [NC_009762] and 1314536 to 1360560 [NC_028859]; incom- plete, positions 1929685 to 1938122 [NC_021323]); in isolate 08- 02300, four prophage regions were identified, of which one was intact (positions 2108983 to 2157602 [NC_008617]; incomplete, positions 407256 to 415795 [NC_021323], 1409855 to 1419493 [NC_019914], and 1957745 to 1788804 [NC_023500]).
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Complete genome sequences of erwinia amylovora phages vB_EamP-S2 and vB_EamM-Bue1

Complete genome sequences of erwinia amylovora phages vB_EamP-S2 and vB_EamM-Bue1

ABSTRACT Phages vB_EamP-S2 (S2) and vB_EamM-Bue1 (Bue1) infect the plant pathogen Erwinia amylovora. S2 has a genome size of 45,495 bp and belongs to the genus SP6virus. The genome size of Bue1, related to Salmonella phage Vil, is 164,037 bp. Both phages possess a depolymerase enzyme, a frequent feature of

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Complete Genome Sequence of the English Isolate of Rat Cytomegalovirus (Murid Herpesvirus 8)

Complete Genome Sequence of the English Isolate of Rat Cytomegalovirus (Murid Herpesvirus 8)

The complete genome sequences of both MuHV-2 and MuHV-1 (MCMV Smith strain) have been published (NC_002512, 230,138 bp [ 7] and NC_004065, 230,278 bp [5]) as well as those of four very closely related isolates of MuHV-1 (6). The RCMV-M and RCMV-E genomes were shown to have significantly different restriction enzyme cleavage patterns, suggesting that they represent different betaherpesvirus species rather than different strains of the same virus (1, 8).

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Complete or high-quality draft genome sequences of six Xanthomonas hortorum strains sequenced with short- and long-read technologies

Complete or high-quality draft genome sequences of six Xanthomonas hortorum strains sequenced with short- and long-read technologies

We report here the whole-genome sequences of six X. hortorum strains (Table 1). The strains were isolated between 1942 and 2008 from a wide range of hosts and in various countries (Table 1). The genome sequences published in this work are either complete genome sequences or high-quality draft genome sequences, and all have five contigs or less (Table 1).

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First results of a national external quality assessment scheme for the detection of SARS-CoV-2 genome sequences

First results of a national external quality assessment scheme for the detection of SARS-CoV-2 genome sequences

identical for all participants and no significant difference in the time of analysis was observed between the group which correctly analysed S3 as positive and that which tested S3 false-negative (p = 0.56; unpaired t-test). The observation that all except one laboratory detected sample S2 correctly, which had the second lowest concentration (CT 33.6), suggests that the sensitivity limit of the respective test systems may conform to viral loads between S2 and S3. To further clarify this point, a positive sample with a viral load between S2 and S3 will be included in future quality assessment rounds for SARS-CoV-2 genome testing.
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First report of two complete Clostridium chauvoei genome sequences and detailed in silico genome analysis

First report of two complete Clostridium chauvoei genome sequences and detailed in silico genome analysis

Complete genome sequence of two Clostridium chauvoei strains was achieved for the type strain and an isolate of German origin which had been isolated from a diseased animal ( Table 2 ). The strategy of microbial genome sequencing with PacBio long reads and HGAP successfully fin- ished both genomes with high coverage and quality values without the need of manual completion or additional short read data. Earlier studies have shown the advantages of using PacBio generated long reads based on single-library and non-hybrid assemblies for completing bacterial genomes ( Brown et al., 2014; Liao et al., 2015 ). The genomic sizes of both, the type strain and the field isolate corroborated the pub- lished genome sequence of the Swiss C. chauvoei field strain JF4335 ( Table 3 ). No plasmid representing contig was obtained for DSM 7528 T but a 3.9-kb plasmid was identi fied in strain 12S0467. Like in other bacterial species the rRNA gene cluster is used as an important ge- netic marker to differentiate and identify C. chauvoei and C. septicum by PCR ( Sasaki et al., 2000 ). Commonly, most of the rRNA genes are posi- tioned close to each other, a constellation which is considered as the major hindrance for genome finishing ( Koren et al., 2013 ). The charac- terization of the region seems to be problematic without long read based sequencing techniques such as the PacBio RS II system capable of generating reads with N50 close to 20 kb ( Rhoads and Au, 2015 ). Using this technique we were able to resolve these dif ficulties, our ge- nome analysis showed the presence of 87 tRNA genes and 9 rRNA gene clusters ( Table 3 ).
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Directed degree sequences

Directed degree sequences

d) We had a conjecture (when the complexity of the dag realization problem was still open) that a combination of the general algorithm in c) and a certain strat- egy leads to a polynomial time algorithm for all sequences. We disproved our conjecture by constructing a counter-example. On the other hand, we show in experiments that a large fraction of systematically constructed dag sequences can be efficiently solved by this strategy. Another striking observation is that this simple disproved linear-time algorithm solves a set of real-world instances from different domains, namely ordered binary decision diagrams (OBDDs), train and flight schedules, as well as instances derived from food-web networks without any exception. The vertex degrees of OBBDs always correspond to opposed sequences. Likewise, we observe that the dag sequences corresponding to the train and flight schedules are opposed as well. Hence, we have a linear-time algo- rithm for their corresponding sequences with a). To explore possible reasons for the observation that so many non-opposed sequences are solved successfully by our strategy we started several experiments leading to interesting insights. This motivates us to develop characteristics like dag density and “distance to provably easy sequences” which can indicate how easy or difficult a given sequence can be realized.
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Complete Genome Sequence of a CTX-M-15-Producing Klebsiella pneumoniae Outbreak Strain from Multilocus Sequence Type 514

Complete Genome Sequence of a CTX-M-15-Producing Klebsiella pneumoniae Outbreak Strain from Multilocus Sequence Type 514

Whole-genome sequencing was performed on a PacBio RSII system (Pacific Biosciences, USA) by a commercial service pro- vider (GATC Biotech, Konstanz, Germany). In addition, genomic DNA was sequenced by applying the Nextera XT library kit and a MiSeq v3 reagent kit with 600 cycles on a MiSeq sequencer (Illu- mina, USA). A total of 53,705 PacBio reads with a mean read length of 6,143 bp were assembled using the RS_HGAP_Assem- bly.3 protocol implemented in SMRT Portal version 2.3.0. Chro- mosomal contigs were scaffolded, and the remaining gaps were closed on the basis of bridging PacBio reads, resulting in a closed circular chromosomal sequence of 5,278 kb. Two additional con- tigs exhibited overlapping ends and thus were circularized to plas- mid sequences with 5 kb and 362 kb, respectively. Gel electropho- resis confirmed the sizes of these two plasmids and revealed the presence of a third plasmid with a size of 4 kb. The sequence of the 4-kb plasmid had not been assembled from PacBio data initially, but it was retrieved by assembling Illumina reads de novo using Geneious version 7.1.4 ( 3 ). Illumina reads were mapped onto all replicons to improve the sequence quality to QV60. Finally, all four replicons were structurally confirmed by mapping the PacBio reads (RS BridgeMapper.3 protocol). Annotation was performed using Prokka 1.8 ( 4 ) and manually supplemented where appro- priate. PacBio sequencing revealed three sequence motifs with methylated adenine residues (N 6 -methyladenine, 6 mA): GATC,
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The complete genome sequence of Rhizobium sp. NGR234 reveals a surprisingly large number of quorum quenching associated genes

The complete genome sequence of Rhizobium sp. NGR234 reveals a surprisingly large number of quorum quenching associated genes

The scope of the present research was to investigate the inventory of QQ associated systems and enzymes comprised by the α-proteobacterium Rhizobium sp. NGR234, which was initiated by the completion of its genome sequence. Illuminating whole genome sequences of unique and ubiquitous microorganisms provides access to a large pool of sequence data for comparative genomics. Where functional based analyses fail to uncover single genes, gene operons or complex correlations responsible for certain processes, genome wide analyses answer these questions. The sequencing, closure and comparative analysis of the genome of unique microbe Rhizobium sp. NGR234 provided deeper insights into mechanisms involved in transport, secretion and communication revealing some puzzles of its broad host range (Schmeisser et al. 2009). Focusing on cell-to-cell communication in NGR234, the genome uncovered one novel QS system and a wealth of genes linked to degradation of AI-1 molecules. One main goal of the research was to employ a function- based approach to confirm these findings. Therefore, a NGR234 cosmid clone library was constructed and screened on cosmids conferring AHL degrading ability. This first approach combined with further motility assays and sequence analyses delivered five genes/loci involved in AHL degradation or modification. Two out of the five proteins were biochemically characterized in detail and subjected to HPLC-MS analysis in order to uncover the underlying cleaving mechanism. Comparing the sequential and functional results there is evidence that the genome of NGR234 comprises a high number of genes involved in QQ and that at least five genes are functional, interfering with QS systems of different biosensor strains. The detailed characterization of two genes, dlhR and qsdR1, proved that the megaplasmid of NGR234 encodes true lactonases not described in earlier studies (Krysciak et al. 2011).
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Complete Genome Sequence of blaCTX-M-27-Encoding Escherichia coli Strain H105 of Sequence Type 131 Lineage C1/H30R

Complete Genome Sequence of blaCTX-M-27-Encoding Escherichia coli Strain H105 of Sequence Type 131 Lineage C1/H30R

10,355 bp was performed using the “RS_HGAP_Assembly.3” included in the SMRT Portal version 2.3.0. Subsequently, Illumina short reads were mapped onto the assem- bled sequences in order to obtain a highly accurate genome with QV60 final quality. The chromosome was adjusted to dnaA as the first gene. Annotation was performed both using Prokka 1.10 (3) and the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html). Antimicrobial re- sistance genes and prophages were identified using Resfinder and PHAST, respectively (4, 5).
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Draft Genome Sequence and Complete Plasmid Sequence of Acinetobacter lwoffii F78, an Isolate with Strong Allergy-Protective Properties

Draft Genome Sequence and Complete Plasmid Sequence of Acinetobacter lwoffii F78, an Isolate with Strong Allergy-Protective Properties

DNA sequencing libraries were prepared using the Nextera XT kit (Illumina, USA) according to the manufacturer’s instructions. Individually tagged libraries were sequenced as a part of a flow cell as 2 ⫻ 300-bp paired-end reads using the Illumina MiSeq plat- form. A total of 12,447,167,642 sequences were produced, and the sequences from each isolate were separately assembled us- ing CLC Genomics Workbench version 7.0.4. The location of open reading frames and the annotation of genes were done

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Draft Genome Sequences of Klebsiella oxytoca Isolates Originating from a Highly Contaminated Liquid Hand Soap Product

Draft Genome Sequences of Klebsiella oxytoca Isolates Originating from a Highly Contaminated Liquid Hand Soap Product

Received 21 June 2015 Accepted 22 June 2015 Published 23 July 2015 Citation Hammerl JA, Lasch P, Nitsche A, Dabrowski PW, Hahmann H, Wicke A, Kleta S, Al Dahouk S, Dieckmann R. 2015. Draft genome sequences of Klebsiella oxytoca isolates originating from a highly contaminated liquid hand soap product. Genome Announc 3(4):e00820-15. doi:10.1128/genomeA.00820-15. Copyright © 2015 Hammerl et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

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Draft Genome Sequences of 59 Endospore-Forming Gram-Positive Bacteria Associated with Crop Plants Grown in Vietnam

Draft Genome Sequences of 59 Endospore-Forming Gram-Positive Bacteria Associated with Crop Plants Grown in Vietnam

According to their draft genome sequences, we have assigned 49 of the isolates with potential to control plant pathogens as representatives of Bacillus altitudinis (strain BT2.2), Bacillus cereus (strains A8, A22, A24, A31, A42, HB3.1, HD1.4B, HD2.4, M2.1B, SN4.3, and TK1), Bacillus pacificus (strain SN4-1), Bacillus subtilis subsp. subtilis (strain GR2.1), Bacillus tequilensis (strain DL2.1), Bacillus tropicus (strains CD3.2 and SN1), Bacillus velezensis (strains A25, A35, BT2.1, BT2.4, CP5.2, CP6, CP7.1A, CP7.1C, CP7.2A, DP1.3B, DP2.2B, EG5.1A, HD1.1, HD2.2, HD2.5, HD3.1B, HD5.1, HD5.2A, KT1, MR2.1A, OL1.1, OR2.1, S1, S2, TK2, TL7, and BP1.2A), Brevibacillus parabrevis (strains HD1.4A and HD3.3A), and Brevibacillus porteri (strains HB1.1, HB1.2, and HB1.4B).
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Popular matchings in complete graphs

Popular matchings in complete graphs

Tata Institute of Fundamental Research, Mumbai; kavitha@tcs.tifr.res.in Abstract. Our input is a complete graph G on n vertices where each vertex has a strict ranking of all other vertices in G. The goal is to construct a matching in G that is “globally stable” or popular. A matching M is popular if M does not lose a head-to-head election against any matching M 0 : here each vertex casts a vote for the matching in {M, M 0 } in which it gets a better assignment. Popular matchings need not exist in the given instance G and the popular matching problem is to decide whether one exists or not. The popular matching problem in G is easy to solve for odd n. Surprisingly, the problem becomes NP-hard for even n, as we show here. This seems to be the first graph theoretic problem that is efficiently solvable when n has one parity and NP-hard when n has the other parity.
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Cytotoxic Effects during Knock Out of Multiple Porcine Endogenous Retrovirus (PERV) Sequences in the Pig Genome by Zinc Finger Nucleases (ZFN)

Cytotoxic Effects during Knock Out of Multiple Porcine Endogenous Retrovirus (PERV) Sequences in the Pig Genome by Zinc Finger Nucleases (ZFN)

Mannheim, Germany). In a second step PCR products were heated to 95°C for dehybridisation and then cooled down slowly for re-annealing. At this stage the wild type sequences and mutat- ed sequence if present will re-anneal building “bubbles” corresponding to the DNA mis- matches, which can be then cut by the surveyor nuclease. 10 μl of each sample were loaded on a 2% agarose gel and the concentration of the PCR amplicon was quantified by band intensity. 40 ng/μl for all samples were estimated. In the third step rehybridized amplicons were treated with the surveyor nuclease. Different combinations of reaction parameters were tested for opti- mization: different DNA amounts, the enhancer concentration (1 or 2 μl) the MgCl 2 concen- tration (0, 0.5 or 1 μl) the nuclease quantity (0.5, 1 or 2 μl), as well as the nuclease working time (20 min, 40 min, 1h or 2h). After stopping the reaction with the stop solution, samples were run on a 2% agarose gel or 10% polyacrylamide gel. In parallel, a G/C control was performed as described by the manufacturer. It consists of two control plasmids with inserts that differ at a single base pair. Treatment with nuclease led to cleavage of the heteroduplexes into two bands (416 and 217 bps).
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Optimists and pessimists in (in)complete markets

Optimists and pessimists in (in)complete markets

On the complete market (gray line), the mechanism is basically the same as for the model with jumps in aggregate consumption discussed in Section II.B. The investors want to speculate against each other because they disagree about the likelihood of jumps. The optimist thinks these are less likely, and so she speculates on her belief by selling the insurance

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Intersection optimization is NP-complete

Intersection optimization is NP-complete

i ≤k |Ai|. We refer to Saaloma and Yu to learn more about state complexity [1, 2]. But this is not the issue addressed here. The question is to find the order in which we have to perform the intersections. And we show that this part of the problem is also inherently difficult. To get rid of the size problem, we consider the ordering problem with regards to some a priori upper bound on the size of automata. The decision problem will be proved NP-complete.

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Black holes are quantum complete

Black holes are quantum complete

with volume regularisation vol(Σ t ) and a regulator concerning the momenta N(Λ) with momentum cut-off Λ. We see, the Hamilton operator admits a contraction semi-group which takes the probability amplitude to zero when we approach the singular hypersurface. The regularisation does not sensitively influence the result. Nevertheless, it might be seen as a sign for the existence of a fundamental parent theory. Quantum gravity should be able to explain how field theory is protected from classical singularities. We interpret our result to the favour of quantum gravity because if quantum field theory cannot reach a classical singularity, this state should not even be formed. A valid quantum gravity should provide a dynamical resolution of the black hole formation not ending in a singularity. We conclude that the Schwarzschild interior is quantum complete for charged fields. When we compare the integral kernels corresponding to the real and the complex field we see that up to constant factors there are identical.
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