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Sunday, July 7, 2019

GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing.

Tandem repeats comprise significant proportion of the human genome including coding and regulatory regions. They are highly prone to repeat number variation and nucleotide mutation due to their repetitive and unstable nature, making them a major source of genomic variation between individuals. Despite recent advances in high throughput sequencing, analysis of tandem repeats in the context of complex diseases is still hindered by technical limitations. We report a novel targeted sequencing approach, which allows simultaneous analysis of hundreds of repeats. We developed a Bayesian algorithm, namely – GtTR – which combines information from a reference long-read dataset with a short…

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Sunday, July 7, 2019

HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning.

Second-generation DNA sequencing techniques generate short reads that can result in fragmented genome assemblies. Third-generation sequencing platforms mitigate this limitation by producing longer reads that span across complex and repetitive regions. However, the usefulness of such long reads is limited because of high sequencing error rates. To exploit the full potential of these longer reads, it is imperative to correct the underlying errors. We propose HECIL-Hybrid Error Correction with Iterative Learning-a hybrid error correction framework that determines a correction policy for erroneous long reads, based on optimal combinations of decision weights obtained from short read alignments. We demonstrate that HECIL…

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Sunday, July 7, 2019

Modular traits of the Rhizobiales root microbiota and their evolutionary relationship with symbiotic Rhizobia.

Rhizobia are a paraphyletic group of soil-borne bacteria that induce nodule organogenesis in legume roots and fix atmospheric nitrogen for plant growth. In non-leguminous plants, species from the Rhizobiales order define a core lineage of the plant microbiota, suggesting additional functional interactions with plant hosts. In this work, genome analyses of 1,314 Rhizobiales isolates along with amplicon studies of the root microbiota reveal the evolutionary history of nitrogen-fixing symbiosis in this bacterial order. Key symbiosis genes were acquired multiple times, and the most recent common ancestor could colonize roots of a broad host range. In addition, root growth promotion is…

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Sunday, July 7, 2019

Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak.

Multi-country outbreaks of foodborne bacterial disease present challenges in their detection, tracking, and notification. As food is increasingly distributed across borders, such outbreaks are becoming more common. This increases the need for high-resolution, accessible, and replicable isolate typing schemes. Here we evaluate a core genome multilocus typing (cgMLST) scheme for the high-resolution reproducible typing of Salmonella enterica (S. enterica) isolates, by its application to a large European outbreak of S. enterica serovar Enteritidis. This outbreak had been extensively characterised using single nucleotide polymorphism (SNP)-based approaches. The cgMLST analysis was congruent with the original SNP-based analysis, the epidemiological data, and whole…

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Sunday, July 7, 2019

First description of novel arginine catabolic mobile elements (ACMEs) types IV and V harboring a kdp operon in Staphylococcus epidermidis characterized by whole genome sequencing.

The arginine catabolic mobile element (ACME) was first described in the methicillin-resistant Staphylococcus aureus strain USA300 and is thought to facilitate survival on skin. To date three distinct ACME types have been characterized comprehensively in S. aureus and/or Staphylococcus epidermidis. Type I harbors the arc and opp3 operons encoding an arginine deaminase pathway and an oligopeptide permease ABC transporter, respectively, type II harbors the arc operon only, and type III harbors the opp3 operon only. To investigate the diversity and detailed genetic organization of ACME, whole genome sequencing (WGS) was performed on 32 ACME-harboring oro-nasal S. epidermidis isolates using MiSeq-…

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Sunday, July 7, 2019

Complete genome sequence of Acinetobacter radioresistens strain LH6, a multidrug-resistant bacteriophage-propagating strain.

Antimicrobial resistance is a major problem worldwide. Understanding the interplay between drug-resistant pathogens, such as Acinetobacter baumannii and related species, potentially acting as environmental reservoirs is critical for preventing the spread of resistance determinants. Here we report the complete genome sequence of a multidrug-resistant bacteriophage-propagating strain of Acinetobacter radioresistens.

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Sunday, July 7, 2019

Complete genome sequences of Canadian epidemic methicillin-resistant Staphylococcus aureus strains CMRSA3 and CMRSA6.

Methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 8 (CC8) sequence type 239 (ST239) represents a predominant hospital-associated MRSA sublineage present worldwide. The Canadian epidemic MRSA strains CMRSA3 and CMRSA6 are moderately virulent members of this group but are closely related to the highly virulent strain TW20. Whole-genome sequencing of CMRSA3 and CMRSA6 was conducted to identify genetic determinants associated with their virulence.

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Sunday, July 7, 2019

Complete genome sequence of Pseudomonas aeruginosa K34-7, a carbapenem-resistant isolate of the high-risk sequence type 233.

Carbapenem-resistant Pseudomonas aeruginosa is defined as a textquotedblleftcriticaltextquotedblright priority pathogen for the development of new antibiotics. Here we report the complete genome sequence of an extensively drug-resistant, Verona integron-encoded metallo-ß-lactamase-expressing isolate belonging to the high-risk sequence type 233.

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Sunday, July 7, 2019

Complete genome sequence of Aeromonas rivipollensis KN-Mc-11N1, isolated from a wild nutria (Myocastor coypus) in South Korea.

We report here the complete genome sequence of Aeromonas rivipollensis KN-Mc-11N1, which was isolated from a wild nutria (Myocastor coypus) in South Korea. Genomic analysis indicated that A. rivipollensis may have zoonotic potential similar to that of other aeromonads, and nutria could be one of the sources of transmission of zoonotic pathogens to humans.

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Sunday, July 7, 2019

Complete genome sequence of a Staphylococcus aureus sequence type 612 isolate from an Australian horse.

Staphylococcus aureus is a serious pathogen of humans and animals. Multilocus sequence type 612 is dominant and highly virulent in South African hospitals but relatively uncommon elsewhere. We present the complete genome sequence of methicillin-resistant Staphylococcus aureus strain SVH7513, isolated from a horse at a veterinary clinic in New South Wales, Australia.

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Sunday, July 7, 2019

Tracing the de novo origin of protein-coding genes in yeast.

De novo genes are very important for evolutionary innovation. However, how these genes originate and spread remains largely unknown. To better understand this, we rigorously searched for de novo genes in Saccharomyces cerevisiae S288C and examined their spread and fixation in the population. Here, we identified 84 de novo genes in S. cerevisiae S288C since the divergence with their sister groups. Transcriptome and ribosome profiling data revealed at least 8 (10%) and 28 (33%) de novo genes being expressed and translated only under specific conditions, respectively. DNA microarray data, based on 2-fold change, showed that 87% of the de novo genes…

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