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May 6, 2019

A High-Quality Genome Assembly from a Single, Field collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System

A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies, however, long-read methods have historically had greater input DNA requirements and higher costs than next generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female Spotted Lanternfly (Lycorma delicatula) using a single PacBio SMRT Cell. The Spotted Lanternfly is an invasive species recently discovered in the northeastern United States, threatening to damage…

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July 1, 2018

Complete genome sequence of a vancomycin-resistant sequence type 203 Enterococcus faecium strain with vanA belonging to complex type 859.

In 2014, the first vancomycin-resistant (encoded by vanA) Enterococcus faecium isolate belonging to sequence type 203 (ST203) and complex type 859 (CT859) was detected in Denmark. In 2016, 64% of the Danish clinical vanA E. faecium isolates belonged to ST203 and CT859. Using Pacific Biosciences (PacBio) RS II sequencing, we describe the genome of ST203 CT859 vanA E. faecium.

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June 1, 2018

Complete genome sequences of three Bacillus amyloliquefaciens strains that inhibit the growth of Listeria monocytogenes in vitro.

Here, we report the complete genome sequences of three Bacillus amyloliquefaciens strains isolated from alfalfa, almond drupes, and grapes that inhibited the growth of Listeria monocytogenes strain 2011L-2857 in vitro We also report multiple gene clusters encoding secondary metabolites that may be responsible for the growth inhibition of L. monocytogenes. Copyright © 2018 Tran et al.

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November 16, 2017

Complete genomic sequences of two Salmonella enterica subsp. enterica serogroup C2 (O:6,8) strains from Central California.

Salmonella enterica subsp. enterica strains RM11060, serotype 6,8:d:-, and RM11065, serotype 6,8:-:e,n,z15, were isolated from environmental samples collected in central California in 2009. We report the complete genome sequences of these two strains. These genomic sequences are distinct and will provide additional data to our understanding of S. enterica genomics.

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August 1, 2017

Zinc resistance within swine associated methicillin resistant staphylococcus aureus (MRSA) Isolates in the USA is associated with MLST lineage.

Zinc resistance in livestock-associated methicillin resistant Staphylococcus aureus (LA-MRSA) sequence type (ST) 398 is primarily mediated by the czrC gene co-located with the mecA gene, encoding methicillin resistance, within the type V SCCmec element. Because czrC and mecA are located within the same mobile genetic element, it has been suggested that the use of in feed zinc as an antidiarrheal agent has the potential to contribute to the emergence and spread of MRSA in swine through increased selection pressure to maintain the SCCmec element in isolates obtained from pigs. In this study we report the prevalence of the czrC gene…

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June 1, 2017

Improved maize reference genome with single-molecule technologies.

Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase…

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March 30, 2017

Complete genome sequences of two genotype A2 small ruminant lentiviruses isolated from infected U.S. sheep.

Two distinct subgroups of genotype A2 small ruminant lentiviruses (SRLVs) have been identified in the United States that infect sheep with specific host transmembrane protein 154 (TMEM154) diplotypes. Here, we report the first two complete genome sequences of SRLV strains infecting U.S. sheep belonging to genotype A2, subgroups 1 and 2. Copyright © 2017 Workman et al.

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February 9, 2017

Complete genome sequence of Edwardsiella hoshinae ATCC 35051.

Edwardsiella hoshinae is a Gram-negative facultative anaerobe that has primarily been isolated from avians and reptiles. We report here the complete and annotated genome sequence of an isolate from a monitor lizard (Varanus sp.), which contains a chromosome of 3,811,650 bp and no plasmids. Copyright © 2017 Reichley et al.

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October 1, 2016

Structural basis for recombinatorial permissiveness in the generation of Anaplasma marginale Msp2 antigenic variants.

Sequential expression of outer membrane protein antigenic variants is an evolutionarily convergent mechanism used by bacterial pathogens to escape host immune clearance and establish persistent infection. Variants must be sufficiently structurally distinct to escape existing immune effectors yet retain core structural elements required for localization and function within the outer membrane. We examined this balance using Anaplasma marginale, which generates antigenic variants in the outer membrane protein Msp2 using gene conversion. The overwhelming majority of Msp2 variants expressed during long-term persistent infection are mosaics, derived by recombination of oligonucleotide segments from multiple alleles to form unique hypervariable regions (HVR). As…

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June 24, 2016

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing.

Zea mays is an important genetic model for elucidating transcriptional networks. Uncertainties about the complete structure of mRNA transcripts limit the progress of research in this system. Here, using single-molecule sequencing technology, we produce 111,151 transcripts from 6 tissues capturing ~70% of the genes annotated in maize RefGen_v3 genome. A large proportion of transcripts (57%) represent novel, sometimes tissue-specific, isoforms of known genes and 3% correspond to novel gene loci. In other cases, the identified transcripts have improved existing gene models. Averaging across all six tissues, 90% of the splice junctions are supported by short reads from matched tissues. In…

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June 6, 2016

Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers.

Next generation sequencing technologies have vastly changed the approach of sequencing of the 16S rRNA gene for studies in microbial ecology. Three distinct technologies are available for large-scale 16S sequencing. All three are subject to biases introduced by sequencing error rates, amplification primer selection, and read length, which can affect the apparent microbial community. In this study, we compared short read 16S rRNA variable regions, V1-V3, with that of near-full length 16S regions, V1-V8, using highly diverse steer rumen microbial communities, in order to examine the impact of technology selection on phylogenetic profiles. Short paired-end reads from the Illumina MiSeq…

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March 7, 2016

Multiple mechanisms responsible for strong Congo-red-binding variants of Escherichia coli O157:H7 strains.

High variability in the expression of csgD-dependent, biofilm-forming and adhesive properties is common among Shiga toxin-producing Escherichia coli. Although many strains of serotype O157:H7 form little biofilm, conversion to stronger biofilm phenotypes has been observed. In this study, we screened different strains of serotype O157:H7 for the emergence of strong Congo-red (CR) affinity/biofilm-forming properties and investigated the underlying genetic mechanisms. Two major mechanisms which conferred stronger biofilm phenotypes were identified: mutations (insertion, deletion, single nucleotide change) in rcsB region and stx-prophage excision from the mlrA site. Restoration of the native mlrA gene (due to prophage excision) resulted in strong biofilm…

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