scholarly journals Complete genome resources for Ralstonia bacterial wilt strains UW763 (phylotype I); Rs5, UW700 (phylotype II); UW386, RUN2474, RUN2279 (phylotype III)

2021 ◽  
Author(s):  
Olivia R. Steidl ◽  
Alicia N. Truchon ◽  
Madeline M. Hayes ◽  
Caitilyn Allen
Keyword(s):  
Single Molecule ◽  
Plant Pathogens ◽  
High Impact ◽  
Vascular Wilt ◽  
Genome Sequences ◽  
Southeastern Us ◽  
Soil Isolate ◽  
Tomato Isolate ◽  
Species Type ◽  
Globally Distributed

We share whole genome sequences of six strains from the Ralstonia solanacearum species complex, a diverse group of beta-Proteobacteria that cause plant vascular wilt diseases. Using single-molecule real-time (SMRT) technology, we sequenced and assembled full genomes of Rs5 and UW700, two phylotype IA-sequevar 7 (IIA-7) strains from the southeastern US that are closely related to the R. solanacearum species type strain, K60, but were isolated >50 years later. Four sequenced strains from Africa include a soil isolate from Nigeria (UW386, III-23), a tomato isolate from Senegal (UW763, I-14), and two potato isolates from the Madagascar highlands (RUN2474, III-19 and RUN2279, III-60). This resource will support studies of the genetic diversity, ecology, virulence, and microevolution of this globally distributed group of high-impact plant pathogens.

scholarly journals Complete Genome Sequences of the Plant Pathogens Ralstonia solanacearum Type Strain K60 and R. solanacearum Race 3 Biovar 2 Strain UW551

2017 ◽  
Vol 5 (40) ◽  
Author(s):  
Madeline M. Hayes ◽  
April M. MacIntyre ◽  
Caitilyn Allen
Keyword(s):  
Bacterial Wilt ◽  
Ralstonia Solanacearum ◽  
Type Strain ◽  
Plant Pathogens ◽  
Brown Rot ◽  
Industrial Agriculture ◽  
Genome Sequences ◽  
Content Type ◽  
Potato Brown Rot ◽  
Globally Distributed

ABSTRACT Ralstonia solanacearum is a globally distributed plant pathogen that causes bacterial wilt diseases of many crop hosts, threatening both sustenance farming and industrial agriculture. Here, we present closed genome sequences for the R. solanacearum type strain, K60, and the cool-tolerant potato brown rot strain R. solanacearum UW551, a highly regulated U.S. select agent pathogen.

scholarly journals Genomic characterization of 99 viruses from the bunyavirus families Nairoviridae, Peribunyaviridae, and Phenuiviridae, including 35 previously unsequenced viruses

2021 ◽  
Vol 17 (3) ◽  
pp. e1009315
Author(s):  
Marylee L. Kapuscinski ◽  
Nicholas A. Bergren ◽  
Brandy J. Russell ◽  
Justin S. Lee ◽  
Erin M. Borland ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Reference Sequence ◽  
Large Sample Size ◽  
Emerging Pathogens ◽  
Genome Sequences ◽  
Pathogenic Potential ◽  
Genomic Characterization ◽  
Response Decisions ◽  
Rapid Characterization

Bunyaviruses (Negarnaviricota: Bunyavirales) are a large and diverse group of viruses that include important human, veterinary, and plant pathogens. The rapid characterization of known and new emerging pathogens depends on the availability of comprehensive reference sequence databases that can be used to match unknowns, infer evolutionary and pathogenic potential, and make response decisions in an evidence-based manner. In this study, we determined the coding-complete genome sequences of 99 bunyaviruses in the Centers for Disease Control and Prevention’s Arbovirus Reference Collection, focusing on orthonairoviruses (family Nairoviridae), orthobunyaviruses (Peribunyaviridae), and phleboviruses (Phenuiviridae) that either completely or partially lacked genome sequences. These viruses had been collected over 66 years from 27 countries from vertebrates and arthropods representing 37 genera. Many of the viruses had been characterized serologically and through experimental infection of animals but were isolated in the pre-sequencing era. We took advantage of our unusually large sample size to systematically evaluate genomic characteristics of these viruses, including reassortment, and co-infection. We corroborated our findings using several independent molecular and virologic approaches, including Sanger sequencing of 197 genome segments, and plaque isolation of viruses from putative co-infected virus stocks. This study contributes to the described genetic diversity of bunyaviruses and will enhance the capacity to characterize emerging human pathogenic bunyaviruses.

scholarly journals Five Closed Salmonella enterica Genome Sequences from a 2017–2018 Multistrain, Multistate Kratom Outbreak

2020 ◽  
Vol 9 (3) ◽  
Author(s):  
Hallie E. Rauch ◽  
Julie Haendiges ◽  
Maria Balkey ◽  
Maria Hoffmann
Keyword(s):  
Dna Sequencing ◽  
Real Time ◽  
Single Molecule ◽  
Salmonella Enterica ◽  
Genome Sequences ◽  
Circular Chromosome ◽  
Content Type ◽  
Single Plasmid

We report here the closed genomes of Salmonella enterica strains from the 2017–2018 multistrain, multistate kratom outbreak using single-molecule real-time DNA sequencing. Four of the genomes consist of one circular chromosome, and the fifth has a circular chromosome and a single plasmid.

scholarly journals Identification of Structural Variants in Two Novel Genomes of Maize Inbred Lines Possibly Related to Glyphosate Tolerance

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 523
Author(s):  
Medhat Mahmoud ◽  
Joanna Gracz-Bernaciak ◽  
Marek Żywicki ◽  
Wojciech Karłowski ◽  
Tomasz Twardowski ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Molecule ◽  
Zea Mays L ◽  
Shikimate Pathway ◽  
High Impact ◽  
Maize Genome ◽  
Structural Variants ◽  
Shikimate Dehydrogenase ◽  
Epsps Gene ◽  
Sequencing Technologies

To study genetic variations between genomes of plants that are naturally tolerant and sensitive to glyphosate, we used two Zea mays L. lines traditionally bred in Poland. To overcome the complexity of the maize genome, two sequencing technologies were employed: Illumina and Single Molecule Real-Time (SMRT) PacBio. Eleven thousand structural variants, 4 million SNPs and approximately 800 thousand indels differentiating the two genomes were identified. Detailed analyses allowed to identify 20 variations within the EPSPS gene, but all of them were predicted to have moderate or unknown effects on gene expression. Other genes of the shikimate pathway encoding bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase and chorismate synthase were altered by variants predicted to have a high impact on gene expression. Additionally, high-impact variants located within the genes involved in the active transport of glyphosate through the cell membrane encoding phosphate transporters as well as multidrug and toxic compound extrusion have been identified.

scholarly journals Draft Genome Sequences of Two Uncultured Armatimonadetes Associated with a Microcystis sp. (Cyanobacteria) Isolate

2017 ◽  
Vol 5 (40) ◽  
Author(s):  
Jason N. Woodhouse ◽  
A. Katharina Makower ◽  
Hans-Peter Grossart ◽  
Elke Dittmann
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Type Strain ◽  
Enrichment Culture ◽  
Draft Genome ◽  
Eutrophic Lake ◽  
Smrt Sequencing ◽  
Genome Sequences ◽  
Terrestrial Environments ◽  
Strain Genome

ABSTRACT Two genome sequences of the phylum Armatimonadetes, derived from terrestrial environments, have been previously described. Here, two additional Armatimonadetes genome sequences were obtained via single-molecule real-time (SMRT) sequencing of an enrichment culture of the bloom-forming cyanobacterium Microcystis sp. isolated from a eutrophic lake (Brandenburg, Germany). The genomes are most closely affiliated with the class Fimbriimonadales, although they are smaller than the 5.6-Mbp type strain genome.

scholarly journals Reevaluation of the Complete Genome Sequence of Magnetospirillum gryphiswaldense MSR-1 with Single-Molecule Real-Time Sequencing Data

2018 ◽  
Vol 6 (17) ◽  
Author(s):  
René Uebe ◽  
Dirk Schüler ◽  
Christian Jogler ◽  
Sandra Wiegand
Keyword(s):  
Single Molecule ◽  
Complete Genome Sequence ◽  
Type Strain ◽  
Point Mutations ◽  
Laboratory Strain ◽  
Sequencing Data ◽  
Genome Sequences ◽  
Content Type ◽  
Magnetospirillum Gryphiswaldense ◽  
Genomic Plasticity

ABSTRACT Magnetospirillum gryphiswaldense is a key organism for understanding magnetosome formation and magnetotaxis. As earlier studies suggested a high genomic plasticity, we (re)sequenced the type strain MSR-1 and the laboratory strain R3/S1. Both sequences differ by only 11 point mutations, but organization of the magnetosome island deviates from that of previous genome sequences.

scholarly journals Genome Sequences and Methylation Patterns of Natrinema versiforme BOL5-4 and Natrinema pallidum BOL6-1, Two Extremely Halophilic Archaea from a Bolivian Salt Mine

2019 ◽  
Vol 8 (33) ◽  
Author(s):  
Priya DasSarma ◽  
Brian P. Anton ◽  
Satyajit L. DasSarma ◽  
Fabiana L. Martinez ◽  
Daniel Guzman ◽  
...  
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Genome Annotation ◽  
Halophilic Archaea ◽  
Salt Mine ◽  
Genome Sequences ◽  
Content Type ◽  
Extremely Halophilic Archaea ◽  
Methylation Patterns

Two extremely halophilic archaea, namely, Natrinema versiforme BOL5-4 and Natrinema pallidum BOL6-1, were isolated from a Bolivian salt mine and their genomes sequenced using single-molecule real-time sequencing. The GC-rich genomes of BOL5-4 and BOL6-1 were 4.6 and 3.8 Mbp, respectively, with large chromosomes and multiple megaplasmids. Genome annotation was incorporated into HaloWeb and methylation patterns incorporated into REBASE.

scholarly journals First Complete Genome Sequences ofStaphylococcus aureussubsp.aureusRosenbach 1884 (DSM 20231T), Determined by PacBio Single-Molecule Real-Time Technology

2015 ◽  
Vol 3 (4) ◽  
Author(s):  
Akino Shiroma ◽  
Yasunobu Terabayashi ◽  
Kazuma Nakano ◽  
Makiko Shimoji ◽  
Hinako Tamotsu ◽  
...  
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Complete Genome ◽  
Genome Sequences

Recent Developments in Artificial Molecular-Machine–Based Active Nanomaterials and Nanosystems

MRS Bulletin ◽  
2008 ◽  
Vol 33 (3) ◽  
pp. 226-231 ◽  
Author(s):  
Tony Jun Huang
Keyword(s):  
Single Molecule ◽  
Interdisciplinary Research ◽  
Recent Progress ◽  
High Strain ◽  
Molecular Machines ◽  
High Impact ◽  
Molecular Machine ◽  
Mechanical Motion ◽  
Structures And Properties ◽  
Recent Developments

AbstractArtificial molecular machines capable of converting chemical, electrochemical, and photochemical energy into mechanical motion represent a high-impact, fast-growing field of interdisciplinary research. These molecular-scale systems utilize a “bottom-up” technology centered upon the design and manipulation of molecular assemblies and are potentially capable of delivering efficient actuation at length scales dramatically smaller than traditional microscale actuators. As actuation materials, molecular machines have many advantages, such as high strain (40%–60%), high force and energy densities, and the capability to maintain their actuation properties from the level of a single molecule to the macroscale. These advantages have inspired researchers to develop molecular-machine–based active nanomaterials and nanosystems, including electroactive and photoactive polymers. This article will discuss the structures and properties of artificial molecular machines, as well as review recent progress on efforts to move molecular machines from solution to surfaces to devices.

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