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      Draft Genome Sequences of Pseudomonas spp. Isolated from Berry Surfaces in Commercial Cranberry Bogs in Massachusetts, USA

      brief-report
      a , a , a , b ,
      Microbiology Resource Announcements
      American Society for Microbiology

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          ABSTRACT

          The surfaces of plants are colonized by a rich diversity of microbes but are largely unexplored. Here, we present the draft genome sequences of five Pseudomonas spp. isolated from cultivated cranberry fruit surfaces. Although the isolates represent four different species, their genomes all contain conserved iron sequestration and uptake genes.

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          Most cited references23

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          RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

          The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.
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            TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy

            Microbial taxonomy is increasingly influenced by genome-based computational methods. Yet such analyses can be complex and require expert knowledge. Here we introduce TYGS, the Type (Strain) Genome Server, a user-friendly high-throughput web server for genome-based prokaryote taxonomy, connected to a large, continuously growing database of genomic, taxonomic and nomenclatural information. It infers genome-scale phylogenies and state-of-the-art estimates for species and subspecies boundaries from user-defined and automatically determined closest type genome sequences. TYGS also provides comprehensive access to nomenclature, synonymy and associated taxonomic literature. Clinically important examples demonstrate how TYGS can yield new insights into microbial classification, such as evidence for a species-level separation of previously proposed subspecies of Salmonella enterica. TYGS is an integrated approach for the classification of microbes that unlocks novel scientific approaches to microbiologists worldwide and is particularly helpful for the rapidly expanding field of genome-based taxonomic descriptions of new genera, species or subspecies.
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              Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

              The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows researchers direct access to tools and data, and the emphasis has changed to user-created genome-groups, with detailed summaries and views of the data that researchers have selected. Perhaps the biggest change has been the enhanced capability for researchers to analyze their private data and compare it to the available public data. Researchers can assemble their raw sequence reads and annotate the contigs using RASTtk. PATRIC also provides services for RNA-Seq, variation, model reconstruction and differential expression analysis, all delivered through an updated private workspace. Private data can be compared by ‘virtual integration’ to any of PATRIC's public data. The number of genomes available for comparison in PATRIC has expanded to over 80 000, with a special emphasis on genomes with antimicrobial resistance data. PATRIC uses this data to improve both subsystem annotation and k-mer classification, and tags new genomes as having signatures that indicate susceptibility or resistance to specific antibiotics.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                Microbiol Resour Announc
                Microbiol Resour Announc
                mra
                Microbiology Resource Announcements
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2576-098X
                8 July 2021
                July 2021
                : 10
                : 27
                : e00204-21
                Affiliations
                [a ]Biomedical Sciences Program, College of Graduate Studies, Midwestern University, Glendale, Arizona, USA
                [b ]College of Veterinary Medicine, Midwestern University, Glendale, Arizona, USA
                University of Arizona
                Author notes

                Marit H. Koszewski and Sheyda Motevalli contributed equally to this work. Author order was determined alphabetically.

                Citation Koszewski MH, Motevalli S, Soby SD. 2021. Draft genome sequences of Pseudomonas spp. isolated from berry surfaces in commercial cranberry bogs in Massachusetts, USA. Microbiol Resour Announc 10:e00204-21. https://doi.org/10.1128/MRA.00204-21.

                Author information
                https://orcid.org/0000-0002-4415-5878
                Article
                MRA00204-21
                10.1128/MRA.00204-21
                8265235
                34236228
                54b570a7-fc2b-4b1b-85ad-b96536f712c9
                Copyright © 2021 Koszewski et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 15 March 2021
                : 11 June 2021
                Page count
                Figures: 1, Tables: 1, Equations: 0, References: 23, Pages: 4, Words: 1887
                Funding
                Funded by: Midwestern University (MWU), FundRef https://doi.org/10.13039/100012807;
                Award Recipient :
                Categories
                Genome Sequences
                Custom metadata
                July 2021

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