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      Draft Genome Sequences of Flavobacterium covae Strains LSU-066-04 and LV-359-01

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          ABSTRACT

          Flavobacterium covae is one of four Flavobacterium spp. that cause columnaris disease in teleost fish. Here, we report the draft genomes of two isolates, LSU-066-04 and LV-359-01, and their predicted virulence factors.

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          CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

          Donovan Parks, Michael Imelfort, Connor Skennerton … (2015)
          Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities.
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            The RAST Server: Rapid Annotations using Subsystems Technology

            Ramy Aziz, Daniela Bartels, Aaron A. Best … (2008)
            Background The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them. Description We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user. In addition, the annotated genome can be browsed in an environment that supports comparative analysis with the annotated genomes maintained in the SEED environment. The service normally makes the annotated genome available within 12–24 hours of submission, but ultimately the quality of such a service will be judged in terms of accuracy, consistency, and completeness of the produced annotations. We summarize our attempts to address these issues and discuss plans for incrementally enhancing the service. Conclusion By providing accurate, rapid annotation freely to the community we have created an important community resource. The service has now been utilized by over 120 external users annotating over 350 distinct genomes.
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              DNA-DNA hybridization values and their relationship to whole-genome sequence similarities.

              Johan Goris, Konstantinos Konstantinidis, Joel Klappenbach … (2007)
              DNA-DNA hybridization (DDH) values have been used by bacterial taxonomists since the 1960s to determine relatedness between strains and are still the most important criterion in the delineation of bacterial species. Since the extent of hybridization between a pair of strains is ultimately governed by their respective genomic sequences, we examined the quantitative relationship between DDH values and genome sequence-derived parameters, such as the average nucleotide identity (ANI) of common genes and the percentage of conserved DNA. A total of 124 DDH values were determined for 28 strains for which genome sequences were available. The strains belong to six important and diverse groups of bacteria for which the intra-group 16S rRNA gene sequence identity was greater than 94 %. The results revealed a close relationship between DDH values and ANI and between DNA-DNA hybridization and the percentage of conserved DNA for each pair of strains. The recommended cut-off point of 70 % DDH for species delineation corresponded to 95 % ANI and 69 % conserved DNA. When the analysis was restricted to the protein-coding portion of the genome, 70 % DDH corresponded to 85 % conserved genes for a pair of strains. These results reveal extensive gene diversity within the current concept of "species". Examination of reciprocal values indicated that the level of experimental error associated with the DDH method is too high to reveal the subtle differences in genome size among the strains sampled. It is concluded that ANI can accurately replace DDH values for strains for which genome sequences are available.
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                Author and article information

                Contributors
                Mark R. Liles:
                ORCID: https://orcid.org/0000-0002-9313-8150
                Frank J. Stewart: Role: Editor
                Journal
                Journal ID (nlm-ta): Microbiol Resour Announc
                Journal ID (iso-abbrev): Microbiol Resour Announc
                Journal ID (publisher-id): mra
                Title: Microbiology Resource Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2576-098X
                Publication date (Electronic, pub): 15 June 2022
                Publication date (Electronic, collection): July 2022
                Publication date PMC-release: 15 June 2022
                Volume: 11
                Issue: 7
                Electronic Location Identifier: e00352-22
                Affiliations
                [a ] Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
                [b ] United States Department of Agriculture, Agricultural Research Service, Aquatic Animal Health Research Unit, Auburn, Alabama, USA
                [c ] United States Department of Agriculture, Agricultural Research Service, Harry K. Dupree Stuttgart National Aquaculture Research Center, Stuttgart, Arkansas, USA
                Montana State University
                Author notes

                The authors declare no conflict of interest.

                Author information
                https://orcid.org/0000-0001-5634-5858
                https://orcid.org/0000-0001-7358-5108
                https://orcid.org/0000-0002-9313-8150
                Article
                Publisher ID: 00352-22 Publisher ID: mra.00352-22
                DOI: 10.1128/mra.00352-22
                PMC ID: 9302162
                PubMed ID: 35703564
                SO-VID: be6d1d07-4da9-454a-bfd9-b84e48ec31e4
                License:

                This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.

                History
                Date received : 18 April 2022
                Date accepted : 2 June 2022
                Page count
                Figures: 0, Tables: 1, Equations: 0, References: 15, Pages: 3, Words: 1814
                Funding
                Funded by: U.S. Department of Agriculture (USDA), FundRef https://doi.org/10.13039/100000199;
                Award ID: 6010-32000-027-014-D
                Award Recipient :
                Funded by: U.S. Department of Agriculture (USDA), FundRef https://doi.org/10.13039/100000199;
                Award ID: 6010-32000-027-000-S
                Award Recipient :
                Categories
                Subject: Genome Sequences
                Compound subject: bacteriology, Bacteriology
                Custom metadata
                cover-date July 2022

                Data availability:

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