Page 76 - Read Online
P. 76

Page 18 of 19                  Kok et al. Microbiome Res Rep 2023;2:30  https://dx.doi.org/10.20517/mrr.2023.16

                   Available from: https://openaccess.wgtn.ac.nz/articles/thesis/American_foulbrood_and_its_causative_agent_Paenibacillus_larvae_in_
                   New_Zealand_s_registered_hives_and_apiaries/17013008. [Last accessed on 26 Jul 2023].
               21.      Dingman DW, Stahly DP. Medium promoting sporulation of Bacillus larvae and metabolism of medium components. Appl Environ
                   Microbiol 1983;46:860-9.  DOI  PubMed  PMC
               22.      de Graaf DC, Alippi AM, Antúnez K, et al. Standard methods for American Foulbrood research. J Apic Res 2013;52:1-28.  DOI
               23.      Dobbelaere W, de Graaf DC, Peeters JE. Development of a fast and reliable diagnostic method for American Foulbrood disease
                   (Paenibacillus larvae subsp. larvae) using a 16S rRNA gene based PCR. Apidologie 2001;32:363-70.  DOI
               24.      Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
                   J Comput Biol 2012;19:455-77.  DOI  PubMed  PMC
               25.      Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes De Novo assembler. Curr Protoc Bioinformatics
                   2020;70:e102.  DOI  PubMed
               26.      Overbeek R, Olson R, Pusch GD, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology
                   (RAST). Nucleic Acids Res 2014;42:D206-14.  DOI  PubMed  PMC
               27.      Brettin T, Davis JJ, Disz T, et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom
                   annotation pipelines and annotating batches of genomes. Sci Rep 2015;5:8365.  DOI  PubMed  PMC
               28.      Aziz RK, Bartels D, Best AA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008;9:75.
                   DOI  PubMed  PMC
               29.      Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30:2068-9.  DOI  PubMed
               30.      Kok DN, Turnbull J, Takeuchi N, Tsourkas PK, Hendrickson HL. In Vitro evolution to increase the titers of difficult bacteriophages:
                   RAMP-UP protocol. Phage 2023;4:68-81.  DOI  PubMed  PMC
               31.      Santos MA. An improved method for the small scale preparation of bacteriophage DNA based on phage precipitation by zinc chloride.
                   Nucleic Acids Res 1991;19:5442.  DOI  PubMed  PMC
               32.      Lazeroff M, Ryder G, Harris SL, Tsourkas PK. Phage commander, an application for rapid gene identification in bacteriophage
                   genomes using multiple programs. Phage 2021;2:204-13.  DOI  PubMed  PMC
               33.      Pope WH, Jacobs-sera D. Annotation of bacteriophage genome sequences using DNA master: an overview. In: Clokie MR, Kropinski
                   AM, Lavigne R, editors. Bacteriophages. New York: Springer; 2018. p. 217-29.  DOI
               34.      Salisbury A, Tsourkas PK. A method for improving the accuracy and efficiency of bacteriophage genome annotation. Int J Mol Sci
                   2019;20:3391.  DOI  PubMed  PMC
               35.      Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their
                   applications. Wellcome Open Res 2018;3:124.  DOI  PubMed  PMC
               36.      Morrissey BJ, Helgason T, Poppinga L, Fünfhaus A, Genersch E, Budge GE. Biogeography of Paenibacillus larvae, the causative
                   agent of American Foulbrood, using a new multilocus sequence typing scheme. Environ Microbiol 2015;17:1414-24.  DOI  PubMed
                   PMC
               37.      Papić B, Diricks M, Kušar D. Analysis of the global population structure of Paenibacillus larvae and outbreak investigation of
                   American Foulbrood using a stable wgMLST scheme. Front Vet Sci 2021;8:582677.  DOI  PubMed  PMC
               38.      Binney BM, Pragert H, Foxwell J, et al. Genomic analysis of the population structure of Paenibacillus larvae in New Zealand. Front
                   Microbiol 2023;14:1161926.  DOI  PubMed  PMC
               39.      Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.
                   Nucleic Acids Res 2007;35:W52-7.  DOI  PubMed  PMC
               40.      Tesson F, Hervé A, Mordret E, et al. Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nat Commun
                   2022;13:2561.  DOI  PubMed  PMC
               41.      Abby SS, Néron B, Ménager H, Touchon M, Rocha EP. MacSyFinder: a program to mine genomes for molecular systems with an
                   application to CRISPR-Cas systems. PLoS One 2014;9:e110726.  DOI  PubMed  PMC
               42.      Oliveira PH, Touchon M, Rocha EP. The interplay of restriction-modification systems with mobile genetic elements and their
                   prokaryotic hosts. Nucleic Acids Res 2014;42:10618-31.  DOI  PubMed  PMC
               43.      Gao  L,  Altae-Tran  H,  Böhning  F,  et  al.  Diverse  enzymatic  activities  mediate  antiviral  immunity  in  prokaryotes.  Science
                   2020;369:1077-84.  DOI  PubMed  PMC
               44.      Bernheim A, Bikard D, Touchon M, Rocha EPC. Atypical organizations and epistatic interactions of CRISPRs and cas clusters in
                   genomes and their mobile genetic elements. Nucleic Acids Res 2020;48:748-60.  DOI  PubMed  PMC
               45.      Doron S, Melamed S, Ofir G, et al. Systematic discovery of antiphage defense systems in the microbial pangenome. Science
                   2018;359:eaar4120.  DOI  PubMed  PMC
               46.      Millman A, Melamed S, Leavitt A, et al. An expanded arsenal of immune systems that protect bacteria from phages. Cell Host
                   Microbe 2022;30:1556-69.  DOI
               47.      Arndt D, Grant JR, Marcu A, et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res
                   2016;44:W16-21.  DOI  PubMed  PMC
               48.      Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res 2011;39:W347-52.  DOI
                   PubMed  PMC
               49.      Tsourkas PK, Yost DG, Krohn A, et al. Complete genome sequences of nine phages capable of infecting Paenibacillus larvae, the
                   causative agent of American Foulbrood disease in honeybees. Genome Announc 2015;3:e01120-15.  DOI  PubMed  PMC
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