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      Whole-Genome Sequencing of Erwinia amylovora Strains from Mexico Detects Single Nucleotide Polymorphisms in rpsL Conferring Streptomycin Resistance and in the avrRpt2 Effector Altering Host Interactions

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          Abstract

          We report draft genome sequences of three Mexican Erwinia amylovora strains. A novel plasmid, pEA78, was identified. Comparative genomics revealed an rpsL chromosomal mutation conferring high-level streptomycin resistance in two strains. In the effector gene avrRpt2, a single nucleotide polymorphism was detected that overcomes fire blight disease resistance in Malus × robusta 5.

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          EDGAR: A software framework for the comparative analysis of prokaryotic genomes

          Jochen Blom, Stefan P Albaum, Daniel Doppmeier … (2009)
          Background The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons. Results To support these studies EDGAR – "Efficient Database framework for comparative Genome Analyses using BLAST score Ratios" – was developed. EDGAR is designed to automatically perform genome comparisons in a high throughput approach. Comparative analyses for 582 genomes across 75 genus groups taken from the NCBI genomes database were conducted with the software and the results were integrated into an underlying database. To demonstrate a specific application case, we analyzed ten genomes of the bacterial genus Xanthomonas, for which phylogenetic studies were awkward due to divergent taxonomic systems. The resultant phylogeny EDGAR provided was consistent with outcomes from traditional approaches performed recently and moreover, it was possible to root each strain with unprecedented accuracy. Conclusion EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes. The software supports a quick survey of evolutionary relationships and simplifies the process of obtaining new biological insights into the differential gene content of kindred genomes. Visualization features, like synteny plots or Venn diagrams, are offered to the scientific community through a web-based and therefore platform independent user interface , where the precomputed data sets can be browsed.
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            Complete genome sequence of the fire blight pathogen Erwinia amylovora CFBP 1430 and comparison to other Erwinia spp.

            Tim Kamber, Brion Duffy, Jochen Blom … (2010)
            Fire blight, caused by the enterobacterium Erwinia amylovora, is a devastating disease of rosaceous plants that has global economic importance for apple and pear production and trade. The complete genome of E. amylovora CFBP 1430 was sequenced, annotated, and compared with the genomes of other Erwinia spp. Several singleton and shared features of the E. amylovora CFBP 1430 genome were identified that offer a first view into evolutionary aspects within the genus Erwinia. Comparative genomics identified or clarified virulence and fitness determinants and secretion systems. Novel insights revealed in the genome of E. amylovora CFBP 1430 hold potential for exploitation to improve the design of more effective fire blight control strategies.
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              Use of antibiotics in plant agriculture.

              Joseph Duffy, Virginia O. Stockwell (2012)
              Antibiotics are essential for control of bacterial diseases of plants, especially fire blight of pear and apple and bacterial spot of peach. Streptomycin is used in several countries; the use of oxytetracycline, oxolinic acid and gentamicin is limited to only a few countries. Springtime antibiotic sprays suppress pathogen growth on flowers and leaf surfaces before infection; after infection, antibiotics are ineffective. Antibiotics are applied when disease risk is high, and consequently the majority of orchards are not treated annually. In 2009 in the United States, 16,465 kg (active ingredient) was applied to orchards, which is 0.12% of the total antibiotics used in animal agriculture. Antibiotics are active on plants for less than a week, and significant residues have not been found on harvested fruit. Antibiotics have been indispensable for crop protection in the United States for more than 50 years without reports of adverse effects on human health or persistent impacts on the environment.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Announc
                Journal ID (iso-abbrev): Genome Announc
                Journal ID (hwp): ga
                Journal ID (pmc): ga
                Journal ID (publisher-id): GA
                Title: Genome Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2169-8287
                Publication date (Electronic): 23 January 2014
                Publication date Collection: Jan-Feb 2014
                Volume: 2
                Issue: 1
                Electronic Location Identifier: e01229-13
                Affiliations
                [a ]Research Group for Environmental Genomics and Systems Biology, Institute for Natural Resources Sciences, Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
                [b ]Plant Protection Division, Agroscope Changins-Wädenswil ACW, Wädenswil, Switzerland
                [c ]FACIATEC, University of Chihuahua, Cuauhtémoc, Chihuahua, Mexico
                [d ]Bioinformatics and Systems Biology, Justus-Liebig-Universität, Giessen, Germany
                [e ]Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
                Author notes
                Address correspondence to Theo H. M. Smits, theo.smits@ 123456zhaw.ch .
                Article
                Publisher ID: genomeA01229-13
                DOI: 10.1128/genomeA.01229-13
                PMC ID: 3900913
                PubMed ID: 24459281
                SO-VID: ddb31d7c-fabd-4b24-b83a-ada02fe6b187
                Copyright © Copyright © 2014 Smits et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

                History
                Date received : 18 December 2013
                Date accepted : 19 December 2013
                Page count
                Pages: 2
                Categories
                Subject: Prokaryotes
                Custom metadata
                cover-date January/February 2014
                access-type free

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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