GENOME ANNOUNCEMENT
Draft Genome Sequence of Streptomyces acidiscabies 84-104, an Emergent Plant Pathogen José C. Huguet-Tapia and Rosemary Loria Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
A draft genome sequence of the plant pathogen Streptomyces acidiscabies 84-104, an emergent plant pathogen, is presented here. The genome is among the largest of streptomycetes, at more than 11 Mb, and encodes a 100-kb pathogenicity island (PAI) shared with other plant-pathogenic streptomycetes. The presence of this conserved PAI, and the remnants of a conserved integrase/recombinase at its 3= end, supports the hypothesis that S. acidiscabies emerged as a plant pathogen as a result of this acquisition.
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lant-pathogenic Streptomyces spp. produce lesions on potato tubers, a disease referred to as potato scab (8, 9). Virulence requires production of a phytotoxin, thaxtomin A, which inhibits synthesis of cellulose, leading to defective plant cell walls. Thaxtomin is a nitrated dipeptide, and its biosynthetic pathway has been described; it is unique in the involvement of a nitric oxide (NO) synthase that provides NO for nitration of the tryptophan moiety (6). Plant-pathogenic Streptomyces spp., such as S. scabies, S. acidiscabies, S. turgidiscabies, and S. ipomoeae, are polyphyletic but share virulence factors, including thaxtomins. Emergence of new plant-pathogenic streptomycetes is hypothesized to involve lateral gene transfer (LGT), and a mobile pathogenicity island (PAI) has been described in S. turgidiscabies (4, 5). S. acidiscabies causes disease in low-pH soils, and it emerged as a new pathogen of potato in the 1950s (7). While genome sequences are available for many saprophytic Streptomyces species (2, 11, 12), relatively few genome sequences are available for pathogenic species. Here we present a draft genome sequence for S. acidiscabies 84-104, an isolate that was obtained from a potato scab lesion in 1984. Sequencing reads were generated with two sequencing platforms: Roche 454 GS FLX (454 GS FLX) and Illumina Genome Analyzer IIx (GAIIx). The 454 GS FLX reads were assembled, and then the GAIIx paired reads were mapped onto this assembly. Glimmer 3.02 (1) was used to predict coding sequences (CDSs), and annotation was carried out using Blast2Go (3). Additional functional classification of CDSs was performed using the COG, Pfam, and Gene Ontology databases. tRNA prediction was conducted using the program tRNAscan-SE 1.21 (10). The draft genome sequence of S. acidiscabies comprises 11,005,945 bp, with a 53-fold average coverage. The assembled genome contains 244 contigs with an N90 of 28 kb and an N50 of 113 kb; the largest contig is 289 kb. The genome contains 75 tRNA genes and encodes 10,070 putative proteins. Of the CDSs, 68% could be assigned to COG families (13); reciprocal BLAST analysis with other Streptomyces genomes indicated that S. acidiscabies 84104 shares 3,006 orthologs with S. coelicolor, S. avermitilis, S. griseous, S. bingchenggensis, and S. scabies. S. acidiscabies and S. scabies share 357 orthologs; many of these genes are located in a syntenic 100-kb PAI previously described for S. scabies and S. turgidiscabies (4). Both S. scabies and S. acidiscabies contain a remnant of the CDS encoding the putative integrase/recombinase located in the 3= end of the PAI in S. turgidiscabies. This finding supports the hypothesis that S. acidiscabies emerged as a plant pathogen as the result of acquisition of this PAI.
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Journal of Bacteriology
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Nucleotide sequence accession numbers. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number AHBF00000000. The version described in this paper is the first version, AHBF01000000. ACKNOWLEDGMENT This work was supported by the National Research Initiative of the USDA Cooperative State Research, Education and Extension Service, grant no. 2010-65110-20416.
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Received 21 December 2011 Accepted 19 January 2012 Address correspondence to Rosemary Loria,
[email protected]. Copyright © 2012, American Society for Microbiology. All Rights Reserved. doi:10.1128/JB.06767-11
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