Draft Genome Sequence of Enterococcus faecalis Strain PF3, Isolated from Adélie Penguin Feces from Antarctica Robert J. Spence,a Ana Pavasovic,b James J. Smith,a Peter J. Prentisa
Enterococcus faecalis is one of the leading causes of nosocomial infections and is a common commensal organism in humans and other animals. In this study, we report a draft genome sequence for the E. faecalis strain PF3, isolated from Adélie penguin feces collected from Warriner Island, Antarctica. Received 15 December 2013 Accepted 19 December 2013 Published 23 January 2014 Citation Spence RJ, Pavasovic A, Smith JJ, Prentis PJ. 2014. Draft genome sequence of Enterococcus faecalis strain PF3, isolated from Adélie penguin feces from Antarctica. Genome Announc. 2(1):e01209-13. doi:10.1128/genomeA.01209-13. Copyright © 2014 Spence et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Peter J. Prentis, [email protected].
E
nterococcus spp. are Gram-positive bacteria commonly found under a wide range of different environmental conditions (1). Within this genus, Enterococcus faecalis is a common commensal organism found in the gastrointestinal tract of warm-blooded animals (2). This species has been isolated from a range of different organisms, including mammals, birds, food industry animals, insects, and plants (3). Here, we completed a draft genome sequence for E. faecalis strain PF3, isolated from Adélie penguin (Pygoscelis adeliae) feces collected on Warriner Island, Antarctica. The genome of E. faecalis PF3 was sequenced on an Ion Proton PGM using a P1 chip with 200-bp chemistry. The raw data comprise 921 megabases with 8,723,410 reads averaging 105.6 bp. De novo assembly was performed using CLC Genomics Workbench 6.02, producing 401 contigs, with an N50 of 59,627 bp and with the largest contig being 201,859 bp. The draft genome that resulted from this assembly is 3,215,729 bp long with a G⫹C content of 37.5%. xBASE annotation (4–9) detected a total of 3,387 genes, of which 3,338 are coding sequences (CDSs), 45 are tRNA genes, and 4 are rRNA genes. Progressive Mauve (10) was used to align E. faecalis PF3 to other E. faecalis reference genomes. Pairwise alignments determined that the PF3 strain shows the greatest homology to the widespread commensal E. faecalis OG1RF strain. The draft genome contains a pathogenicity island, multiple plasmid sequences, and three clusters of regularly interspaced short palindromic repeat (CRISPR)-associated genes. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AZIA00000000. The version described in this paper is version AZIA01000000. ACKNOWLEDGMENTS This work was supported by the Australian Antarctic Division and carried out at Queensland University of Technology, Australia.
January/February 2014 Volume 2 Issue 1 e01209-13
REFERENCES 1. Franz CM, Huch M, Abriouel H, Holzapfel W, Gálvez A. 2011. Enterococci as probiotics and their implications in food safety. Int. J. Food Microbiol. 151:125–140. http://dx.doi.org/10.1016/j.ijfoodmicro.2011.08.014. 2. Paulsen IT, Banerjei L, Myers GS, Nelson KE, Seshadri R, Read TD, Fouts DE, Eisen JA, Gill SR, Heidelberg JF, Tettelin H, Dodson RJ, Umayam L, Brinkac L, Beanan M, Daugherty S, DeBoy RT, Durkin S, Kolonay J, Madupu R, Nelson W, Vamathevan J, Tran B, Upton J, Hansen T, Shetty J, Khouri H, Utterback T, Radune D, Ketchum KA, Dougherty BA, Fraser CM. 2003. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 299:2071–2074. http: //dx.doi.org/10.1126/science.1080613. 3. Devriese L, Baele M, Butaye P. 2006. The genus Enterococcus, p 163–174. In Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (ed), The prokaryotes: a handbook on the biology of bacteria, vol 4. Bacteria: Firmicutes, Cyanobacteria. Springer-Verlag New York, Inc., New York, NY. 4. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673– 679. http://dx.doi.org/10.1093/bioinformatics/btm009. 5. Chaudhuri RR, Loman NJ, Snyder LAS, Bailey CM, Stekel DJ, Pallen MJ. 2008. xBASE2: a comprehensive resource for comparative bacterial genomics. Nucleic Acids Res. 36(Database issue):543–546. http://dx.doi .org/10.1093/nar/gkm928. 6. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100 –3108. http://dx.doi.org/10.1093 /nar/gkm160. 7. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. 2004. Versatile and open software for comparing large genomes. Genome Biol. 5:R12. http://dx.doi.org/10.1186/gb-2004-5-2-r12. 8. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389 –3402. http: //dx.doi.org/10.1093/nar/25.17.3389. 9. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955–964. http://dx.doi.org/10.1093/nar/25.5.0955. 10. Darling AE, Mau B, Perna NT. 2010. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5:e11147. http://dx.doi.org/10.1371/journal.pone.0011147.
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Science and Engineering Faculty, Queensland University of Technology, Brisbane, Queensland, Australiaa; Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australiab
Enterococcus faecalis is one of the leading causes of nosocomial infections and is a common commensal organism in humans and other animals. In this study, we report a draft genome sequence for the E. faecalis strain PF3, isolated from Adélie penguin feces collected from Warriner Island, Antarctica. Received 15 December 2013 Accepted 19 December 2013 Published 23 January 2014 Citation Spence RJ, Pavasovic A, Smith JJ, Prentis PJ. 2014. Draft genome sequence of Enterococcus faecalis strain PF3, isolated from Adélie penguin feces from Antarctica. Genome Announc. 2(1):e01209-13. doi:10.1128/genomeA.01209-13. Copyright © 2014 Spence et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Peter J. Prentis, [email protected].
E
nterococcus spp. are Gram-positive bacteria commonly found under a wide range of different environmental conditions (1). Within this genus, Enterococcus faecalis is a common commensal organism found in the gastrointestinal tract of warm-blooded animals (2). This species has been isolated from a range of different organisms, including mammals, birds, food industry animals, insects, and plants (3). Here, we completed a draft genome sequence for E. faecalis strain PF3, isolated from Adélie penguin (Pygoscelis adeliae) feces collected on Warriner Island, Antarctica. The genome of E. faecalis PF3 was sequenced on an Ion Proton PGM using a P1 chip with 200-bp chemistry. The raw data comprise 921 megabases with 8,723,410 reads averaging 105.6 bp. De novo assembly was performed using CLC Genomics Workbench 6.02, producing 401 contigs, with an N50 of 59,627 bp and with the largest contig being 201,859 bp. The draft genome that resulted from this assembly is 3,215,729 bp long with a G⫹C content of 37.5%. xBASE annotation (4–9) detected a total of 3,387 genes, of which 3,338 are coding sequences (CDSs), 45 are tRNA genes, and 4 are rRNA genes. Progressive Mauve (10) was used to align E. faecalis PF3 to other E. faecalis reference genomes. Pairwise alignments determined that the PF3 strain shows the greatest homology to the widespread commensal E. faecalis OG1RF strain. The draft genome contains a pathogenicity island, multiple plasmid sequences, and three clusters of regularly interspaced short palindromic repeat (CRISPR)-associated genes. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AZIA00000000. The version described in this paper is version AZIA01000000. ACKNOWLEDGMENTS This work was supported by the Australian Antarctic Division and carried out at Queensland University of Technology, Australia.
January/February 2014 Volume 2 Issue 1 e01209-13
REFERENCES 1. Franz CM, Huch M, Abriouel H, Holzapfel W, Gálvez A. 2011. Enterococci as probiotics and their implications in food safety. Int. J. Food Microbiol. 151:125–140. http://dx.doi.org/10.1016/j.ijfoodmicro.2011.08.014. 2. Paulsen IT, Banerjei L, Myers GS, Nelson KE, Seshadri R, Read TD, Fouts DE, Eisen JA, Gill SR, Heidelberg JF, Tettelin H, Dodson RJ, Umayam L, Brinkac L, Beanan M, Daugherty S, DeBoy RT, Durkin S, Kolonay J, Madupu R, Nelson W, Vamathevan J, Tran B, Upton J, Hansen T, Shetty J, Khouri H, Utterback T, Radune D, Ketchum KA, Dougherty BA, Fraser CM. 2003. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 299:2071–2074. http: //dx.doi.org/10.1126/science.1080613. 3. Devriese L, Baele M, Butaye P. 2006. The genus Enterococcus, p 163–174. In Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (ed), The prokaryotes: a handbook on the biology of bacteria, vol 4. Bacteria: Firmicutes, Cyanobacteria. Springer-Verlag New York, Inc., New York, NY. 4. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673– 679. http://dx.doi.org/10.1093/bioinformatics/btm009. 5. Chaudhuri RR, Loman NJ, Snyder LAS, Bailey CM, Stekel DJ, Pallen MJ. 2008. xBASE2: a comprehensive resource for comparative bacterial genomics. Nucleic Acids Res. 36(Database issue):543–546. http://dx.doi .org/10.1093/nar/gkm928. 6. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100 –3108. http://dx.doi.org/10.1093 /nar/gkm160. 7. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. 2004. Versatile and open software for comparing large genomes. Genome Biol. 5:R12. http://dx.doi.org/10.1186/gb-2004-5-2-r12. 8. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389 –3402. http: //dx.doi.org/10.1093/nar/25.17.3389. 9. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955–964. http://dx.doi.org/10.1093/nar/25.5.0955. 10. Darling AE, Mau B, Perna NT. 2010. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5:e11147. http://dx.doi.org/10.1371/journal.pone.0011147.
Genome Announcements
genomea.asm.org 1
Downloaded from http://genomea.asm.org/ on June 11, 2015 by NYU MEDICAL CENTER LIBRARY
Science and Engineering Faculty, Queensland University of Technology, Brisbane, Queensland, Australiaa; Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australiab
