Volume 11 Supplement 4

UT-ORNL-KBRIN Bioinformatics Summit 2010

Open Access

Sequence and annotation of the Wizard007 mycobacterium phage genome

  • Ejike Anyanwu1,
  • Kaitlyn Cole1,
  • Karlee Driver1,
  • Anthony Falcone1,
  • Elizabeth Farnsworth1,
  • Benjamin Howard1,
  • Brittney Howard1,
  • Courtney Howard1,
  • Rodney King1,
  • Jordan Olberding1,
  • Mackenzie Perkins1,
  • Claire Rinehart1Email author,
  • Heidi Sayre1,
  • Tyler Scaff1,
  • Sarah Schrader1,
  • Prasanna Tamarapu Parthasarathy1 and
  • Cynthia Tope1
BMC Bioinformatics201011(Suppl 4):P15

DOI: 10.1186/1471-2105-11-S4-P15

Published: 23 July 2010

Material and methods

The Wizard007 bacteriophage was isolated from a soil sample taken at N36° 49’36.8” W87° 29’42.5” in Hopkinsville, KY. It was plaque purified on Mycobacterium smegmatis and DNA was isolated using the Promega Wizard DNA purification kit. The DNA was sequenced at the Virginia Commonwealth University by Roche 454 DNA sequencing. The genome quality was confirmed in Consed [1] and found to be 51,034 bp in length. Genes were called from the assembled sequence with a workflow consisting of Glimmer [2], GeneMark [3], tRNAscan [4], and SDFinder to identify potential gene features. Gbrowse [5], Apollo [6], and BLAST [7] were used to call and annotate genes. A 10 base 3’ overhang was found at the ends by ligating the genomic DNA and sequencing a PCR product produced across the ligated ends.

Results and conclusion

Wizard007 is 95% similar to the Mycobacterium phage Peaches (NC_013694) when comparing the number of gene BLAST hits. The first 41,000 bp and the genes contained therein match Peaches’ organization and sequence very closely. The 3’ end of Wizard007 lacks 4 coding sequences that are found in Peaches (CDS 69, 74, 75, & 78) and it has one coding sequence that is not called in Peaches (gp 76). Additionally there are two coding sequences in Peaches (CDS 83 & 84) that do not match Wizard007 (gp 77 & 79).

Declarations

Acknowledgements

Funding for the DNA sequencing of Wizard007 was provided by the WKU Bioinformatics and Information Science Center. Supplies and technical support for the isolation and genome annotation were provided by the Howard Hughes Medical Institute Science Education Alliance National Genome Research Initiative.

Authors’ Affiliations

(1)
Department of Biology, Western Kentucky University

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Copyright

© Rinehart et al; licensee BioMed Central Ltd. 2010

This article is published under license to BioMed Central Ltd.

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