Open Access Research article

Repertoire of novel sequence signatures for the detection of Candidatus Liberibacter asiaticus by quantitative real-time PCR

Sunitha Kogenaru12, Qing Yan1, Nadia Riera1, M Caroline Roper3, Xiaoling Deng4, Timothy A Ebert5, Michael Rogers5, Michael E Irey6, Gerhard Pietersen7, Charles M Rush8 and Nian Wang1*

Author Affiliations

1 Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred 33850, USA

2 Present address: Division of Nephrology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109-0676, USA

3 Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA

4 Department of Plant Pathology, South China Agricultural University, Guangzhou, Guangdong, P. R. China

5 Department of Entomology and Nematology, Citrus Research and Education Center, IFAS, University of Florida, Lake Alfred 33850, USA

6 US Sugar Corporation, Clewiston, FL 33440, USA

7 Department of Microbiology & Plant Pathology, ARC-Plant Protection Research Institute, University of Pretoria, Pretoria, South Africa

8 Texas A&M AgriLife Research and Extension Center, Texas A&M University, Amarillo, USA

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BMC Microbiology 2014, 14:39  doi:10.1186/1471-2180-14-39

Published: 17 February 2014

Additional files

Additional file 1:

PERL script 1 facilitates the similarity search in an automated fashion. This script performs similarity searches against the specified nucleotide sequence database using a stand-alone BLAST program for each of the input gene sequences from the Las genome.

Format: TXT Size: 4KB Download file

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Additional file 2:

PERL script 2 facilitates the identification of unique genes to Las. This script facilitates the identification of unique genes by automatically parsing all the BLAST output files generated from the Additional file 1 PERL script 1and returns the unique gene sequences with no similarity to the DNA sequences of other organisms.

Format: TXT Size: 3KB Download file

Open Data

Additional file 3: Figure S1:

Snapshot of the unique genes identified by bioinformatics is shown in the context of the whole genome of Las. The absolute positions of the regions are shown. The novel unique regions of Las identified in this study are shown in bluish green, while the currently known targets are colored in green.

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Additional file 4: Table S1:

Custom designed primer pairs specific to the unique sequences of Las identified by bioinformatic analysis. The forward and reverse primer pair for each of the unique genic regions is given. The product size for each of the primers is shown along with the %GC content.

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