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Bioinformation. 2012; 8(19): 950–952.
Published online Oct 1, 2012. doi:  10.6026/97320630008950
PMCID: PMC3488838
RKN Lethal DB: A database for the identification of Root Knot Nematode (Meloidogyne spp.) candidate lethal genes
Ahmed Ismail,1 Benjamin F Matthews,2 and Nadim W Alkharouf1*
1Department of Computer and Information Sciences, Towson University, 8000 York Road, Towson, MD 21252, USA
2Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, USA
*Nadim W Alkharouf: nalkharouf/at/towson.edu
Received September 4, 2012; Accepted September 7, 2012.
Abstract
Root Knot nematode (RKN; Meloidogyne spp.) is one of the most devastating parasites that infect the roots of hundreds of plant species. RKN cannot live independently from their hosts and are the biggest contributors to the loss of the world's primary foods. RNAi gene silencing studies have demonstrated that there are fewer galls and galls are smaller when RNAi constructs targeted to silence certain RKN genes are expressed in plant roots. We conducted a comparative genomics analysis, comparing RKN genes of six species: Meloidogyne Arenaria, Meloidogyne Chitwoodi, Meloidogyne Hapla, Meloidogyne Incognita, Meloidogyne Javanica, and Meloidogyne Paranaensis to that of the free living nematode Caenorhabditis elegans, to identify candidate genes that will be lethal to RKN when silenced or mutated. Our analysis yielded a number of such candidate lethal genes in RKN, some of which have been tested and proven to be effective in soybean roots. A web based database was built to house and allow scientists to search the data. This database will be useful to scientists seeking to identify candidate genes as targets for gene silencing to confer resistance in plants to RKN.
Availability
The database can be accessed from http://bioinformatics.towson.edu/RKN/
Keywords: RKN, Meloidogyne, web based database, RNAi, C. elegans
Articles from Bioinformation are provided here courtesy of
Biomedical Informatics Publishing Group