An integrated pipeline for the development of novel panels of mapped microsatellite markers for Leishmania donovani complex, Leishmania braziliensis and Leishmania major
- 27 March 2008
- journal article
- research article
- Published by Cambridge University Press (CUP) in Parasitology
- Vol. 135 (5), 567-574
- https://doi.org/10.1017/s0031182008004186
Abstract
SUMMARY: A panel of microsatellites mapped to the Leishmania genome might make it possible to find associations between specific loci and phenotypic traits. To identify such loci, a Perl programme was written that scans the sequence of a genome and writes all loci containing microsatellites to a MySQL database. The programme was applied to the sequences of the L. braziliensis, L. infantum and L. major genomes. The database is publicly available over the internet: http://www.genomics.liv.ac.uk/tryps/resources.html ‘Microsatellite Locus Extractor’, and allows the selection of mapped microsatellites that meet user-defined criteria from a specified region of the selected genome. The website also incorporates a primer design pipeline that will design primers to amplify the selected loci. Using this pipeline 12 out of 17 primer sets designed against the L. infantum genome generated polymorphic PCR products. A tailed primer protocol was used to label all microsatellite primers with a single set of labelled primers. To avoid the culture of parasites prior to genotyping, sets of nested PCR primers were developed to amplify parasite DNA eluted from microscope slides. The limit of detection was approximately 1·6 parasite equivalents. However, only 6/56 DNA from slides stored at ambient temperature for over 6 months gave positive PCR results.Keywords
This publication has 14 references indexed in Scilit:
- USE OF MULTIPLE DISPLACEMENT AMPLIFICATION TO INCREASE THE DETECTION AND GENOTYPING OF TRYPANOSOMA SPECIES SAMPLES IMMOBILIZED ON FTA FILTERSThe American Journal of Tropical Medicine and Hygiene, 2007
- APPLICATION OF MICROSATELLITE GENOTYPING TO THE STUDY OF A RESTRICTED LEISHMANIA INFANTUM FOCUS: DIFFERENT GENOTYPE COMPOSITIONS IN ISOLATES FROM DOGS AND SAND FLIESThe American Journal of Tropical Medicine and Hygiene, 2007
- Visceral leishmaniasis with duodenal involvement: three immunocompetent cases from southern IranPathogens and Global Health, 2006
- Practical Approach for Typing Strains of Leishmania infantum by Microsatellite AnalysisJournal of Clinical Microbiology, 2002
- Polymorphic microsatellite repeats are not conserved between Leishmania donovani and Leishmania majorMolecular Ecology Notes, 2002
- M13-Tailed Primers Improve the Readability and Usability of Microsatellite Analyses Performed with Two Different Allele- Sizing MethodsBioTechniques, 2001
- Primer3 on the WWW for General Users and for Biologist ProgrammersMethods in molecular biology (Clifton, N.J.), 1999
- Intra and inter-specific microsatellite variation in the Leishmania subgenus VianniaMolecular and Biochemical Parasitology, 1999
- Universal and rapid salt-extraction of high quality genomic DNA for PCR- based techniquesNucleic Acids Research, 1997
- A highly sensitive and rapid procedure for direct PCR detection of Leishmania infantum within human peripheral blood mononuclear cellsActa Tropica, 1995