Genome-wide identification and characterization of coding single-nucleotide polymorphisms in Trypanosoma cruzi

ACKERMANN A, COSENTINO R, PANUNZI L, CARMONA S, AGÜERO F

Woods Hole, MA, USA

Congreso; Molecular Parasitology Meeting; 2008

Marine Biological Laboratory

AbstractUsing the reference genome sequence of T. cruzi as a starting point, together with other sequences present in the public domain we have identified > 260,000 candidate single-nucleotide polymorphisms in the annotated coding regions of the CL-Brener clone of T. cruzi. The compiled dataset contains mRNAs, ESTs, and genomic sequences from different strains and isolates of T. cruzi. Candidate SNPs were assigned different scores (range 0-1), based on the support available from the sequences that contain the polymorphic site. Based on this analysis we found > 190,000 SNPs with a score > 0.7. Candidate SNPs were further classified into synonymous/nonsynonymous based on the effect they showed at the protein level. To validate our scoring strategy we have selected coding regions containing ~ 100 candidate SNPs to perform a small scale resequencing validation experiment. Using this approach we have been able to validate ~ 89% of the putative SNPs that had a score > 0.4. Also, because we have resequenced the selected regions in a panel of strains representative of different evolutionary lineages of T. cruzi, we have been able to discover many new SNPs (approximately three times the number of SNPs detected between allelic variants of the CL-Brener strain). Finally, all the information collected and generated by this project has been integrated into a searchable database, that can be accessed at http://snps.tcruzi.org.