A Genome-Wide Analysis of Genetic Diversity in Trypanosoma cruzi Intergenic Regions

Background:trypanosoma cruzi is the causal agent of chagas disease. recently,the genomes of representative strains from two major evolutionary lineages were sequenced,allowing the construction of a detailed genetic diversity map for this important parasite. however this map is focused on coding regions of the genome,leaving a vast space of regulatory regions uncharacterized in terms of their evolutionary conservation and/or divergence.methodology:using data from the hybrid cl brener and sylvio x10 genomes (from the tcvi and tci discrete typing units,respectively),we identified intergenic regions that share a common evolutionary ancestry,and are present in both cl brener haplotypes (tcii-like and tciii-like) and in the tci genome; as well as intergenic regions that were conserved in only two of the three genomes/haplotypes analyzed. the genetic diversity in these regions was characterized in terms of the accumulation of indels and nucleotide changes.principal findings:based on this analysis we have identified i) a core of highly conserved intergenic regions,which remained essentially unchanged in independently evolving lineages; ii) intergenic regions that show high diversity in spite of still retaining their corresponding upstream and downstream coding sequences; iii) a number of defined sequence motifs that are shared by a number of unrelated intergenic regions. a fraction of indels explains the diversification of some intergenic regions by the expansion/contraction of microsatellite-like repeats. © 2014 panunzi,agüero.