Conservation and diversity of intergenic regions of Trypanosoma cruzi

PANUNZI L; AGÜERO F

Foz do Iguacu

Congreso; XXVII Annual Meeting of the Brazilian Society of Protozoology; 2011

Sociedade Brasileira de Protozoologia

Trypanosoma cruzi (TC) is an old species, with a number of well defined evolutionary lineages. Knowledge of its genome plasticity is important to understand regulatory processes at several levels (transcriptional, post-transcriptional, translational). The first genome from the TC species was derived from a hybrid strain (CL-Brener) and contains information from two divergent parental genomes. In this study we analyzed the sequence diversity of intergenic regions (IGRs) in the TC genome by aligning the assembled sequences of both Esmeraldo-like and Non Esmeraldo-like alleles of the CL Brener genome. We found a conserved group of 2,948 IGRs, whose upstream and downstream coding sequences (CDSs) were orthologous, syntenic and had expected start/stop codons (allelic IGRs). We also identified 10 groups of variable size corresponding to IGRs associated with unrelated loci (i.e. non-allelic, non-homologous). These IGRs showed significant portions of sequence similarity. In some cases, the copies of this region were more conserved in one parental allele (e.g. Esmeraldo-like) but exhibited high sequence variation in the other (e.g. non Esmeraldo-like). In other grouped IGRs, the conserved region was shared by both alleles, highlighting a different genomic arrangement of CDS and IGRs. We also analyzed the distribution of size, base composition and sequence diversity of every pair of allelic IGRs, and CDSs. When considering the length of CDSs and IGRs, we found a strong correlation between paired CDS and IGR alleles, although a higher heterogeneity was evident in the length of paired IGRs. The mean length of allelic IGRs was 636 nt and only 3.15% of them presented a strictly identical length, with 6.9% of outliers. Whereas 68.22% of allelic CDSs were of identical length, with 3.64% of outliers and a mean length of 1436 nt. The alignments showed a global mean coverage of 88.1% for IGRs and 97.74% for CDSs, and a mean length difference of 8.9% and 2.16%, indicating not only length conservation but also a relatively large sequence similarity. When looking at SNPs, allelic IGRs presented an average of nearly 5% SNPs and 11.88% indels, whereas allelic CDSs exhibited a lower rate for both (1.99% SNPs and 2.2% indels). The transition/transversion ratio was 1.97 and 2.93 in allelic IGRs and CDSs, respectively, suggesting a preferential type of nucleotide substitution. The mean base frequencies were similar between haplotypes in CDSs (~25% for each base), but there was a significant bias in the observed frequency of T (35.95%) and C (16.77%) nucleotides in allelic IGRs.