Shotgun sequencing analysis of Trypanosoma cruzi I Sylvio X10/1 and comparison with T. cruzi VI CL Brener

Abstract

Trypanosoma cruzi is the causative agent of Chagas disease, which affects more than 9 million people in Latin America. We have generated a draft genome sequence of the TcI strain Sylvio X10/1 and compared it to the TcVI reference strain CL Brener to identify lineage-specific features. We found virtually no differences in the core gene content of CL Brener and Sylvio X10/1 by presence/absence analysis, but 6 open reading frames from CL Brener were missing in Sylvio X10/1. Several multicopy gene families, including DGF, mucin, MASP and GP63 were found to contain substantially fewer genes in Sylvio X10/1, based on sequence read estimations. 1,861 small insertion-deletion events and 77,349 nucleotide differences, 23% of which were non-synonymous and associated with radical amino acid changes, further distinguish these two genomes. There were 336 genes indicated as under positive selection, 145 unique to T. cruzi in comparison to T. brucei and Leishmania. This study provides a framework for further comparative analyses of two major T. cruzi lineages and also highlights the need for sequencing more strains to understand fully the genomic composition of this parasite.

Figure 1. Sequence identity of Sylvio X10/1 contigs compared to non-Esmeraldo and Esmeraldo.

Shows the percentage identity (horizontal axis) of the best Sylvio X10/1 versus CL Brener BLAST hit and the combined alignment length on the vertical axis. The black line (triangles) represent Sylvio X10/1 compared to non-Esmeraldo and blue lines (circles) represent Sylvio X10/1 compared to Esmeraldo. Both comparisons have a similar overall distribution of identities but Sylvio X10/1 compared to non-Esmeraldo is shifted to a slightly higher sequence identity. Sylvio X10/1 compared to non-Esmeraldo has a peak at 97% sequence identity and Sylvio X10/1 compared to Esmeraldo has a peak at 96% sequence identity.

Figure 2. Nucleotide differences and dN/dS estimations.

Black lines (circles) represent Sylvio X10/1 compared to non-Esmeraldo, blue lines (triangles) represent Sylvio X10/1 compared to Esmeraldo and red lines (crosses) represent non-Esmeraldo compared to Esmeraldo. A) Shows the distribution of single nucleotide differences (ND) in genes, normalized to show the number of ND per 1000 bp. Sylvio X10/1-Esmeraldo show the largest number of ND, and have 25 ND/kb/gene in average. B) Shows the ratios of non-synonymous and synonymous nucleotide variation (horizontal axis shows dN/dS) between the comparisons as a fraction of the genes examined (vertical axis). All comparisons have average dN/dS around 0.40 and the shape of the curves has a similar appearance. About 95% of the examined genes have a ratio below 1, implying that the genes are under purifying selection and 336 genes show evidence of positive selection (dN/dS >1).

Figure 3. Gene content comparison between Sylvio X10/1 and CL Brener.

Shows estimations of gene content between Sylvio X10/1 and CL Brener as percent of the total data. Searches was performed on the read libraries of Sylvio X10/1 and CL Brener. DGF, mucin, MASP, GP63, RHS, 90 and kinesin are more expanded in CL Brener. The sialidase family is indicated to be slightly smaller in Sylvio X10/1.