Genomic assemblies of newly sequenced Trypanosoma cruzi strains reveal new genomic expansion and greater complexity

Abstract

Chagas disease is a complex illness caused by the protozoan Trypanosoma cruzi displaying highly diverse clinical outcomes. In this sense, the genome sequence elucidation and comparison between strains may lead to disease understanding. Here, two new T. cruzi strains, have been sequenced, Y using Illumina and Bug2148 using PacBio, assembled, analyzed and compared with the T. cruzi annotated genomes available to date. The assembly stats from the new sequences show effective improvement of T. cruzi genome over the actual ones. Such as, the largest contig assembled (1.3 Mb in Bug2148) in de novo attempts and the highest mean assembly coverage (71X for Y). Our analysis reveals a new genomic expansion and greater complexity for those multi-copy gene families related to infection process and disease development, such as Trans-sialidases, Mucins and Mucin Associated Surface Proteins, among others. On one side, we demonstrate that multi-copy gene families are located near telomeric regions of the “chromosome-like” 1.3 Mb contig assembled of Bug2148, where they likely suffer high evolutive pressure. On the other hand, we identified several strain-specific single copy genes that might help to understand the differences in infectivity and physiology among strains. In summary, our results indicate that T. cruzi has a complex genomic architecture that may have promoted its evolution.

Nanopore sequencing significantly improves genome assembly of the eukaryotic protozoan parasite Trypanosoma cruzi

“…Even though trypanosomatid genomes are small, their assembly and annotation have been Long-read sequencing using PacBio has been proven useful to improve the quality of T. cruzi genome assemblies (Berná et al 2018;Callejas-Hernández et al 2018), however, the innovative Nanopore technology has been not implemented to sequence trypanosomatid genomes so far despite presenting several comparative advantages over PacBio. Nanopore is cheaper, easy to use in any laboratory, requires less amount of genomic DNA and sequencing yield can be monitored in real-time.…”

An Evolutionary View of Trypanosoma Cruzi Telomeres

“…In T cruzi apart from the TS family other gene families suffered big expansions, namely RHS, DFG-1, MASP, and MUC and these genes tend to form clusters at multiple locations in the genome, in some cases covering whole chromosomes (El-Sayed et al, 2005;Weatherly et al, 2009;Berna et al, 2018;Callejas-Hernández et al, 2018). Except for MUC and MASP families, these expanded families are often found at chromosomal terminal locations (El-Sayed et al, 2005;Weatherly et al, 2009;Moraes Barros et al, 2012;Callejas-Hernández et al, 2018). Therefore it is not surprising to detect members of these families when T. cruzi telomeres and subtelomeres are cloned (Chiurillo et al, 1999;Freitas-Junior et al, 1999).…”

Trypanosoma cruzi Genome 15 Years Later: What Has Been Accomplished?

“…These authors defined 41 pairs of chromosomes as well as two artificially assembled contigs that could not be assigned at any chromosome. More recently, through long sequence reads obtained by the PACBio technology several laboratories have succeeded in closing some of the gaps in the original genome draft [ 30 , 34 , 35 , 36 , 37 , 38 ].…”

“…Copy Number Variations [ 3 , 34 , 35 , 37 , 38 , 44 , 48 , 49 , 50 ] originated by gene duplication, ectopic recombination, unequal-crossing-over, gene mobilization via transposons, chromosome duplications, and others, may contribute to variants with a selective advantage. As stated before, T. cruzi ’s genes coding for surface proteins are notably expanded [ 30 , 34 , 35 , 36 , 49 , 50 ] and some variants have already been adapted to processes related to the infectivity and interaction with the host [ 51 , 52 , 53 , 54 ]. In addition to complete genes, the T. cruzi genome harbors an enormous repertoire of pseudogenes, which could be seen as a futile waste of energy and are likely to be reservoirs for the generation of gene variants.…”