Biology subjects

Diaz-Viraque, F.

Publications and source records attributed to Diaz-Viraque, F..

7 recordsLinked to original sources

bioRxiv2025

Trypanosoma cruzi Has 32 Chromosomes: A Telomere-to-Telomere Assembly Defines Its Karyotype.

Trypanosoma cruzi, the causative agent of Chagas disease, exhibits remarkable genomic variability and possesses an expanded genome rich in multigene families. However, its precise chromosomal composition has remained elusive due to the challenges posed by extensive repetitive regions. Using PacBio HiFi long-read sequencing, we assembled the complete nuclear genome of the Dm28c strain into 32 telomere-to-telomere chromosomes. This assembly revealed conserved chromosomal structures and synteny patterns when compared to the independently sequenced Dm25 strain, indicating that the 32-chromosome karyotype is a stable and conserved feature of T. cruzi. The species is diploid for all chromosomes, except for chromosome 16, which is consistently tetraploid in all strains analyzed, and homologous to chromosome 31 of Leishmania, also tetraploid. Through a comprehensive annotation pipeline, we refined gene content and resolved haplotypes, resulting in an approximately 25% reduction in core gene redundancy. All chromosomes display a conserved, compartmentalized architecture comprising core, disruptive, and newly defined subtelomeric regions. Subtelomeres, enriched in RHS, TS, and DGF-1 genes and depleted in MASP and mucins, constitute a distinct third genomic compartment, that is transcriptionally active, and represents the main source of genome variability among strains. Altogether, this work defines the complete chromosomal complement of T. cruzi, establishing a robust framework for comparative genomics and enabling detailed studies into genome organization, antigenic variability, and evolutionary dynamics across strains and clades. This assembly redefines the genomic reference landscape and opens new avenues for exploring T. cruzi biology, pathogenic diversity, and adaptive mechanisms.

genomics↗

bioRxiv2023

Genomic organization of Trypanosoma cruzi tRNA genes

An often neglected class of genes in large-scale genome analyses is the non-protein-coding genes. In particular, due to the incompleteness of the genome assembly, it had not been possible to determine the genomic organization of the tRNA genes in Trypanosoma cruzi --a eukaryotic unicellular pathogen causative of disabling human Chagas disease--. Here, we analyzed the genic content and distribution of tRNA genes in the nuclear genome of different strains compared with the genome organization of other related trypanosomatids. We found synteny in most of the tDNAs clusters between T. cruzi and Trypanosoma brucei, demonstrating the importance of the genome location of these Pol III transcribed genes. The vast majority of the isoacceptor species are encoded by two genes, except for tDNASeC, which is present as a tandem of 11 copies in the core compartment, associated with well-positioned nucleosomes. Finally, we describe a group of tRNA genes located at chromatin folding domain boundaries, possibly acting as chromatin insulators in T. cruzi.

genomics↗

bioRxiv2023

3D genome organization drives gene expression in trypanosomes

In trypanosomes --eukaryotic unicellular pathogens that cause disabling human and animal diseases-- very few transcriptional regulatory elements have been described and it is largely accepted that they regulate gene expression mainly post-transcriptionally. In this regard, the role of the spatial organization of the genome on gene expression and vice versa remains practically unexplored. The genome of these parasites is partitioned into core (highly conserved syntenic) and species-specific disruptive regions (synteny disruption), containing multigene families encoding for surface glycoproteins. By mapping genome-wide chromatin interactions we demonstrate that these regions constitute 3D compartments (C and D). These chromatin compartments present significant differences in DNA methylation, nucleosome positioning and chromatin interactions, affecting genome expression dynamics. We show that the genome is organized into chromatin folding domains and transcription is dramatically determined by the local chromatin structure. Our results support a model in which epigenetic mechanisms dramatically impact gene expression in these eukaryotic pathogens.

microbiology↗

bioRxiv2021

Maxicircle architecture and evolutionary insights into Trypanosoma cruzi complex

We sequenced maxicircles from T. cruzi strains representative of the species evolutionary diversity by using long-read sequencing, which allowed us to uncollapse their repetitive regions, finding that their real lengths range from 35 to 50 kb. T. cruzi maxicircles have a common architecture composed of four regions: coding region (CR), AT-rich region, short (SR) and long repeats (LR). Distribution of genes, both in order and in strand orientation are conserved, being the main differences the presence of deletions affecting genes coding for NADH dehydrogenase subunits, reinforcing biochemical findings that indicate that complex I is not functional in T. cruzi. Moreover, the presence of complete minicircles into maxicircles of some strains lead us to think about the origin of minicircles. Finally, a careful phylogenetic analysis was conducted using coding regions of maxicircles from up to 29 strains, and 1023 single copy nuclear genes from all of the DTUs, clearly establishing that taxonomically T. cruzi is a complex of species composed by group 1 that contains clades A, B and D, and group 2 containing clade C. No significant differences were found in hybrid strains that justify the existence of TcV and Tc VI as separate clades: our results indicate that a unique event of hybridization between TcII and TcIII occurred. Three variants of maxicircles exist in T. cruzi: a, b and c, in correspondence with clades A, B, and C from mitochondrial phylogenies. While A and C carry maxicircles a and c respectively, both clades B and D carry b maxicircle variant; hybrid strains also carry the b- variant. We then propose a new nomenclature that is self-descriptive and makes use of both the phylogenetic relationships and the maxicircle variants present in T. cruzi.

genomics↗

bioRxiv2020

Multiple introductions, regional spread and local differentiation during the first week of COVID-19 epidemic in Montevideo, Uruguay

BackgroundAfter its emergence in China in December 2019, the new coronavirus disease (COVID-19) caused by SARS-CoV-2, has rapidly spread infecting more than 3 million people worldwide. South America is among the last regions hit by COVID-19 pandemic. In Uruguay, first cases were detected on March 13 th 2020 presumably imported by travelers returning from Europe. MethodsWe performed whole-genome sequencing of 10 SARS-CoV-2 from patients diagnosed during the first week (March 16th to 19th) of COVID-19 outbreak in Uruguay. Then, we applied genomic epidemiology using a global dataset to reconstruct the local spatio-temporal dynamics of SARS-CoV-2. ResultsOur phylogeographic analysis showed three independent introductions of SARS-CoV-2 from different continents. Also, we evidenced regional circulation of viral strains originally detected in Spain. Introduction of SARS-CoV-2 in Uruguay could date back as early as Feb 20th. Identification of specific mutations showed rapid local genetic differentiation. ConclusionsWe evidenced early independent introductions of SARS-CoV-2 that likely occurred before first cases were detected. Our analysis set the bases for future genomic epidemiology studies to understand the dynamics of SARS-CoV-2 in Uruguay and the Latin America and the Caribbean region.

microbiology↗

bioRxiv2018

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

Chagas disease was described by Carlos Chagas, who first identified the parasite Trypanosoma cruzi from a two-year-old girl called Berenice. Many T. cruzi sequencing projects based on short reads have demonstrated that genome assembly and downstream comparative analyses are extremely challenging in this species, given that half of its genome is composed of repetitive sequences. Here, we report de novo assemblies, annotation and comparative analyses of the Berenice strain using a combination of Illumina short reads and MinION long reads. Our work demonstrates that Nanopore sequencing improves T. cruzi assembly contiguity and increases the assembly size in ~16 Mb. Specifically, we found that assembly improvement also refines the completeness of coding regions for both single copy genes and repetitive transposable elements. Beyond its historical and epidemiological importance, Berenice constitutes a fundamental resource since it now represents the best-quality assembly available for TcII, a highly prevalent lineage causing human infections in South America. The availability of Berenice genome expands the known genetic diversity of T. cruzi and facilitates more comprehensive evolutionary inferences. Our work represents the first report of Nanopore technology used to resolve complex protozoan genomes, supporting its subsequent application for improving trypanosomatid and other highly repetitive genomes.

genomics↗

bioRxiv2018

The Tritryps comparative repeatome: insights on repetitive element evolution in Trypanosomatid pathogens

The major human pathogens Trypanosoma cruzi, Trypanosoma brucei and Leishmania major are collectively known as the Tritryps. The initial comparative analysis of their genomes has uncovered that Tritryps share a great number of genes, but repetitive DNA seems to be extremely variable between them. However, the in-depth characterization of repetitive DNA in these pathogens has been in part neglected, mainly due to the well-known technical challenges of studying repetitive sequences from de novo assemblies using short reads. Here, we compared the repetitive DNA repertories between the Tritryps genomes using genome-wide, low-coverage Illumina sequencing coupled to RepeatExplorer analysis. Our work demonstrates that this extensively implemented approach for studying higher eukaryote repeatomes is also useful for protozoan parasites like trypanosomatids, as we recovered previously observed differences in the presence and amount of repetitive DNA families. Additionally, our estimations of repetitive DNA abundance were comparable to those obtained from enhanced-quality assemblies using longer reads. Importantly, our methodology allowed us to describe a previously unknown transposable element in Leishmania major (TATE family), highlighting its potential to accurately recover distinctive features from poorly characterized repeatomes. Together, our results support the application of this low-cost, low-coverage sequencing approach for the extensive characterization of repetitive DNA evolutionary dynamics in trypanosomatid and other protozooan genomes.

genomics↗