Biology subjects

Chiribao, M. L.

Publications and source records attributed to Chiribao, M. L..

4 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↗

bioRxiv2024

Exploring the Genomic Landscape of the GP63 family in Trypanosoma cruzi: Evolutionary Dynamics and Functional Peculiarities

We analyzed the complete set of GP63 sequences from the parasitic protozoa Trypanosoma cruzi. Our analysis allowed us to refine annotation of sequences previously identified as functional and pseudogenes. Concerning the latter, we unified pseudogenic fragments derived from the same functional gene and excluded sequences incorrectly annotated as GP63 pseudogenes. We were able to identify eleven GP63 gene groups, which are sharply defined and have a high intra-group sequence identity. The sequences of each group showed a strong preference for genomic compartments. Some groups are located in the core and others in disruptive compartments of the T. cruzi genome. Groups located in the core compartment often contain tandem arrays of GP63 genes. On the contrary, genes from groups located in the disruptive compartment tend to be surrounded by genes encoding surface proteins such as MASP, mucins and trans-sialidases. Analysis of the immediate GP63 environments showed differences that may be the result of different genomic dynamics in these two compartments. Interestingly, each GP63 group showed a particular mRNA expression profile and some groups contain members that are differentially expressed between life cycle stages, being expressed at higher levels in trypomastigotes than in the replicative forms. This suggests that these groups of GP63 proteins may play a relevant role in the infective stage. The analysis of the M8 domain, that defines the GP63 protein family, allowed us to recognize that each group presented peculiarities in the conserved sites as well as in the presence of the predicted signal peptide and GPI anchor site. Phylogenetic analysis of the GP63 sequences, including other species of the genus Trypanosoma as well as other kinetoplastids, showed that ten of the 11 groups of T. cruzi not only are also present in the other Trypanosoma species but also are exclusive of genus, suggesting that the diversification of these subfamilies took place before speciation. However, each species then followed a different evolutionary path, amplifying specific groups in unique ways. Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. Impact statementOur study contributes to the understanding of the GP63 gene family in Trypanosoma cruzi, a crucial protein for the parasites infectivity and evolution. We refined the annotation of GP63 sequences, identifying eleven distinct gene groups with distinctive preferences for genomic compartments -some in the core, others in the disruptive compartment. This distribution hints at varied genomic dynamics and potential roles in the parasites life cycle, especially since some groups show enhanced expression in infective stages, suggesting their importance in disease transmission. Our exploration into the GP63 sequences M8 domain revealed group-specific peculiarities in conserved sites and structural motifs, emphasizing functional diversity. Phylogenetic analysis across Trypanosoma species highlighted the evolutionary uniqueness of these gene subfamilies within the genus, underscoring their role in the species distinct evolutionary paths and amplification patterns.

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↗

bioRxiv2018

Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi

Although the genome of Trypanosoma cruzi, the causative agent of Chagas disease, was first made available in 2005, with additional strains reported later, the intrinsic genome complexity of this parasite (abundance of repetitive sequences and genes organized in tandem) has traditionally hindered high-quality genome assembly and annotation. This also limits diverse types of analyses that require high degree of precision. Long reads generated by third-generation sequencing technologies are particularly suitable to address the challenges associated with T. cruzi{acute}s genome since they permit directly determining the full sequence of large clusters of repetitive sequences without collapsing them. This, in turn, allows not only accurate estimation of gene copy numbers but also circumvents assembly fragmentation. Here, we present the analysis of the genome sequences of two T. cruzi clones: the hybrid TCC (DTU TcVI) and the non-hybrid Dm28c (DTU TcI), determined by PacBio SMRT technology. The improved assemblies herein obtained permitted us to accurately estimate gene copy numbers, abundance and distribution of repetitive sequences (including satellites and retroelements). We found that the genome of T. cruzi is composed of a \"core compartment\" and a \"disruptive compartment\" which exhibit opposite gene and GC content composition. New tandem and disperse repetitive sequences were identified, including some located inside coding sequences. Additionally, homologous chromosomes were separately assembled, allowing us to retrieve haplotypes as separate contigs instead of a unique mosaic sequence. Finally, manual annotation of surface multigene families MUC and trans-sialidases allows now a better overview of these complex groups of genes.

genomics↗