Biology subjects

Alvarez-Valin, F.

Publications and source records attributed to Alvarez-Valin, F..

4 recordsLinked to original sources

bioRxiv2026

The modular origin and evolutionary expansion of the enigmatic DGF-1 protein family in trypanosomatids

Large multigene families are a hallmark of trypanosomatid genomes and play major roles in genome plasticity and parasite adaptation. Among them, the Dispersed Gene Family 1 (DGF-1) of Trypanosoma cruzi remains one of the least understood because of its large size, repetitiveness, and fragmented annotations. Here, using a high-quality long-read assembly of T. cruzi, we performed comprehensive re-annotation and structural characterization of DGF-1. We identified seven tandemly repeated structural modules, here termed ribs, that form the extracellular region. This is followed by a distinct C-terminal membrane-associated region containing a conserved hat domain and multiple transmembrane helices. These domains are highly conserved across paralogous copies and the 7 ribs cluster according to positional identity rather than gene origin, indicating that the canonical seven-rib architecture predates the expansion of the family. DGF-1 proteins are present in the early-branching trypanosomatid species Paratrypanosoma confusum and several other trypanosomatids but absent in Leishmania and African trypanosomes, consistent with multiple independent secondary losses. Comparative analyses across Euglenozoa indicate that the DGF-1 architecture did not originate in free-living bodonids. Instead, Bodo saltans contains proteins with rib-like domains and others containing the membrane-associated region, whereas the first complete DGF-1 architecture appears in P. confusum. Phylogenetic and comparative genomic analyses indicate that the family subsequently underwent lineage-specific losses and independent expansions, the largest expansion occurring in T. cruzi. Together, these findings reconstruct the evolutionary emergence of the DGF-1 architecture from pre-existing structural modules and provide a framework for one of the largest and most enigmatic gene families in trypanosomatids.

evolutionary biology↗

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↗

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↗

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↗