Biology subjects

Pita, S.

Publications and source records attributed to Pita, S..

9 recordsLinked to original sources

bioRxiv2026

Increasing threat: Rhynchophorus ferrugineus invaded mainland America through Uruguay.

Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae) is one of the most dangerous palm pests worldwide. Here we report the invasion process of R. ferrugineus in Uruguay. Beyond morphological and molecular identification, we infer the geographic origin of the invasive population, describe the succession of introduced and native palms attacked, provide an easy-to-use key to differentiate the invader R. ferrugineus from the native Rhynchophorus palmarum, and model the ecological niche of R. ferrugineus in Uruguay and neighboring countries. First detected in 2022, the Uruguayan population of the weevil is the first to establish on mainland America, following the earlier island records from Curacao and Aruba. Phylogenetic analysis showed that the Uruguayan R. ferrugineus sequences clustered within a single clade, most closely related to sequences from southern China, and clearly distinct from the sequences of Curacao and Aruba, indicating at least two independent introduction events into the Americas from different source regions. After four years, R. ferrugineus has spread across an area of nearly 80,000 square kilometers and in January 2026 it reached Argentina, invading two points near the border with Uruguay. Over the first two years after the invasion, attacks focused on Phoenix canariensis, yet the three most common native palms in Uruguay, Butia odorata, Butia yatay, and Syagrus romanzoffiana, are currently being attacked. The diagnostic key to differentiate the pair R. palmarum / R. ferrugineus is based on three characters: the tip of the rostrum, the tegminal plate, and the ratio between the interocular space and the width of the rostrum at the base. Niche models showed that Uruguay and the neighboring areas of Argentina and Brazil are suitable for R. ferrugineus, and these are precisely the areas where both the highly susceptible P. canariensis and the native B. odorata, B. yatay, and S. romanzoffiana are present. Neighboring countries should therefore be prepared for the expansion of R. ferrugineus in the short term.

zoology↗

bioRxiv2026

Novel Methylation Markers in a Prostate Cancer Cohort are Associated with Disease Development and Relapse

Prostate cancer remains one of the most common cancers among men globally. While significant strides have been made in diagnosis and treatment, understanding the complex genetic and epigenetic underpinnings of the disease remains crucial for guiding intervention and developing more personalized and effective therapies. The importance of DNA methylation in prostate cancer has been known for some time, but important facets of the modulation of the epigenome during carcinogenesis remain obscure, partly because the bulk of cancer methylation data have been produced using microarray technologies. Here we utilise the TruSeq methyl capture method (EPICseq) to profile the, previously defined, UK Prostate ICGC cohort of well-annotated primary prostate cancers. To this we add methylation sequencing of benign tissue from the same men. These data allow us to identify differentially methylated regions distinguishing cancerous and non-cancerous prostate tissue, while identifying numerous genes whose methylation profiles can perform that task as well as distinguishing between classes of prostate cancer. We describe a describe a methylation-based control mechanism for prostate-cancer-associated SNPs, and show that this seems a likely mechanism of action for a SNP near the MMP7 gene. We describe three novel molecular signatures that arise from different aspects of the biology of prostate cancer revealed by sequencing. Each is shown to be an independent classifier of cancers into groups with different expected times to relapse. These consist of patterns in driver gene methylation, strand-specific methylation, and signal arising in mitochondrial reads. We show that these signatures, combined with existing molecular tools, provide a powerful predictor of time to recurrence. By substantially enhancing understanding of prostate cancer risk, detection, and prognosis, we pave the way for the development of clinical practices that will benefit patients and improve outcomes.

cancer biology↗

bioRxiv2025

Reconstructing Sordida subcomplex (Hemiptera, Reduviidae, Triatominae) phylogeny across species distribution range

The conformation of the Sordida subcomplex has been a topic of prolonged debate, with diverse methodological approaches employed to discern its constituent species. Up to now, Triatoma sordida, T. garciabesi and T. rosai comprise part of this subcomplex. Distinguishing and identifying these three species pose significant challenges due to their pronounced morphological similarity, overlapping distributions, and presence of natural hybrids. This study aims to uncover the genetic diversity and geographic spread of these three species by analyzing a mitochondrial cytochrome b gene fragment and complementing it with chromosomal studies across natural populations from an extensive geographical range, including Argentina, Bolivia, Brazil, and Paraguay. Phylogenetic analyses revealed genetic distances that suggest the presence of at least six putative species, rather than the three currently recognized. The present findings underscore the potency and significance of molecular analyses from natural populations for species identification and highlight the limitations of morphology in classifying Triatominae species.

genetics↗

bioRxiv2024

CHAMP delivers accurate taxonomic profiles of the prokaryotes, eukaryotes, and bacteriophages in the human microbiome

Accurate taxonomic profiling of the human microbiome composition is crucial for linking microbial species to health outcomes. Therefore, we created the Clinical Microbiomics Human Microbiome Profiler (CHAMP), a comprehensive tool designed for the profiling of prokaryotes, eukaryotes, and viruses across all body sites. Boasting a reference database derived from 30,382 human microbiome samples, CHAMP covers 6,567 prokaryotic and 244 eukaryotic species as well as 64,003 viruses. We used a diverse set of in silico metagenomes and DNA mock communities to benchmark CHAMP against the established profiling tools MetaPhlAn 4, Bracken 2, mOTUs 3, and Phanta. CHAMP demonstrated unparalleled species recall, F1 score, and significantly reduced false positives compared to all other tools benchmarked. Indeed, the false positive relative abundance (FPRA) for CHAMP was, on average, 50-fold lower than the second-best performing profiler. CHAMP also proved to be more robust than the other tools to low sequencing depths, highlighting its application for low biomass samples. Taken together, this establishes CHAMP as a best-in-class human microbiome profiler of prokaryotes, eukaryotes, and viruses in diverse and complex communities across low and high biomass samples. CHAMP profiling is offered as a service by Clinical Microbiomics A/S and available for a fee at https://cosmosidhub.com.

bioinformatics↗

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

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↗

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↗