Browsing by Autor "Diosque, Patricio"

Now showing 1 - 5 of 5

Genome data vs MLST for exploring intraspecific evolutionary history in bacteria: Much is not always better.
(2021) Floridia-Yapur, Noelia; Rusman, Fanny; Diosque, Patricio; Tomasini, Nicolás
Genome-based phylogeny has been proposed to be more accurate than phylogeny based in a few genes as MLST-based phylogeny. However, much is not always better. Here we analyzed 368 complete genomes corresponding to 9 bacterial species in order to address intraspecific phylogeny. The studied species were: Burkholderia pseudomallei, Campylobacter jejuni, Chlamydia trachomatis, Helicobacter pylori, Klebsiella pneumoniae, Listeria monocytogenes, Salmonella enterica, Staphylococcus aureus and Streptococcus pyogenes. The intra-specific phylogenies were inferred using the complete genome sequences of different strains of these species and their MLST schemes. A supermatrix approach was used to infer maximum likelihood phylogenies in both cases. The phylogenetic incongruence between the supermatrix-based genome or MLST tree and individual trees (constructed from genome fragments or MLST genes, respectively) was analyzed. In supermatrix-based trees for genomes, most branches showed a high branch support; however, a high number of branches also showed high percentage of topologically incongruent individual trees. Interestingly, genome and MLST trees showed similar levels of incongruence in the phylogeny for each bacteria specie. Both genome and MLST approaches showed that C. trachomatis and S. aureus have a tree-like evolutionary history (low levels of internal incongruence). Instead, B. pseudomallei and S. pyogenes show high levels of incongruence (network-like evolutionary story) probably caused by HGT (horizontal gene transfer). Concluding, our analysis showed that: high branch supports obtained in genome phylogenies could be an artifact probably caused by data size; MLST is valid to address intraspecific phylogenetic structure; and, each species has its own evolutionary history, which could be affected by HGT to different extents.
MLSTest: novel software for multi-locus sequence data analysis in eukaryotic organisms.
(2013) Tomasini, Nicolás; Lauthier, Juan J; Llewellyn, Martin S; Diosque, Patricio
Multi-locus sequence typing (MLST) is a frequently used genotyping method whose goal is the unambiguous assignment of microorganisms to genetic clusters. MLST typically involves analysis of DNA sequence results generated from several house-keeping gene loci. MLST remains the gold standard for molecular typing of many bacterial pathogens. Eukaryotic pathogens have also been the subject of MLST, however, few tools are available to deal with diploid sequence data. Here we present novel software for MLST data analysis tailored towards diploid Eukaryotes: MLSTest. This software meets various methods used in MLST and introduces some novel methodologies for the evaluation of the data set. In addition to construction of allelic profiles and basic clustering analysis, the MLSTest looks for network structures that suggest genetic exchange in BURST graphs. Additionally, it uses several simple methods for tree construction with the advantage of managing heterozygous or three-state sites. Additionally, the software analyses whether concatenation of fragments from different genes is suitable for the data set using different tests (bionj-incongruence length difference test, Templeton test). It evaluates how the incongruence is distributed across the tree using a variation of the localized incongruence length difference test based on a modified neighbour joining algorithm. We tested the last method in simulated datasets. We showed that is conservative (adequate type I error rate) and moderately to highly powerful as well as useful to localize incongruences in two bacterial and two eukaryotic MLST datasets. MLSTest was also designed for developing MLST schemes. It thus has tools to optimize locus combinations and to reduce the number of targets required for typing. MLSTest also analyses whether the discriminatory power of the typing scheme is increased by including more loci. We evaluated the software over simulated and real datasets from bacterial and eukaryotic microorganisms. The software is freely available at http://www.ipe.unsa.edu.ar/software.
Phylogenomics of Trypanosoma cruzi: Few evidence of TcI/TcII mosaicism in TcIII challenges the hypothesis of an ancient TcI/TcII hybridization.
(2017) Tomasini, Nicolás; Diosque, Patricio
Phylogenetic relationships among major lineages of Trypanosoma cruzi are still debatable. Particularly, it is controversial the origin of two main lineages: TcIII and TcIV. Some authors proposed that these lineages have been the result of an ancient hybridization between TcI and TcII, and this was one of the most accepted evolutionary models in the scientific community for several years. In the present paper we analyse several genomes of T. cruzi in order to examine if there is evidence supporting that TcIII is an ancient TcI/TcII hybrid. Our results show that TcIII is mainly related to TcI and not to TcII and there is few evidence of mosaicism for TcIII. Our results challenge the hypothesis of the ancient TcI/TcII hybridization.
Preponderant clonal evolution of Trypanosoma cruzi I from Argentinean Chaco revealed by Multilocus Sequence Typing (MLST).
(2014) Tomasini, Nicolás; Lauthier, Juan J; Monje Rumi, María M; Ragone, Paula G; Alberti D'Amato, Anahí M; Brandán, Cecilia Pérez; Basombrío, Miguel A; Diosque, Patricio
Trypanosoma cruzi has been historically classified as a species with preponderant clonal evolution (PCE). However, with the advent of highly polymorphic markers and studies at geographically reduced scales, the PCE in T. cruzi was challenged. In fact, some studies have suggested that recombination in T. cruzi lineage I (TcI) is much more frequent than previously believed. Further analyses of TcI populations from different geographical regions of Latin America are needed to examine this hypothesis. In the present study, we contribute to this topic by analyzing the population structure of TcI from a restricted geographical area in the Chaco region, Argentina. We analyzed TcI isolates from different hosts and vectors using a Multilocus Sequence Typing (MLST) approach. These isolates were previously characterized by sequencing the spliced leader intergenic region (SL-IR). Low levels of incongruence and well-supported clusters for MLST dataset were obtained from the analyses. Moreover, high linkage disequilibrium was found and five repeated and overrepresented genotypes were detected. In addition, a good correspondence between SL-IR and MLST was observed which is expected under PCE. However, recombination is not ruled out because five out of 28 pairs of loci were incompatible with strict clonality and one possible genetic exchange event was detected. Overall, our results represent evidence of PCE in TcI from the study area. Finally, considering our findings we discuss the scenario for the genetic structure of TcI.
Trypanosoma cruzi: infectivity modulation of a clone after passages through different hosts.
(2006) Pérez Brandán, Cecilia; Padilla, Angel Marcelo; Diosque, Patricio; Basombrío, Miguel Angel
Although Trypanosoma cruzi virulence can be modified through passages in vivo or long-term in vitro culture, the mechanisms involved are poorly understood. Here we report modifications in the infectivity of a T. cruzi clone after passages in different hosts without detectable changes in parasite genetic patterns. A clone was obtained from a T. cruzi IIe isolate and showed to be less virulent than the original isolate (p<0.05). This clone was enzymatically similar to the original isolate as shown by multilocus enzyme electrophoresis. Infection of this clone was compared by successive passages in mice and guinea pigs. The mouse-passaged subline became more virulent for both host species compared to the guinea pig-passaged subline (p<0.05). The clone line displayed similar random amplified polymorphic DNA patterns before and after passages in different hosts suggesting that alterations in virulence could be a result of a differential expression of virulence factors.