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The origin of parasitism gene in nematodes: evolutionary analysis through the construction of domain trees.

ABSTRACT: Inferring evolutionary history of parasitism genes is important to understand how evolutionary mechanisms affect the occurrences of parasitism genes. In this study, we constructed multiple domain trees for parasitism genes and genes under free-living conditions. Further analyses of horizontal gene transfer (HGT)-like phylogenetic incongruences, duplications, and speciations were performed based on these trees. By comparing these analyses, the contributions of pre-adaptations were found to be more important to the evolution of parasitism genes than those of duplications, and pre-adaptations are as crucial as previously reported HGTs to parasitism. Furthermore, speciation may also affect the evolution of parasitism genes. In addition, Pristionchus pacificus was suggested to be a common model organism for studies of parasitic nematodes, including root-knot species. These analyses provided information regarding mechanisms that may have contributed to the evolution of parasitism genes.

SUBMITTER: Yang Y

PROVIDER: S-EPMC3836563 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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The origin of parasitism gene in nematodes: evolutionary analysis through the construction of domain trees.

Yang Yizi Y Luo Damin D

Evolutionary bioinformatics online 20131106

Inferring evolutionary history of parasitism genes is important to understand how evolutionary mechanisms affect the occurrences of parasitism genes. In this study, we constructed multiple domain trees for parasitism genes and genes under free-living conditions. Further analyses of horizontal gene transfer (HGT)-like phylogenetic incongruences, duplications, and speciations were performed based on these trees. By comparing these analyses, the contributions of pre-adaptations were found to be mor ...[more]

PMID: 24277980

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Project description:An ample variety of parasitic associations are found between mollusks and nematodes, in which the mollusks may act as intermediate, paratenic or definitive hosts. Some free-living nematodes, in particular those of the order Rhabditida, are also found frequently in terrestrial mollusks. The present study reviews the results of the parasitological testing on samples of terrestrial mollusks conducted at the Brazilian National Reference Laboratory for Schistosomiasis and Malacology between 2008 and 2021. The samples were supplied primarily by the public health authorities from the different regions of Brazil, but also by research institutions and general population. The mollusks were processed individually and the obtained larvae were identified from their morphology and, whenever necessary, by molecular analysis. A total of 1,919 service orders were registered during the period, including 19,758 mollusk specimens collected from 23 of the 26 Brazilian states, as well as the Federal District, totalizing 145 municipalities. There was a marked predominance of the synanthropic species that are widely distributed in Brazil-Achatina fulica (87.08%), Bulimulus tenuissimus (4.18%), Bradybaena similaris (2.06%), and Sarasinula linguaeformis (1.50%). Of the 16,750 terrestrial mollusks examined, nematodes were recorded in 1,308 service orders, with the predominance of the superfamily Metastrongyloidea, in 616 service orders. They included Angiostrongylus cantonensis, rat lungworm, which was found in 252 samples, and Aelurostrongylus abstrusus in 145 samples. Free-living nematodes were found in 952 samples, Ancylostoma caninum and Cruzia tentaculata (previously identified as Strongyluris sp.) in one and 275 samples, respectively, and other parasites in 210 samples (not identified). The results highlight the diversity of the associations between nematodes and terrestrial mollusks in Brazil, in particular invasive and synanthropic species, with emphasis on the giant African land snail, Achatina fulica. They demonstrate the prominent role of this species of mollusk in the transmission of medically-important nematodes, which affect the health of both humans and animals, in particular eosinophilic meningitis, which is caused by Angiostrongylus cantonensis. This reinforces the need for more studies, and justify the growing demand for information as well as parasitological diagnosis of this mollusk, given its wide distribution in Brazil and its impact as an urban pest.

Project description:BackgroundA long recognized problem is the inference of the supertree S that amalgamates a given set {G(j)} of trees G(j), with leaves in each G(j) being assigned homologous elements. We ground on an approach to find the tree S by minimizing the total cost of mappings ?(j) of individual gene trees G(j) into S. Traditionally, this cost is defined basically as a sum of duplications and gaps in each ?(j). The classical problem is to minimize the total cost, where S runs over the set of all trees that contain an exhaustive non-redundant set of species from all input G(j).ResultsWe suggest a reformulation of the classical NP-hard problem of building a supertree in terms of the global minimization of the same cost functional but only over species trees S that consist of clades belonging to a fixed set P (e.g., an exhaustive set of clades in all G(j)). We developed a deterministic solving algorithm with a low degree polynomial (typically cubic) time complexity with respect to the size of input data. We define an extensive set of elementary evolutionary events and suggest an original definition of mapping ? of tree G into tree S. We introduce the cost functional c(G, S, f) and define the mapping ? as the global minimum of this functional with respect to the variable f, in which sense it is a generalization of classical mapping ?. We suggest a reformulation of the classical NP-hard mapping (reconciliation) problem by introducing time slices into the species tree S and present a cubic time solving algorithm to compute the mapping ?. We introduce two novel definitions of the evolutionary scenario based on mapping ? or a random process of gene evolution along a species tree.ConclusionsDeveloped algorithms are mathematically proved, which justifies the following statements. The supertree building algorithm finds exactly the global minimum of the total cost if only gene duplications and losses are allowed and the given sets of gene trees satisfies a certain condition. The mapping algorithm finds exactly the minimal mapping ?, the minimal total cost and the evolutionary scenario as a minimum over all possible distributions of elementary evolutionary events along the edges of tree S. The algorithms and their effective software implementations provide useful tools in many biological studies. They facilitate processing of voluminous tree data in acceptable time still largely avoiding heuristics. Performance of the tools is tested with artificial and prokaryotic tree data.ReviewersThis article was reviewed by Prof. Anthony Almudevar, Prof. Alexander Bolshoy (nominated by Prof. Peter Olofsson), and Prof. Marek Kimmel.

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The origin of parasitism gene in nematodes: evolutionary analysis through the construction of domain trees.

Publications

The origin of parasitism gene in nematodes: evolutionary analysis through the construction of domain trees.

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