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ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes

Horizontal gene transfer (HGT) plays an important role for evolutionary innovations within prokaryotic communities and is a crucial event for their survival. Several computational approaches have arisen to identify HGT events in recipient genomes. However, this has been proven to be a complex task d...

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Autores principales: Sánchez-Soto, Daniela, Agüero-Chapin, Guillermin, Armijos-Jaramillo, Vinicio, Perez-Castillo, Yunierkis, Tejera, Eduardo, Antunes, Agostinho, Sánchez-Rodríguez, Aminael
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7397055/
https://www.ncbi.nlm.nih.gov/pubmed/32645885
http://dx.doi.org/10.3390/genes11070756
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author Sánchez-Soto, Daniela
Agüero-Chapin, Guillermin
Armijos-Jaramillo, Vinicio
Perez-Castillo, Yunierkis
Tejera, Eduardo
Antunes, Agostinho
Sánchez-Rodríguez, Aminael
author_facet Sánchez-Soto, Daniela
Agüero-Chapin, Guillermin
Armijos-Jaramillo, Vinicio
Perez-Castillo, Yunierkis
Tejera, Eduardo
Antunes, Agostinho
Sánchez-Rodríguez, Aminael
author_sort Sánchez-Soto, Daniela
collection PubMed
description Horizontal gene transfer (HGT) plays an important role for evolutionary innovations within prokaryotic communities and is a crucial event for their survival. Several computational approaches have arisen to identify HGT events in recipient genomes. However, this has been proven to be a complex task due to the generation of a great number of false positives and the prediction disagreement among the existing methods. Phylogenetic reconstruction methods turned out to be the most reliable ones, but they are not extensible to all genes/species and are computationally demanding when dealing with large datasets. In contrast, the so-called surrogate methods that use heuristic solutions either based on nucleotide composition patterns or phyletic distribution of BLAST hits can be applied easily to the genomic scale, but they fail in identifying common HGT events. Here, we present ShadowCaster, a hybrid approach that sequentially combines nucleotide composition-based predictions by support vector machines (SVMs) under the shadow of phylogenetic models independent of tree reconstruction, to improve the detection of HGT events in prokaryotes. ShadowCaster successfully predicted close and distant HGT events in both artificial and bacterial genomes. ShadowCaster detected HGT related to heavy metal resistance in the genome of Rhodanobacter denitrificans with higher accuracy than the most popular state-of-the-art computational approaches, encompassing most of the predicted cases made by other methods. ShadowCaster is released at the GitHub platform as an open-source software under the GPLv3 license.
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spelling pubmed-73970552020-08-05 ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes Sánchez-Soto, Daniela Agüero-Chapin, Guillermin Armijos-Jaramillo, Vinicio Perez-Castillo, Yunierkis Tejera, Eduardo Antunes, Agostinho Sánchez-Rodríguez, Aminael Genes (Basel) Article Horizontal gene transfer (HGT) plays an important role for evolutionary innovations within prokaryotic communities and is a crucial event for their survival. Several computational approaches have arisen to identify HGT events in recipient genomes. However, this has been proven to be a complex task due to the generation of a great number of false positives and the prediction disagreement among the existing methods. Phylogenetic reconstruction methods turned out to be the most reliable ones, but they are not extensible to all genes/species and are computationally demanding when dealing with large datasets. In contrast, the so-called surrogate methods that use heuristic solutions either based on nucleotide composition patterns or phyletic distribution of BLAST hits can be applied easily to the genomic scale, but they fail in identifying common HGT events. Here, we present ShadowCaster, a hybrid approach that sequentially combines nucleotide composition-based predictions by support vector machines (SVMs) under the shadow of phylogenetic models independent of tree reconstruction, to improve the detection of HGT events in prokaryotes. ShadowCaster successfully predicted close and distant HGT events in both artificial and bacterial genomes. ShadowCaster detected HGT related to heavy metal resistance in the genome of Rhodanobacter denitrificans with higher accuracy than the most popular state-of-the-art computational approaches, encompassing most of the predicted cases made by other methods. ShadowCaster is released at the GitHub platform as an open-source software under the GPLv3 license. MDPI 2020-07-07 /pmc/articles/PMC7397055/ /pubmed/32645885 http://dx.doi.org/10.3390/genes11070756 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Sánchez-Soto, Daniela
Agüero-Chapin, Guillermin
Armijos-Jaramillo, Vinicio
Perez-Castillo, Yunierkis
Tejera, Eduardo
Antunes, Agostinho
Sánchez-Rodríguez, Aminael
ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes
title ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes
title_full ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes
title_fullStr ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes
title_full_unstemmed ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes
title_short ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes
title_sort shadowcaster: compositional methods under the shadow of phylogenetic models to detect horizontal gene transfers in prokaryotes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7397055/
https://www.ncbi.nlm.nih.gov/pubmed/32645885
http://dx.doi.org/10.3390/genes11070756
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