Next Article in Journal
The Need for Establishing a Universal CTG Sizing Method in Myotonic Dystrophy Type 1
Next Article in Special Issue
Vertical and Horizontal Transmission of ESBL Plasmid from Escherichia coli O104:H4
Previous Article in Journal
Actions of L-thyroxine (T4) and Tetraiodothyroacetic Acid (Tetrac) on Gene Expression in Thyroid Cancer Cells
Previous Article in Special Issue
Direct Visualization of Horizontal Gene Transfer by Transformation in Live Pneumococcal Cells Using Microfluidics
Open AccessArticle

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

1
Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, Loja 110108, Ecuador
2
CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Porto, Portugal
3
Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
4
Grupo de Bio-Quimioinformática & Carrera de Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias Agropecuarias, Universidad de Las Américas, Quito EC170125, Ecuador
5
Grupo de Bio-Quimioinformática & Escuela de Ciencias Físicas y Matemáticas, Universidad de Las Américas, Quito EC170125, Ecuador
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Genes 2020, 11(7), 756; https://doi.org/10.3390/genes11070756
Received: 9 June 2020 / Revised: 27 June 2020 / Accepted: 30 June 2020 / Published: 7 July 2020
(This article belongs to the Special Issue Horizontal Gene Transfer in Bacteria)
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. View Full-Text
Keywords: horizontal gene transfer; parametric method; implicit phylogenetic model; hybrid approach horizontal gene transfer; parametric method; implicit phylogenetic model; hybrid approach
Show Figures

Graphical abstract

MDPI and ACS Style

Sánchez-Soto, D.; Agüero-Chapin, G.; Armijos-Jaramillo, V.; Perez-Castillo, Y.; Tejera, E.; Antunes, A.; Sánchez-Rodríguez, A. ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes. Genes 2020, 11, 756. https://doi.org/10.3390/genes11070756

AMA Style

Sánchez-Soto D, Agüero-Chapin G, Armijos-Jaramillo V, Perez-Castillo Y, Tejera E, Antunes A, Sánchez-Rodríguez A. ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes. Genes. 2020; 11(7):756. https://doi.org/10.3390/genes11070756

Chicago/Turabian Style

Sánchez-Soto, Daniela; Agüero-Chapin, Guillermin; Armijos-Jaramillo, Vinicio; Perez-Castillo, Yunierkis; Tejera, Eduardo; Antunes, Agostinho; Sánchez-Rodríguez, Aminael. 2020. "ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes" Genes 11, no. 7: 756. https://doi.org/10.3390/genes11070756

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Search more from Scilit
 
Search
Back to TopTop