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HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes
Horizontal gene transfer (HGT) is a fast-track mechanism that allows genetically unrelated organisms to exchange genes for rapid environmental adaptation. We developed a new phyletic distribution-based software, HGT-Finder, which implements a novel bioinformatics algorithm to calculate a horizontal...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4626719/ https://www.ncbi.nlm.nih.gov/pubmed/26473921 http://dx.doi.org/10.3390/toxins7104035 |
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author | Nguyen, Marcus Ekstrom, Alex Li, Xueqiong Yin, Yanbin |
author_facet | Nguyen, Marcus Ekstrom, Alex Li, Xueqiong Yin, Yanbin |
author_sort | Nguyen, Marcus |
collection | PubMed |
description | Horizontal gene transfer (HGT) is a fast-track mechanism that allows genetically unrelated organisms to exchange genes for rapid environmental adaptation. We developed a new phyletic distribution-based software, HGT-Finder, which implements a novel bioinformatics algorithm to calculate a horizontal transfer index and a probability value for each query gene. Applying this new tool to the Aspergillus fumigatus, Aspergillus flavus, and Aspergillus nidulans genomes, we found 273, 542, and 715 transferred genes (HTGs), respectively. HTGs have shorter length, higher guanine-cytosine (GC) content, and relaxed selection pressure. Metabolic process and secondary metabolism functions are significantly enriched in HTGs. Gene clustering analysis showed that 61%, 41% and 74% of HTGs in the three genomes form physically linked gene clusters (HTGCs). Overlapping manually curated, secondary metabolite gene clusters (SMGCs) with HTGCs found that 9 of the 33 A. fumigatus SMGCs and 31 of the 65 A. nidulans SMGCs share genes with HTGCs, and that HTGs are significantly enriched in SMGCs. Our genome-wide analysis thus presented very strong evidence to support the hypothesis that HGT has played a very critical role in the evolution of SMGCs. The program is freely available at http://cys.bios.niu.edu/HGTFinder/HGTFinder.tar.gz. |
format | Online Article Text |
id | pubmed-4626719 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-46267192015-11-12 HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes Nguyen, Marcus Ekstrom, Alex Li, Xueqiong Yin, Yanbin Toxins (Basel) Article Horizontal gene transfer (HGT) is a fast-track mechanism that allows genetically unrelated organisms to exchange genes for rapid environmental adaptation. We developed a new phyletic distribution-based software, HGT-Finder, which implements a novel bioinformatics algorithm to calculate a horizontal transfer index and a probability value for each query gene. Applying this new tool to the Aspergillus fumigatus, Aspergillus flavus, and Aspergillus nidulans genomes, we found 273, 542, and 715 transferred genes (HTGs), respectively. HTGs have shorter length, higher guanine-cytosine (GC) content, and relaxed selection pressure. Metabolic process and secondary metabolism functions are significantly enriched in HTGs. Gene clustering analysis showed that 61%, 41% and 74% of HTGs in the three genomes form physically linked gene clusters (HTGCs). Overlapping manually curated, secondary metabolite gene clusters (SMGCs) with HTGCs found that 9 of the 33 A. fumigatus SMGCs and 31 of the 65 A. nidulans SMGCs share genes with HTGCs, and that HTGs are significantly enriched in SMGCs. Our genome-wide analysis thus presented very strong evidence to support the hypothesis that HGT has played a very critical role in the evolution of SMGCs. The program is freely available at http://cys.bios.niu.edu/HGTFinder/HGTFinder.tar.gz. MDPI 2015-10-09 /pmc/articles/PMC4626719/ /pubmed/26473921 http://dx.doi.org/10.3390/toxins7104035 Text en © 2015 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 license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Nguyen, Marcus Ekstrom, Alex Li, Xueqiong Yin, Yanbin HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes |
title | HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes |
title_full | HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes |
title_fullStr | HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes |
title_full_unstemmed | HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes |
title_short | HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes |
title_sort | hgt-finder: a new tool for horizontal gene transfer finding and application to aspergillus genomes |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4626719/ https://www.ncbi.nlm.nih.gov/pubmed/26473921 http://dx.doi.org/10.3390/toxins7104035 |
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