Next Article in Journal
The Effects of Shiga Toxin 1, 2 and Their Subunits on Cytokine and Chemokine Expression by Human Macrophage-Like THP-1 Cells
Next Article in Special Issue
Menadione-Induced Oxidative Stress Re-Shapes the Oxylipin Profile of Aspergillus flavus and Its Lifestyle
Previous Article in Journal
Main Ustilaginoidins and Their Distribution in Rice False Smut Balls
Previous Article in Special Issue
Suppression of Aflatoxin Biosynthesis in Aspergillus flavus by 2-Phenylethanol Is Associated with Stimulated Growth and Decreased Degradation of Branched-Chain Amino Acids
Article Menu

Export Article

Open AccessArticle
Toxins 2015, 7(10), 4035-4053; doi:10.3390/toxins7104035

HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes

1
Department of Computer Science, Northern Illinois University, DeKalb, IL 60115-2857, USA
2
Department of Biological Sciences, Northern Illinois University, Montgomery Hall 325A, DeKalb, IL 60115-2857, USA
3
College of Life Sciences, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, Inner Mongolia, China
*
Author to whom correspondence should be addressed.
Academic Editor: Jiujiang Yu
Received: 15 August 2015 / Revised: 22 September 2015 / Accepted: 23 September 2015 / Published: 9 October 2015
View Full-Text   |   Download PDF [630 KB, uploaded 9 October 2015]   |  

Abstract

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. View Full-Text
Keywords: horizontal gene transfer; HGT; gene clusters; secondary metabolism; Aspergillus; bioinformatics; software horizontal gene transfer; HGT; gene clusters; secondary metabolism; Aspergillus; bioinformatics; software
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Supplementary material

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Nguyen, M.; Ekstrom, A.; Li, X.; Yin, Y. HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes. Toxins 2015, 7, 4035-4053.

Show more citation formats Show less citations formats

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Toxins EISSN 2072-6651 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top