Format

Send to

Choose Destination
Toxins (Basel). 2015 Oct 9;7(10):4035-53. doi: 10.3390/toxins7104035.

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

Author information

1
Department of Computer Science, Northern Illinois University, DeKalb, IL 60115-2857, USA. z1605032@students.niu.edu.
2
Department of Computer Science, Northern Illinois University, DeKalb, IL 60115-2857, USA. z1664374@students.niu.edu.
3
Department of Biological Sciences, Northern Illinois University, Montgomery Hall 325A, DeKalb, IL 60115-2857, USA. xueqiongli@imau.edu.cn.
4
College of Life Sciences, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, Inner Mongolia, China. xueqiongli@imau.edu.cn.
5
Department of Biological Sciences, Northern Illinois University, Montgomery Hall 325A, DeKalb, IL 60115-2857, USA. yyin@niu.edu.

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.

KEYWORDS:

Aspergillus; HGT; bioinformatics; gene clusters; horizontal gene transfer; secondary metabolism; software

PMID:
26473921
PMCID:
PMC4626719
DOI:
10.3390/toxins7104035
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Multidisciplinary Digital Publishing Institute (MDPI) Icon for PubMed Central
Loading ...
Support Center