title: HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes.
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.
authors.affiliation: Department of Computer Science, Northern Illinois University, DeKalb, IL 60115-2857, USA. z1605032@students.niu.edu.
authors.forename: Marcus
authors.initials: M
authors.lastname: Nguyen
authors.affiliation: Department of Computer Science, Northern Illinois University, DeKalb, IL 60115-2857, USA. z1664374@students.niu.edu.
authors.forename: Alex
authors.initials: A
authors.lastname: Ekstrom
authors.affiliation: Department of Biological Sciences, Northern Illinois University, Montgomery Hall 325A, DeKalb, IL 60115-2857, USA. xueqiongli@imau.edu.cn.|College of Life Sciences, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, Inner Mongolia, China. xueqiongli@imau.edu.cn.
authors.forename: Xueqiong
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Biological Sciences, Northern Illinois University, Montgomery Hall 325A, DeKalb, IL 60115-2857, USA. yyin@niu.edu.
authors.forename: Yanbin
authors.initials: Y
authors.lastname: Yin
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D000465:Algorithms; D001230:Aspergillus / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D005800:Genes, Fungal; D016681:Genome, Fungal; D005810:Multigene Family; D010802:Phylogeny; D012984:Software; D013045:Species Specificity
keywords: Aspergillus; HGT; bioinformatics; gene clusters; horizontal gene transfer; secondary metabolism; software