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.
Highlights
Horizontal gene transfer (HGT) is a major force that shapes the genome evolution in prokaryotes, which creates genomic innovations in response to environmental adaptation [1]
Cellulases were found to be transferred from bacteria to nematodes [4], bacterial toxin genes were transferred into eukaryotes [5], and antibacterial lysozymes were transferred into various eukaryotes and archaea [6]
We looked at the results of the genome-wide analysis of horizontally transferred genes (HTGs) in terms of their functions, sequence features, and gene clustering
Summary
Horizontal gene transfer (HGT) is a major force that shapes the genome evolution in prokaryotes, which creates genomic innovations in response to environmental adaptation [1]. The most accurate, golden-standard method to identify horizontally transferred genes (HTGs) is the gene-by-gene phylogenetic analysis, which compares the target gene phylogeny with a well-established species phylogeny to identify genes with incongruences [16,19,23]. Softwares published implementing the phyletic distribution method: Pyphy [26], PhyloGenie [27], DarkHorse [28], and HGTector [29] All these tools were originally designed to find HTGs in prokaryotes, do not have a rigorous statistical assessment of the predictions, and require extensive human intervention. HGT-Finder: (i) can be used for HGT detection in both prokaryotes and eukaryotes, (ii) can report a statistical P value for each gene to indicate how likely it is to be horizontally transferred, and (iii) is fully automated (requires minimal human intervention), as well as very easy to install and run. We compared HGT-Finder predictions with previously published HGT results and tools
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