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 .

Phylogeny and genomics of SAUL, an enigmatic bacterial lineage frequently associated with marine sponges

“…To further investigate the magnitude of HGT events within SAUL genomes, we identified candidate transferred genes using HGT-Finder (Nguyen et al, 2015). Very few putative transferred genes were found in SAUL genomes (7 and 5 for bin_aplysina and bin_petrosia respectively), likely corresponding to ancestral HGT events (R 0.4).…”

“…SAUL genomes were searched using blastn (v 12.6.0) against the GenBank NR database. The BLAST output was subjected to HGT-Finder (R threshold ranging from 0.2 to 0.9, Q value < 0.05) to identify HGT candidates (Nguyen et al, 2015). Clustered regularly interspaced short palindromic repeats (CRISPR) were identified using CRISPR-Finder (Grissa et al, 2008) in CRISPRs web server with default settings.…”

ShadowCaster: compositional methods under the shadow of phylogenetic models for the detection of horizontal gene transfer events in prokaryotes

“…Nevertheless, explicit phylogenetic methods (tree building-based) are not practical at large-scale (e.g. comprising entire gene repertoires), because they are computationally expensive and time consuming [12]. In this sense, several methods having rather implicit phylogenetic approaches, have arisen.…”

“…These methods are mainly based on phyletic distribution derived from BLAST searches in order to speed up alien gene detection in multiple genomes/taxa since they bypassed gene tree reconstruction e.g. DarkHorse [13], HGTector [14] and HGT-Finder [12]. Table 1 shows the state-of-the-art of HGT detection methods that rely on different information sources and when applied to the same dataset often generate partially overlapping predictions.…”

Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life

“…The hgt index method was first used to determine genes of non-metazoan origin in the transcriptome of the bdelloid rotifer Adineta ricciae [27] and later used to infer the contribution of HGT to the transcriptomes of several different metazoan species, including vertebrates [11]. A refined scoring method has been recently proposed that not only takes into account sequence similarity between receiver and candidate donors, measured in BLAST bit score, but also taxonomic distance measured as the number of step in the NCBI's taxonomic lineage to reach the common ancestor of the query and subject species [28]. The software is publicly available and has been initially developed to identify HGT in fungal genomes.…”