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.

Keywords: Aspergillus; HGT; bioinformatics; gene clusters; horizontal gene transfer; secondary metabolism; software.

Figure 1

The use of statistical distribution to calculate P values. The x-axis shows the X value. The blue curve is the distribution of the X values of 9577 Aspfu proteins. The red curve is the theoretical distribution that has the same mean and standard deviation as the blue curve. The green line is drawn to indicate the cutoff value; any X value larger than that in the blue curve will have a P value <0.01.

Figure 2

The number of HTGs predicted using different R thresholds. The x-axis is the R threshold and the y-axis is the number of HTGs. The last column shows the total number of HTGs after removing overlaps. # means “number”.

Figure 3

The percentage of HTGs that have more than 50% BLAST hits from non-eukaryotic species using different R thresholds. The x-axis is the R thresholds and the y-axis is the percentage of HTGs.

Figure 4

The percentage of Aspfu HTGs that have more than 50% BLAST hits from non-Eukaryotic species using different R thresholds. The x-axis is the R threshold and the y-axis is the percentage of HTGs.

Figure 5

Phylogeny of Aspfl1|27612|7000001155802518 (GenBank ID: AFLA_091530) as an example of HTG. The query protein (in pink)’s homologs are restricted to very few fungal species, two other Aspergillus species and a few Fusarium species. The rest of the homologs are all from Proteobacteria. The boxes on the right show the taxonomic distance (D) in green and sequence similarity (R) in red. The black triangle on the top represents the collapsed Proteobacteria homologs.

Figure 6

The percentage of HTGs that form physically linked gene clusters on chromosomes. The x-axis is the N thresholds and the y-axis is the percentage of HTGs. N is used to define gene clusters. For example if two HTGs are separated by less than N non-HTGs, these N + 2 genes will belong to one gene cluster. More HTGs will be included until the N threshold is not met. N is explored from 0 to 7 in this figure.

Figure 7

Diagram representation of HTGCs and SMGCs in Aspni. The top graph is a Circos plot [42] of the chromosomal distribution of HTGCs and SMGCs in Aspni. The outmost numbers are the IDs of SMGCs, which were extracted from [40]. The functional descriptions of these SMGCs are available in Table S6. The bottom linear graph, as an example of overlapping between HTGCs and SMGCs, shows the detailed genomic neighborhood of SMGC 5 and 6 (cyan frames) as well as the overlapping HTGC 11 (red frame).