Whole genome evaluation of horizontal transfers in the pathogenic fungus Aspergillus fumigatus

Abstract

Background: Numerous cases of horizontal transfers (HTs) have been described for eukaryote genomes, but in contrast to prokaryote genomes, no whole genome evaluation of HTs has been carried out. This is mainly due to a lack of parametric methods specially designed to take the intrinsic heterogeneity of eukaryote genomes into account. We applied a simple and tested method based on local variations of genomic signatures to analyze the genome of the pathogenic fungus Aspergillus fumigatus.

Results: We detected 189 atypical regions containing 214 genes, accounting for about 1 Mb of DNA sequences. However, the fraction of atypical DNA detected was smaller than the average amount detected in the same conditions in prokaryote genomes (3.1% vs 5.6%). It appeared that about one third of these regions contained no annotated genes, a proportion far greater than in prokaryote genomes. When analyzing the origin of these HTs by comparing their signatures to a home made database of species signatures, 3 groups of donor species emerged: bacteria (40%), fungi (25%), and viruses (22%). It is to be noticed that though inter-domain exchanges are confirmed, we only put in evidence very few exchanges between eukaryotic kingdoms.

Conclusions: In conclusion, we demonstrated that HTs are not negligible in eukaryote genomes, bearing in mind that in our stringent conditions this amount is a floor value, though of a lesser extent than in prokaryote genomes. The biological mechanisms underlying those transfers remain to be elucidated as well as the biological functions of the transferred genes.

Figure 1

Representation of the distance of each 5 kb window to the host genome for the 8 chromosomes of A. fumigatus. The red line indicates the threshold, all the windows above this line are considered as atypical. Black boxes represent the non-sequenced parts of the chromosomes [78].

Figure 2

Detail of the c3r2 region lacking annotated genes.

Figure 3

Phylogenetic trees for gene/protein AFUA.2G12710 and AFUA.6G09720 and their respective SSU rRNA trees. A. fumigatus and N. fischieri were highlighted in blue, main incongruencies between SSU rRNA tree and protein tree are indicated with red arrows or bars. Numbers at nodes correspond to the number of bootstrap trees out of 1000 supporting that node when this number is inferior to 500.

Figure 4

Sample signatures of regions associated with the signature of their best neighbor (the distance between them is given in arbitrary units).

Figure 5

Summary of the origin of atypical regions by domain and by family.