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Open Access Research article

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

Ludovic V Mallet1, Jennifer Becq2 and Patrick Deschavanne1*

Author Affiliations

1 Molécules thérapeutiques in silico (MTI), INSERM UMR-M 973, Université Paris Diderot - Paris 7, Bât Lamarck, 35 rue Hélène Brion, 75205, Paris Cedex 13, France

2 DSIMB, INSERM UMR-S 665, Université Paris Diderot - Paris 7, INTS, 6 rue Alexandre Cabanel, 75739 Paris Cedex 15, France

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BMC Genomics 2010, 11:171  doi:10.1186/1471-2164-11-171

Published: 12 March 2010

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.