Comparative genomics reveals substantial divergence in metal sensitive and metal tolerant isolates of the ericoid mycorrhizal fungus Oidiodendron maius

Abstract

Some heavy metal tolerant fungal isolates capable of forming ericoid mycorrhiza can also confer increased metal tolerance to the host plant. One of these fungal isolates, Oidiodendron maius Zn, has been characterized and a few molecular mechanisms underlying its metal tolerant phenotype have been identified. Here, we investigate the genomic divergences between the available genome of O. maius Zn and the genomes of metal tolerant and sensitive isolates of O. maius, with the aim of identifying genes or intergenic regions possibly involved in the display of the tolerance. The resequenced genomes of 8 tolerant and 10 sensitive isolates were mapped on the reference, O. maius Zn, yielding 357 gene models from the reference that were either missing or too polymorphic to be identified in the genomes of the sensitive isolates. These regions included genes with functions related to defense mechanisms and with unknown functions. One third of the predicted gene models turned out to be highly polymorphic, including many enriched GO terms, i.e. DNA/RNA metabolism and modification, chromosome/chromatin organization, protein biosynthesis, metabolism and function, energy consumption/transfer and mitochondrion. Overall, our findings indicate that the tolerant phenotype in O. maius likely arises from multiple genetic adaptations rather than a singular mechanism.

Keywords: Oidiodendron; Comparative genomics; Metals; Mycorrhizal fungi; Polymorphism.

Fig. 1

Principal component analysis performed on the isolates’ biomass data. The first dimension separates the isolates tolerant to Cr/Ni from the others, while the second dimension separates the Zn/Cd tolerant isolates from the others. The sensitive isolates, in light blue, are separated from the two above mentioned groups. The red triangle and the blue dot represent the mean point of the group of the sensitive and tolerant isolates, respectively

Fig. 2

Phylogeny of the O. maius strains considered in this study based on the alignment of all the polymorphic positions in the full genome. The metal-sensitive isolates are in green, while the tolerant ones are in red (unrooted neighbor joining tree, with bootstrap values as node labels)

Fig. 3

Diverging genes found in diverging genome regions. Upper panel: each point represents the F_st calculated for each gene harbored in a diverging window represented in the lower panel. The genes above the red dashed line are highly polymorphic (Fst > 0.5) and those indicated by pentagons fall in the F_st-outlier windows. Lower panel: each point represents the F_st calculated for a 10 Kb genome window, with a minimum threshold of 0.5. The red dashed line indicates the value that separates the statistical outliers (see methods section), that are also indicated by a pentagon. Different colors indicate the position of the window/gene in a different genome scaffold