Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi

Abstract

Background: Helitrons are class-II eukaryotic transposons that transpose via a rolling circle mechanism. Due to their ability to capture and mobilize gene fragments, they play an important role in the evolution of their host genomes. We have used a bioinformatics approach for the identification of helitrons in two Pleurotus ostreatus genomes using de novo detection and homology-based searching. We have analyzed the presence of helitron-captured genes as well as the expansion of helitron-specific helicases in fungi and performed a phylogenetic analysis of their conserved domains with other representative eukaryotic species.

Results: Our results show the presence of two helitron families in P. ostreatus that disrupt gene colinearity and cause a lack of synteny between their genomes. Both putative autonomous and non-autonomous helitrons were transcriptionally active, and some of them carried highly expressed captured genes of unknown origin and function. In addition, both families contained eukaryotic, bacterial and viral domains within the helitron's boundaries. A phylogenetic reconstruction of RepHel helicases using the Helitron-like and PIF1-like helicase conserved domains revealed a polyphyletic origin for eukaryotic helitrons.

Conclusion: P. ostreatus helitrons display features similar to other eukaryotic helitrons and do not tend to capture host genes or gene fragments. The occurrence of genes probably captured from other hosts inside the helitrons boundaries pose the hypothesis that an ancient horizontal transfer mechanism could have taken place. The viral domains found in some of these genes and the polyphyletic origin of RepHel helicases in the eukaryotic kingdom suggests that virus could have played a role in a putative lateral transfer of helitrons within the eukaryotic kingdom. The high similarity of some helitrons, along with the transcriptional activity of its RepHel helicases indicates that these elements are still active in the genome of P. ostreatus.

Figure 1

Pipeline for helitron identification in the P. ostreatus PC9 and PC15 genomes.

Figure 2

Structural and enzymatic features of the P. ostreatus helitron families. Alignments of the 5′ and 3′ boundaries of the helitron families HELPO1 (A) and HELPO2 (C). Schematic representation of the structural hallmarks, coding features and conserved domains (CDD, cutoff E-value <0.01) of the different elements belonging to the HELPO1 (B) and HELPO2 (D) families.

Figure 3

Helitrons break the synteny between the P. ostreatus PC15 and PC9 genomes. The distribution of helitrons in the chromosomes of the dikaryotic strain N001 is shown in A (PC15 elements are shown in blue and in PC9 elements are shown in red). Truncated elements are marked with a ‘*’. An ACT [32] comparison of the squared region between PC15 and PC9 is shown in B. The lack of gene colinearity between PC9 and PC15 in the squared region of chromosomeVII is shown in C (coordinates: 1,528,715-1,479,715). In the synteny plot, coding regions are represented in purple, and inter-genic regions in pink. Arrows labeled IR represent the inverted repeats found in a 37.2 kb region duplicated in PC15 and absent in PC9 genome. Blue arrows underneath synteny plot represent predicted genes.

Figure 4

Helitron length polymorphisms in allelic copies of the HELPO1.3 subfamily. Regions in red are highly conserved. Blue triangles represent inverted repeats, and the black square represents a satellite sequence (the number of repeats is shown in parentheses). Empty arrows represent predicted ORFs.

Figure 5

Transcriptional profiles of helitron-specific helicases and captured genes. Five representative RNA-seq profiles of the helitron families and subfamilies (A to E). The gene models predicted by JGI are shown in blue. Empty arrows represent manually annotated genes. The expression of the N00, PC9 and PC15 RepHel helicases and captured genes by RT-qPCR is shown in F. The Y axis of F represents the arbitrary units (RQ ) relative to the expression of the reference gene pep.

Figure 6

Phylogenetic reconstruction of the eukaryotic Pif1-like helicase domain. Green represents helitrons from the Plant kingdom, yellow from the Animal kingdom, and blue from the Fungal kingdom. Light blue represents the phylum Basidiomycota and dark blue represents the phylum Ascomycota.