Somatic transposition and meiotically driven elimination of an active helitron family inPleurotus ostreatus

Abstract

Helitrons constitute a superfamily of DNA transposons that were discovered in silico and are widespread in most eukaryotic genomes. They are postulated to mobilize through a “rolling-circle” mechanism, but the experimental evidence of their transposition has been described only recently. Here, we present the inheritance patterns of HELPO1 and HELPO2 helitron families in meiotically derived progeny of the basidiomycete Pleurotus ostreatus. We found distorted segregation patterns of HELPO2 helitrons that led to a strong under-representation of these elements in the progeny. Further investigation of HELPO2 flanking sites showed that gene conversion may contribute to the elimination of such repetitive elements in meiosis, favouring the presence of HELPO2 vacant loci. In addition, the analysis of HELPO2 content in a reconstructed pedigree of subclones maintained under different culture conditions revealed an event of helitron somatic transposition. Additional analyses of genome and transcriptome data indicated that P. ostreatus carries active RNAi machinery that could be involved in the control of transposable element proliferation. Our results provide the first evidence of helitron mobilization in the fungal kingdom and highlight the interaction between genome defence mechanisms and invasive DNA.

Transposon-associated epigenetic silencing duringPleurotus ostreatuslife cycle

“… 30 Also, the plant-pathogen Puccinia striiformis produces 20–22 nt sRNA likely involved in PTGS. 33 In this sense, P. ostreatus contains a highly conserved, transcriptionally active RNAi machinery composed of Argonaute, Dicer and RNA-dependent RNA polymerase proteins 36 (18 proteins sharing 93–100% similarity between PC9 and PC15 strains).…”

“…S1 ). N001-HyB is a dikaryotic strain regenerated ad hoc by mating PC9 and PC15 in 2014, 36 which contains the same genetic complement as N001. All strains were cultured in Erlenmeyer flasks containing 200 ml of Malt Extract (ME, 20 g/l) in the dark, at 24°C under orbital shaking (125 rpm).…”

“… 35 Regarding the potential RNAi activity of P. ostreatus , preliminary data suggests the presence of the RNAi machinery core, which has been detected in silico by screening for Neurospora MSUD and quelling orthologous proteins. 36 Using high-throughput sequencing, we describe the genome-wide epigenetic (DNA methylation and small RNAs) and transcriptional (mRNA) profiles of two compatible P. ostreatus monokaryons as well as dikaryons at different stages during fruit body development. Our results support the evidence of strain-specific DNA methylation and small RNA production primarily involved in the repression of transposons activity.…”

Helitron’s Periodicities Identification in C.Elegans based on the Smoothed Spectral Analysis and the Frequency Chaos Game Signal Coding

“…They were discovered by in silico genomesequence analysis. Newly discovered in all eukaryotic genomes [4]- [7], helitrons have shown a remarkable ability to capture gene sequences [8], [9]. In fact, on a large scale, these elements are suggested to duplicate and shuffle exon domains [10]- [12].…”

“…Helitrons are present in various organisms: like plants (such as corn, maize, rice, Arabidopsis Thaliana) [13], nematodes (such as the worm Caenorhabditis elegans) [14], fungus [15], [16] and animals [17] (such as lucifugus [8] and specifically in the vertebrates genomes like the fishes Danio rerio and Sphoeroides nephelus [16]). Approximately, the helitron DNA constitutes at most 2% of the A. thaliana, the C.elegans and the maize genomes [12], [14], [18] and 4.23% of the silkworm genome [19].…”