Biology subjects

de la Pena, M.

Publications and source records attributed to de la Pena, M..

4 recordsLinked to original sources

bioRxiv2026

A viroid-like RNA can be transmitted among different Trichoderma species affecting their antagonistic capacity

Viroids are small, circular non-coding RNAs that autonomously replicate in plants, exploiting host cellular machinery for replication and spread. Recent studies reveal that viroid-like agents can infect filamentous fungi, suggesting cross-kingdom interactions. In this study, we report the discovery and the characterization of TsvlRNA1 in Trichoderma spirale, a transmissible viroid-like RNA containing a hammerhead ribozyme in one polarity strand. Bioinformatic data, molecular validation, and reverse genetics experiments demonstrate that TsvlRNA1 is circular with an active ribozyme essential for replication. TsvlRNA1 replicates autonomously and transmits horizontally between Trichoderma species, eliciting 21-23 nt viroid-derived small RNAs consistent with RNA silencing targeting. The biocontrol capacity of Trichoderma against Rhizoctonia solani is variably modulated by TsvlRNA1, with effects ranging from positive to negative depending on host strain. In T. spirale, data suggests genotype-by-agent interactions influence antagonistic potential negatively. TsvlRNA1 transmission via horizontal routes is prevalent, and the viroid-like RNA fails to infect plant hosts experimentally. These results highlight so-far the underappreciated ecological and functional diversity of viroid-like agents in fungi, with implications for fungal biology, biocontrol, and genotype-phenotype relationships in eukaryotes. ImportanceSpecies of the fungal genus Trichoderma play a central role in sustainable agriculture by controlling fungal plant pathogens and supporting plant growth. For this reason, Trichoderma-based products represent a substantial share of the global market for microbial biofungicides. Viroids are the smallest known infectious agents, and their presence in filamentous fungi has only recently been discovered. Consequently, little is known about their biology, transmission, or interactions with fungal hosts. In this study, we describe TsvlRNA1, a viroid-like RNA associated with T. spirale, representing only the second viroid-like RNA to be biologically characterized in fungi. We show that TsvlRNA1 can influence the ability of Trichoderma to inhibit Rhizoctonia solani, a major plant pathogen, demonstrating its biological relevance. Unexpectedly, TsvlRNA1 can be transmitted between different Trichoderma species. This finding raises concerns about the possible transfer of genetic traits between fungi, including those related to fungicide resistance, with important implications for agricultural biocontrol. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/702247v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1b6de6eorg.highwire.dtl.DTLVardef@c52141org.highwire.dtl.DTLVardef@a61fcorg.highwire.dtl.DTLVardef@1a6f0a4_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Diversity and impact of single-stranded RNA viruses in Czech Heterobasidion populations

Heterobasidion annosum sensu lato comprises some of the most devastating conifer pathogens conifers. Exploring virocontrol as a potential strategy to mitigate economic losses caused by these fungi holds promise for the future. In this study, we conducted a comprehensive screening for viruses in a 98 H. annosum s.l. specimens from different regions of Czechia aiming to identify viruses inducing hypovirulence. Initial examination for dsRNA presence was followed by RNA-Seq analyses using pooled RNA libraries constructed from H. annosum and Heterobasidion parviporum, with diverse bioinformatic pipelines employed for virus discovery. Our study uncovered 25 distinct ssRNA viruses, including two ourmia-like viruses, one mitovirus, one fusarivirus, one tobamo-like virus, one cogu-like virus, one bisegmented narna-like virus and one segment of another narna-like virus, and 17 ambi-like viruses, for which hairpin and hammerhead ribozymes were detected. Coinfections of up to 10 viruses were observed in six Heterobasidion isolates, while another six harbored a single virus. 73% of the isolates analyzed by RNA-Seq were virus-free. These findings show that the virome of Heterobasidion populations in Czechia is highly diverse and differs from that in the boreal region. We further investigated the host effects of certain identified viruses through comparisons of the mycelial growth rate and proteomic analyses and found that certain tested viruses caused growth reductions of up to 22% and significant alterations in the host proteome profile. Their intraspecific transmission rates ranged from 0% to 33%. Further studies are needed to fully understand the biocontrol potential of these viruses in planta. ImportanceO_LIFirst report of a fusarivirus, a tobamo- and a cogu-like virus in Heterobasidion C_LIO_LICertain viruses caused mycelial growth reduction in H. annosum host strains C_LIO_LIViral infections lead to proteome changes in Heterobasidion C_LI

microbiology↗

bioRxiv2023

Diversity of RNA viruses in declining Mediterranean forests

Global change alters forestry habitats and facilitates the entry of new pathogens that dont share a co-evolution history with the forest, leading them into a spiral of decline. As a result, relationships between forests organisms get disbalanced. Under this scenario, RNA viruses are of particular interest, as they participate in many of such relationships thanks to their ability to infect a wide range of hosts, even from different kingdoms of life. For this reason, the study of RNA viruses is essential to understand how viral flow across different hosts might occur, and to prevent possible outbreaks of diseases in the future. In this work the RNA virus diversity found in trees, arthropods and fungi from declining Mediterranean forests is described. To this extent, three habitats (Quercus ilex, Castanea sativa and Pinus radiata) were sampled and RNAseq was performed on tree tissues, arthropods and fungi. 146 viral sequences were detected by searching for matches to conserved motifs of the RNA-dependent RNA polymerase (RdRP) using Palmscan. Up to 15 viral families were identified, with Botourmiaviridae (28.7%) and Partitiviridae (9.6%) being the most abundant. In terms of genome type, ssRNA(+) viruses were the most represented (83.5%), followed by dsRNA (15%) and two ssRNA(-) representatives. Viruses belonging to families with cross-kingdom capabilities such as Hypoviridae (1), Mitoviridae (6) and Narnaviridae (5) were also found. Distribution of viruses across ecosystems was: Q.ilex (57.5%), P.radiata (26.7%) and C.sativa (15.8%). Interestingly, two RdRP sequences had no matches in available viral databases. This work constitutes a starting point to gain insight into virus evolution and diversity occurring in forests affected by decline, as well as searching for novel viruses that might be participating in unknown infectious pathways.

microbiology↗

bioRxiv2022

Extant hybrids of RNA viruses and viroid-like elements

Earths life may have originated as self-replicating RNA. Some of the simplest current RNA replicators are RNA viruses, defined by linear RNA genomes encoding an RNA-dependent RNA polymerase (RdRP), and subviral agents with single-stranded, circular RNA genomes, such as viroids encoding paired self-cleaving ribozymes. Amongst a massive expansion of candidate viroid and viroid-like elements, we report that fungal pathogens, ambiviruses, are viroid-like elements which undergo rolling circle replication and encode their own viral RdRP, thus they are a distinct hybrid infectious agent. These findings point to a deep evolutionary history between modern RNA viruses and sub-viral elements and offer new perspectives on the evolution of primordial infectious agents, and RNA life. One-Sentence SummaryNovel infectious agents resembling self-cleaving viroid-like RNAs whilst encoding a viral RNA-dependent RNA polymerase.

microbiology↗