Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes DOI Creative Commons
Kerrigan B. Gilbert, Emily Holcomb, Robyn L. Allscheid

et al.

PLoS ONE, Journal Year: 2019, Volume and Issue: 14(7), P. e0219207 - e0219207

Published: July 24, 2019

The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature mycoviral infections focused study primarily pathogenic and/or economically important fungi. As most that are known infect possess either single-stranded or double-stranded genomes, transcriptomic data provides opportunity query for diverse fungal samples without any a priori knowledge virus infection. Here we describe systematic survey all datasets from belonging subphylum Pezizomycotina. Using simple but effective computational pipeline uses reads discarded during normal RNA-seq analyses, followed by identification viral RNA-dependent polymerase (RdRP) motif de novo assembled contigs, 59 44 different were identified. Among identified, 88% determined be new species 68% are, our knowledge, first described species. Comprehensive analyses both nucleotide inferred protein sequences characterize phylogenetic relationships between these set support classification up four families two genera. Thus results provide deeper understanding scope while also increasing hosts. Further, this demonstrates suitability analyzing facilitate rapid discovery viruses.

Language: Английский

Role of Arbuscular Mycorrhizal Fungi in Regulating Growth, Enhancing Productivity, and Potentially Influencing Ecosystems under Abiotic and Biotic Stresses DOI Creative Commons
Abdul Wahab, Murad Muhammad, Asma Munir

et al.

Plants, Journal Year: 2023, Volume and Issue: 12(17), P. 3102 - 3102

Published: Aug. 29, 2023

Arbuscular mycorrhizal fungi (AMF) form symbiotic relationships with the roots of nearly all land-dwelling plants, increasing growth and productivity, especially during abiotic stress. AMF improves plant development by improving nutrient acquisition, such as phosphorus, water, mineral uptake. tolerance resilience to stressors drought, salt, heavy metal toxicity. These benefits come from arbuscular interface, which lets fungal partners exchange nutrients, signalling molecules, protective chemical compounds. Plants' antioxidant defence systems, osmotic adjustment, hormone regulation are also affected infestation. responses promote performance, photosynthetic efficiency, biomass production in stress conditions. As a result its positive effects on soil structure, cycling, carbon sequestration, contributes maintenance resilient ecosystems. The AMFs ecological stability species- environment-specific. AMF's growth-regulating, productivity-enhancing role alleviation under is reviewed. More research needed understand molecular mechanisms that drive AMF-plant interactions their stresses. triggers plants' morphological, physiological, Water development, improved symbiosis. In colonization modulates defense mechanisms, hormonal regulation. circumstances. AMF-mediated enhanced essential oils (EOs), superoxide dismutase (SOD), peroxidase (POD), ascorbate (APX), hydrogen peroxide (H2O2), malondialdehyde (MDA), phosphorus (P). Understanding how increases adaptation reduces will help sustain agriculture, ecosystem management, climate change mitigation. have gained prominence agriculture due multifaceted roles promoting health productivity. This review delves into influences absorption, challenging environmental We further explore extent bolsters

Language: Английский

Citations

186

Molecular dialogues between Trichoderma and roots: Role of the fungal secretome DOI
Artemio Mendoza‐Mendoza, Rinat Zaid,

Robert Lawry

et al.

Fungal Biology Reviews, Journal Year: 2018, Volume and Issue: 32(2), P. 62 - 85

Published: Jan. 19, 2018

Language: Английский

Citations

176

Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi DOI Creative Commons
Dániel G. Knapp,

Julianna B. Németh,

Kerrie Barry

et al.

Scientific Reports, Journal Year: 2018, Volume and Issue: 8(1)

Published: April 16, 2018

Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes two common DSE semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced analyzed another 32 ascomycetes different lifestyles. (Helotiales) P. (Pleosporales) have 70.46 Mb 54.99 22,766 18,750 gene models, respectively. The majority DSE-specific protein clusters lack functional annotation no similarity to characterized proteins, implying that they evolved unique genetic innovations. Both possess an expanded number carbohydrate active enzymes (CAZymes), including plant cell wall degrading (PCWDEs). Those similar in three other DSE, contributed signal for separation principal component analyses CAZymes, indicating shared genomic traits fungi. Number secreted proteases lipases, aquaporins, genes linked melanin synthesis also relatively high our In spite certain similarities between we observed low levels convergence their family evolution. This suggests that, despite originating from same habitat, these along evolutionary trajectories display considerable differences within lifestyle.

Language: Английский

Citations

173

The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response DOI Creative Commons
Omri M. Finkel, Isai Salas-González, Gabriel Castrillo

et al.

PLoS Biology, Journal Year: 2019, Volume and Issue: 17(11), P. e3000534 - e3000534

Published: Nov. 13, 2019

Phosphate starvation response (PSR) in nonmycorrhizal plants comprises transcriptional reprogramming resulting severe physiological changes to the roots and shoots repression of plant immunity. Thus, plant-colonizing microorganisms-the microbiota-are exposed direct influence by soil's phosphorus (P) content itself as well indirect effects soil P on microbial niches shaped plant. The individual contribution these factors microbiota assembly remains unknown. To disentangle effects, we planted PSR-deficient Arabidopsis mutants a long-term managed gradient compared composition their shoot root wild-type across different concentrations. PSR-deficiency had larger effect both bacterial fungal plant-associated than concentrations shoots. dissect plant-microbe interactions under variable conditions, conducted reconstitution experiment. Using 185-member synthetic community (SynCom) wide concentration an agar matrix, demonstrated shift bacteria from neutral or positive interaction negative one, measured rosette size. This phenotypic was accompanied composition: genus Burkholderia specifically enriched tissue starvation. Through drop-out experiment, that absence SynCom, accumulated higher ortophosphate (Pi) levels colonized with full SynCom but only Pi conditions. Therefore, Pi-stressed are susceptible colonization latent opportunistic competitors found within microbiome, thus exacerbating plant's

Language: Английский

Citations

167

Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes DOI Creative Commons
Kerrigan B. Gilbert, Emily Holcomb, Robyn L. Allscheid

et al.

PLoS ONE, Journal Year: 2019, Volume and Issue: 14(7), P. e0219207 - e0219207

Published: July 24, 2019

The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature mycoviral infections focused study primarily pathogenic and/or economically important fungi. As most that are known infect possess either single-stranded or double-stranded genomes, transcriptomic data provides opportunity query for diverse fungal samples without any a priori knowledge virus infection. Here we describe systematic survey all datasets from belonging subphylum Pezizomycotina. Using simple but effective computational pipeline uses reads discarded during normal RNA-seq analyses, followed by identification viral RNA-dependent polymerase (RdRP) motif de novo assembled contigs, 59 44 different were identified. Among identified, 88% determined be new species 68% are, our knowledge, first described species. Comprehensive analyses both nucleotide inferred protein sequences characterize phylogenetic relationships between these set support classification up four families two genera. Thus results provide deeper understanding scope while also increasing hosts. Further, this demonstrates suitability analyzing facilitate rapid discovery viruses.

Language: Английский

Citations

166