ArticleFrontiers in microbiology2016
Visual Comparative Omics of Fungi for Plant Biomass Deconstruction.
Article in Frontiers in microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Functional proteomic analysis of Streptomyces sp. F-3 reveals its potential to effectively degrade waste-yeast.Applied microbiology and biotechnology · 2025Article
- Methionine oxidation of carbohydrate-active enzymes during white-rot wood decay.Applied and environmental microbiology · 2024Article
- OMICS and Other Advanced Technologies in Mycological Applications.Journal of fungi (Basel, Switzerland) · 2023Review
- Speciation Underpinned by Unexpected Molecular Diversity in the Mycorrhizal Fungal Genus Pisolithus.Molecular biology and evolution · 2023Article
- The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley.The ISME journal · 2022Article
- Hybrid Assembly Improves Genome Quality and Completeness ofJournal of fungi (Basel, Switzerland) · 2022Article
- Activity-based protein profiling reveals dynamic substrate-specific cellulase secretion by saprotrophic basidiomycetes.Biotechnology for biofuels and bioproducts · 2022Article
- A Transcriptomic Atlas of the Ectomycorrhizal FungusMicroorganisms · 2021Article
- Harnessing microbial wealth for lignocellulose biomass valorization through secretomics: a review.Biotechnology for biofuels · 2021Review
- Evolution of Fungal Carbohydrate-Active Enzyme Portfolios and Adaptation to Plant Cell-Wall Polymers.Journal of fungi (Basel, Switzerland) · 2021Review
- Desert truffle genomes reveal their reproductive modes and new insights into plant-fungal interaction and ectendomycorrhizal lifestyle.The New phytologist · 2021Article
- Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus.DNA research : an international journal for rapid publication of reports on genes and genomes · 2020Article
- Insights into the cellulose degradation mechanism of the thermophilic fungusBiotechnology for biofuels · 2020Article
- Insights into an unusual Auxiliary Activity 9 family member lacking the histidine brace motif of lytic polysaccharide monooxygenases.The Journal of biological chemistry · 2019Article
- Genomic Analyses Provide Insights Into the Evolutionary History and Genetic Diversity ofFrontiers in microbiology · 2019Article
- Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce.BMC genomics · 2018Article
- Lytic xylan oxidases from wood-decay fungi unlock biomass degradation.Nature chemical biology · 2018Article
- Lavender- and lavandin-distilled straws: an untapped feedstock with great potential for the production of high-added value compounds and fungal enzymes.Biotechnology for biofuels · 2018Article
- Integrative visual omics of the white-rot fungusBiotechnology for biofuels · 2018Article
- The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown.PloS one · 2017Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Wood-decay fungi contain the cellular mechanisms to decompose such plant cell wall components as cellulose, hemicellulose, and lignin. A multi-omics approach to the comparative analysis of wood-decay fungi gives not only new insights into their strategies for decomposing recalcitrant plant biomass, but also an understanding of how to exploit these mechanisms for biotechnological applications. We have developed an analytical workflow, Applied Biomass Conversion Design for Efficient Fungal Green Technology (ABCDEFGT), to simplify the analysis and interpretation of transcriptomic and secretomic data. ABCDEFGT utilizes self-organizing maps for grouping genes with similar transcription patterns, and an overlay with secreted proteins. The key feature of ABCDEFGT is simple graphic outputs of genome-wide transcriptomic and secretomic topographies, which enables visual inspection without a priori of the omics data and facilitates discoveries of co-regulated genes and proteins. Genome-wide omics landscapes were built with the newly sequenced fungal species Pycnoporus coccineus, Pycnoporus sanguineus, and Pycnoporus cinnabarinus grown on various carbon sources. Integration of the post-genomic data revealed a global overlap, confirming the pertinence of the genome-wide approach. ABCDEFGT was evaluated by comparison with the latest clustering method for ease of output interpretation, and ABCDEFGT gave a better biological representation of fungal behaviors. The genome-wide multi-omics strategy allowed us to determine the potential synergy of particular enzymes decomposing cellulose, hemicellulose, and lignin such as Lytic Polysaccharide Monooxygenases, modular enzymes associated with a cellulose binding module1, and Class II Peroxidase isoforms co-regulated with oxido-reductases. Overall, ABCDEFGT was capable of visualizing genome-wide transcriptional and secretomic profiles for intuitive interpretations and is suitable for exploration of newly-sequenced organisms.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.