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Transcriptomic atlas of mushroom development highlights an independent origin of complex multicellularity

https://doi.org/10.1101/349894
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Fruiting-Body Development in Ascomycetes
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Fruiting-Body Development in Ascomycetes
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Transcriptional regulation of laccase and cellulase in relation to fruit body formation in the mycelium of Lentinula edodes on a sawdust-based substrate
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An endo-β-1,6-glucanase involved in Lentinula edodes fruiting body autolysis
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Cerato-platanins: a fungal protein family with intriguing properties and application potential
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The transcriptional regulator c2h2 accelerates mushroom formation in Agaricus bisporus
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Restriction enzyme-mediated DNA integration in Coprinus cinereus
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Characterization of the genome of the basidiomycete Schizophyllum commune
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RING-type E3 ligases: Master manipulators of E2 ubiquitin-conjugating enzymes and ubiquitination
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A bioinformatics analysis of 3400 lytic polysaccharide oxidases from family AA9
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Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi
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Plant Development Is Regulated by a Family of Auxin Receptor F Box Proteins
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How do Agaricomycetes shape their fruiting bodies? 1. Morphological aspects of development
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Copper radical oxidases and related extracellular oxidoreductases of wood-decay Agaricomycetes
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Mushrooms: A rich source of the antioxidants ergothioneine and glutathione
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Le.MAPK and its interacting partner, Le.DRMIP, in fruiting body development in Lentinula edodes
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A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages
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Basidiospore germination in some mycorrhiza-forming hymenomycetes
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Reliability Measures for Membrane Protein Topology Prediction Algorithms
inferredcites →https://doi.org/10.1016/s0953-7562(09)81121-0openalex-snapshot
Glycogen metabolism in relation to fruit body maturation in Coprinus cinereus
inferredcites →https://doi.org/10.1017/s0953756298007552openalex-snapshot
Hydrophobins line air channels in fruiting bodies of Schizophyllum commune and Agaricus bisporus
inferredcites →https://doi.org/10.1038/nature09016openalex-snapshot
The Ectocarpus genome and the independent evolution of multicellularity in brown algae
inferredcites →https://doi.org/10.1038/nbt.1621openalex-snapshot
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
inferredcites →https://doi.org/10.1038/nbt.1643openalex-snapshot
Genome sequence of the model mushroom Schizophyllum commune
inferredcites →https://doi.org/10.1038/ncomms14444openalex-snapshot
Innovation and constraint leading to complex multicellularity in the Ascomycota
inferredcites →https://doi.org/10.1038/ng.3223openalex-snapshot
Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists
inferredcites →https://doi.org/10.1038/nmeth.1701openalex-snapshot
SignalP 4.0: discriminating signal peptides from transmembrane regions
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The origin of Metazoa: a unicellular perspective
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Unearthing the roots of ectomycorrhizal symbioses
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Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria
inferredcites →https://doi.org/10.1038/s41598-017-00483-3openalex-snapshot
Transcription factors of Schizophyllum commune involved in mushroom formation and modulation of vegetative growth
inferredcites →https://doi.org/10.1038/s41598-017-15112-2openalex-snapshot
A role for small secreted proteins (SSPs) in a saprophytic fungal lifestyle: Ligninolytic enzyme regulation in Pleurotus ostreatus
inferredcites →https://doi.org/10.1038/srep33640openalex-snapshot
Schizophyllum commune has an extensive and functional alternative splicing repertoire
inferredcites →https://doi.org/10.1039/b702155kopenalex-snapshot
Fungal photoreceptors: sensory molecules for fungal development and behaviour
inferredcites →https://doi.org/10.1073/pnas.0812043106openalex-snapshot
Evolution of F-box genes in plants: Different modes of sequence divergence and their relationships with functional diversification
inferredcites →https://doi.org/10.1073/pnas.1003391107openalex-snapshot
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea ( Coprinus cinereus )
inferredcites →https://doi.org/10.1073/pnas.1017351108openalex-snapshot
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
inferredcites →https://doi.org/10.1073/pnas.1308173110openalex-snapshot
Fungal adhesion protein guides community behaviors and autoinduction in a paracrine manner
inferredcites →https://doi.org/10.1074/jbc.m109.076075openalex-snapshot
Identification, Characterization, and Biosynthesis of a Novel N-Glycan Modification in the Fruiting Body of the Basidiomycete Coprinopsis cinerea
inferredcites →https://doi.org/10.1080/00275514.1993.12026294openalex-snapshot
Hymenophore Development and Evolution in Lentinus
inferredcites →https://doi.org/10.1093/bioinformatics/bti1022openalex-snapshot
Clustering short time series gene expression data
inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot
edgeR : a Bioconductor package for differential expression analysis of digital gene expression data
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/molbev/msv012openalex-snapshot
Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis
inferredcites →https://doi.org/10.1093/nar/30.7.1575openalex-snapshot
An efficient algorithm for large-scale detection of protein families
inferredcites →https://doi.org/10.1093/nar/gkm259openalex-snapshot
WoLF PSORT: protein localization predictor
inferredcites →https://doi.org/10.1093/nar/gkq256openalex-snapshot
Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing
inferredcites →https://doi.org/10.1093/nar/gkt1178openalex-snapshot
The carbohydrate-active enzymes database (CAZy) in 2013
inferredcites →https://doi.org/10.1093/nar/gkt1183openalex-snapshot
MycoCosm portal: gearing up for 1000 fungal genomes
inferredcites →https://doi.org/10.1093/nar/gkv007openalex-snapshot
limma powers differential expression analyses for RNA-sequencing and microarray studies
inferredcites →https://doi.org/10.1098/rstb.2012.0003openalex-snapshot
Diversity, classification and function of the plant protein kinase superfamily
inferredcites →https://doi.org/10.1099/mic.0.000143openalex-snapshot
Purification, characterization and synergism in autolysis of a group of 1,3-β-glucan hydrolases from the pilei of Coprinopsis cinerea fruiting bodies
inferredcites →https://doi.org/10.1104/pp.106.076679openalex-snapshot
Lentinula edodes tlg1 Encodes a Thaumatin-Like Protein That Is Involved in Lentinan Degradation and Fruiting Body Senescence
inferredcites →https://doi.org/10.1111/brv.12418openalex-snapshot
Complex multicellularity in fungi: evolutionary convergence, single origin, or both?
inferredcites →https://doi.org/10.1111/j.1365-2958.2011.07776.xopenalex-snapshot
Transcription factor genes of Schizophyllum commune involved in regulation of mushroom formation
inferredcites →https://doi.org/10.1126/science.1075762openalex-snapshot
The Protein Kinase Complement of the Human Genome
inferredcites →https://doi.org/10.1126/stke.2001.113.re22openalex-snapshot
Plant Receptor-Like Kinase Gene Family: Diversity, Function, and Signaling
inferredcites →https://doi.org/10.1128/aem.05581-11openalex-snapshot
Endo-β-1,3-Glucanase GLU1, from the Fruiting Body of Lentinula edodes, Belongs to a New Glycoside Hydrolase Family
inferredcites →https://doi.org/10.1128/aem.65.2.389-395.1999openalex-snapshot
Novel Interaction between Laccase and Cellobiose Dehydrogenase during Pigment Synthesis in the White Rot Fungus Pycnoporus cinnabarinus
inferredcites →https://doi.org/10.1128/mmbr.00035-14openalex-snapshot
Plant-Polysaccharide-Degrading Enzymes from Basidiomycetes
inferredcites →https://doi.org/10.1128/mmbr.00037-06openalex-snapshot
A Biochemical Guide to Yeast Adhesins: Glycoproteins for Social and Antisocial Occasions
inferredcites →https://doi.org/10.1128/mmbr.64.2.316-353.2000openalex-snapshot
Life History and Developmental Processes in the BasidiomyceteCoprinus cinereus
inferredcites →https://doi.org/10.1146/annurev.earth.031208.100209openalex-snapshot
The Multiple Origins of Complex Multicellularity
inferredcites →https://doi.org/10.1146/annurev.phyto.112408.132637openalex-snapshot
Fungal Effector Proteins
inferredcites →https://doi.org/10.1186/1471-2105-7-191openalex-snapshot
STEM: a tool for the analysis of short time series gene expression data
inferredcites →https://doi.org/10.1186/1471-2105-9-392openalex-snapshot
PredGPI: a GPI-anchor predictor
inferredcites →https://doi.org/10.1186/1471-2164-11-133openalex-snapshot
Comparative analysis of fungal protein kinases and associated domains
inferredcites →https://doi.org/10.1186/1471-2164-11-663openalex-snapshot
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads
inferredcites →https://doi.org/10.1186/1471-2164-15-492openalex-snapshot
Comparative transcriptomics of the model mushroom Coprinopsis cinerea reveals tissue-specific armories and a conserved circuitry for sexual development
inferredcites →https://doi.org/10.1186/1754-6834-6-41openalex-snapshot
Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes
inferredcites →https://doi.org/10.1186/gb-2010-11-3-r25openalex-snapshot
A scaling normalization method for differential expression analysis of RNA-seq data
inferredcites →https://doi.org/10.1186/s12864-015-1251-8openalex-snapshot
Deep RNA sequencing reveals a high frequency of alternative splicing events in the fungus Trichoderma longibrachiatum
inferredcites →https://doi.org/10.1242/dev.015842openalex-snapshot
An Arabidopsis F-box protein acts as a transcriptional co-factor to regulate floral development
inferredcites →https://doi.org/10.1271/bbb.80213openalex-snapshot
Purification and Characterization of a Novel Exo-β-1,3-1,6-glucanase from the Fruiting Body of the Edible Mushroom Enoki (Flammulina velutipes)
inferredcites →https://doi.org/10.1371/annotation/ed5d46f6-3442-4a89-a505-78befd507436openalex-snapshot
Correction: Plasticity of the β-Trefoil Protein Fold in the Recognition and Control of Invertebrate Predators and Parasites by a Fungal Defence System
inferredcites →https://doi.org/10.1371/journal.pone.0089813openalex-snapshot
Identification of a Fungi-Specific Lineage of Protein Kinases Closely Related to Tyrosine Kinases
inferredcites →https://doi.org/10.1371/journal.pone.0122296openalex-snapshot
A Novel Expansin Protein from the White-Rot Fungus Schizophyllum commune
inferredcites →https://doi.org/10.1371/journal.pone.0132628openalex-snapshot
Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing
inferredcites →https://doi.org/10.1371/journal.pone.0141586openalex-snapshot
Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea
inferredcites →https://doi.org/10.1371/journal.pone.0160336openalex-snapshot
Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation
inferredcites →https://doi.org/10.1371/journal.ppat.1002700openalex-snapshot
Hydrophobins—Unique Fungal Proteins
inferredcites →https://doi.org/10.1371/journal.ppat.1002706openalex-snapshot
Plasticity of the β-Trefoil Protein Fold in the Recognition and Control of Invertebrate Predators and Parasites by a Fungal Defence System
inferredcites →https://doi.org/10.2307/3760704openalex-snapshot
Hymenophore Development and Evolution in Lentinus
inferredcites →https://doi.org/10.3389/fgene.2017.00053openalex-snapshot
Transcription Factors in Fungi: TFome Dynamics, Three Major Families, and Dual-Specificity TFs
inferredcites →https://doi.org/10.3389/fmicb.2015.01278openalex-snapshot
Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins
inferredcites →https://doi.org/10.3390/molecules20058144openalex-snapshot
Hitting the Sweet Spot: Glycans as Targets of Fungal Defense Effector Proteins
inferredcites →https://doi.org/10.5604/17331331.1215609openalex-snapshot
Complex Biochemical Analysis of Fruiting Bodies from Newly Isolated Polish Flammulina velutipes Strains
inferredcites →https://doi.org/10.5941/myco.2011.39.4.243openalex-snapshot
The Ubiquitin-Proteasome System and F-box Proteins in Pathogenic Fungi

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Aspergillus nidulans in the post-genomic era: a top-model filamentous fungus for the study of signaling and homeostasis mechanisms
inferred← citeshttps://doi.org/10.1016/j.fbr.2020.07.002openalex-snapshot
Fungi took a unique evolutionary route to multicellularity: Seven key challenges for fungal multicellular life
inferred← citeshttps://doi.org/10.1017/9781108776387.013openalex-snapshot
Development and Morphogenesis
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Comparative genomics reveals the origin of fungal hyphae and multicellularity
inferred← citeshttps://doi.org/10.1038/s41598-019-44133-2openalex-snapshot
High-throughput targeted gene deletion in the model mushroom Schizophyllum commune using pre-assembled Cas9 ribonucleoproteins
inferred← citeshttps://doi.org/10.1093/molbev/msaa077openalex-snapshot
Unmatched Level of Molecular Convergence among Deeply Divergent Complex Multicellular Fungi
inferred← citeshttps://doi.org/10.1101/546531openalex-snapshot
Comparative genomics reveals the origin of fungal hyphae and multicellularity
inferred← citeshttps://doi.org/10.1101/550103openalex-snapshot
The genome of Auriculariopsis ampla sheds light on fruiting body development and wood-decay of bark-inhabiting fungi
inferred← citeshttps://doi.org/10.1111/brv.12605openalex-snapshot
Fungal evolution: cellular, genomic and metabolic complexity
inferred← citeshttps://doi.org/10.1155/2021/6656365openalex-snapshot
[Retracted] Genome Assembly and Analyses of the Macrofungus Macrocybe gigantea
inferred← citeshttps://doi.org/10.3390/genes9120570openalex-snapshot
UrdA Controls Secondary Metabolite Production and the Balance between Asexual and Sexual Development in Aspergillus nidulans
inferred← citeshttps://doi.org/10.3390/jof11050346openalex-snapshot
Whole-Genome Characterization of Inonotus hispidus from Ulmus macrocarpa and Its Comparative Genomics with Strains from Morus alba and Acer truncatum
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