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Haplotype-Resolved Genome Analyses Reveal Genetically Distinct Nuclei within a Commercial Cultivar of Lentinula edodes

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What this work says

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

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Using Repeat Masker to Identify Repetitive Elements in Genomic Sequences
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Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences
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Prediction of complete gene structures in human genomic DNA
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The Fungal Cell Wall
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Growth, Differentiation and Sexuality
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Monokaryotization by protoplasting heterothallic species of edible mushrooms
inferredcites →https://doi.org/10.1007/s12275-018-8030-6openalex-snapshot
Diversity of A mating type in Lentinula edodes and mating type preference in the cultivated strains
inferredcites →https://doi.org/10.1007/s13238-013-3037-6openalex-snapshot
Co-evolution of plant LTR-retrotransposons and their host genomes
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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
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Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
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The Genomic Impact of European Colonization of the Americas
inferredcites →https://doi.org/10.1016/j.fgb.2016.06.001openalex-snapshot
A detailed analysis of the recombination landscape of the button mushroom Agaricus bisporus var. bisporus
inferredcites →https://doi.org/10.1016/j.fgb.2021.103614openalex-snapshot
Comparative transcriptome analysis of abnormal cap and healthy fruiting bodies of the edible mushroom Lentinula edodes
inferredcites →https://doi.org/10.1016/j.funbio.2019.12.008openalex-snapshot
Characterization of brown film formed by Lentinula edodes
inferredcites →https://doi.org/10.1016/j.gene.2017.10.061openalex-snapshot
De novo transcriptomic analysis during Lentinula edodes fruiting body growth
inferredcites →https://doi.org/10.1016/j.jare.2021.09.008openalex-snapshot
Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes
inferredcites →https://doi.org/10.1016/j.jbiotec.2016.02.032openalex-snapshot
Whole genome de novo sequencing and genome annotation of the world popular cultivated edible mushroom, Lentinula edodes
inferredcites →https://doi.org/10.1016/j.jgg.2021.01.002openalex-snapshot
Identifying a melanogenesis-related candidate gene by a high-quality genome assembly and population diversity analysis in Hypsizygus marmoreus
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Hi–C: A comprehensive technique to capture the conformation of genomes
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1016/s0168-9525(00)02093-xopenalex-snapshot
Repbase Update: a database and an electronic journal of repetitive elements
inferredcites →https://doi.org/10.1038/75556openalex-snapshot
Gene Ontology: tool for the unification of biology
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.2727openalex-snapshot
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
inferredcites →https://doi.org/10.1038/s41588-020-0699-xopenalex-snapshot
Haplotype-resolved genome analyses of a heterozygous diploid potato
inferredcites →https://doi.org/10.1073/pnas.1721381115openalex-snapshot
Nucleus-specific expression in the multinuclear mushroom-forming fungus Agaricus bisporus reveals different nuclear regulatory programs
inferredcites →https://doi.org/10.1073/pnas.1817822116openalex-snapshot
Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi
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De novo identification of repeat families in large genomes
inferredcites →https://doi.org/10.1093/bioinformatics/btp120openalex-snapshot
TopHat: discovering splice junctions with RNA-Seq
inferredcites →https://doi.org/10.1093/bioinformatics/btp157openalex-snapshot
Infernal 1.0: inference of RNA alignments
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InterProScan 5: genome-scale protein function classification
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Genomic analyses of two Italian oyster mushroom Pleurotus pulmonarius strains
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Correlation of Genetic and Physical Maps at the A Mating-Type Locus of Coprinus cinereus
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THE STRUCTURE OF THE A MATING TYPE LOCUS IN COPRINUS LAGOPUS
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/25.5.955openalex-snapshot
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
inferredcites →https://doi.org/10.1093/nar/27.2.573openalex-snapshot
Tandem repeats finder: a program to analyze DNA sequences
inferredcites →https://doi.org/10.1093/nar/30.1.276openalex-snapshot
The Pfam Protein Families Database
inferredcites →https://doi.org/10.1093/nar/gkg095openalex-snapshot
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
inferredcites →https://doi.org/10.1093/nar/gkh379openalex-snapshot
AUGUSTUS: a web server for gene finding in eukaryotes
inferredcites →https://doi.org/10.1093/nar/gki458openalex-snapshot
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints
inferredcites →https://doi.org/10.1093/nar/gkl200openalex-snapshot
AUGUSTUS: ab initio prediction of alternative transcripts
inferredcites →https://doi.org/10.1093/nar/gkm286openalex-snapshot
LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons
inferredcites →https://doi.org/10.1093/nar/gkm960openalex-snapshot
The Pfam protein families database
inferredcites →https://doi.org/10.1093/nar/gkr1293openalex-snapshot
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
inferredcites →https://doi.org/10.1093/nar/gkr988openalex-snapshot
KEGG for integration and interpretation of large-scale molecular data sets
inferredcites →https://doi.org/10.1093/nar/gku1243openalex-snapshot
The InterPro protein families database: the classification resource after 15 years
inferredcites →https://doi.org/10.1094/phyto-77-669openalex-snapshot
Potential Applications of Random DNA Probes and Restriction Fragment Length Polymorphisms in the Taxonomy of the Fusaria
inferredcites →https://doi.org/10.1101/gr.263566.120openalex-snapshot
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
inferredcites →https://doi.org/10.1101/gr.6743907openalex-snapshot
MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
inferredcites →https://doi.org/10.1101/gr.88502openalex-snapshot
Automated De Novo Identification of Repeat Sequence Families in Sequenced Genomes
inferredcites →https://doi.org/10.1111/ahg.12364openalex-snapshot
Improved assembly and variant detection of a haploid human genome using single‐molecule, high‐fidelity long reads
inferredcites →https://doi.org/10.1128/microbiolspec.funk-0046-2016openalex-snapshot
Fungal Sex: The Basidiomycota
inferredcites →https://doi.org/10.1142/9789812799623_0012openalex-snapshot
SCORING PAIRWISE GENOMIC SEQUENCE ALIGNMENTS
inferredcites →https://doi.org/10.1155/2008/619832openalex-snapshot
Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics
inferredcites →https://doi.org/10.1159/000084979openalex-snapshot
Repbase Update, a database of eukaryotic repetitive elements
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2105-14-33openalex-snapshot
HTQC: a fast quality control toolkit for Illumina sequencing data
inferredcites →https://doi.org/10.1186/1471-2105-6-31openalex-snapshot
Automated generation of heuristics for biological sequence comparison
inferredcites →https://doi.org/10.1186/gb-2004-5-2-r12openalex-snapshot
Versatile and open software for comparing large genomes
inferredcites →https://doi.org/10.1371/journal.pone.0005524openalex-snapshot
Chromosomal Rearrangements between Serotype A and D Strains in Cryptococcus neoformans
inferredcites →https://doi.org/10.1371/journal.pone.0022249openalex-snapshot
Comparative Genomics of the Mating-Type Loci of the Mushroom Flammulina velutipes Reveals Widespread Synteny and Recent Inversions
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/10.1534/g3.116.034637openalex-snapshot
Advances in Understanding Mating Type Gene Organization in the Mushroom-Forming FungusFlammulina velutipes
inferredcites →https://doi.org/10.24465/msb.27.3_93openalex-snapshot
Three-dimensional analysis of ectomycorrhizas formed in Pinus thunbergii roots inoculated with Rhizopogon roseolus
inferredcites →https://doi.org/10.3389/fmicb.2019.01987openalex-snapshot
Variations in Nuclear Number and Size in Vegetative Hyphae of the Edible Mushroom Lentinula edodes
inferredcites →https://doi.org/10.3390/jof6040269openalex-snapshot
Immunomodulatory Effects of Edible and Medicinal Mushrooms and Their Bioactive Immunoregulatory Products

What points at this work

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

inferred← citeshttps://doi.org/10.3897/imafungus.16.161411zenodo-depositor-declared
Haplotype-resolved genomes of Phlebopus portentosus reveal nuclear differentiation, TE-mediated variation, and saprotrophic potential
inferred← citeshttps://doi.org/10.1007/978-981-97-0680-8_9openalex-snapshot
Genome Assembly of Tea Plants (Camellia spp.)
inferred← citeshttps://doi.org/10.1007/s00253-023-12624-yopenalex-snapshot
Multi-stage nuclear transcriptomic insights of morphogenesis and biparental role changes in Lentinula edodes
inferred← citeshttps://doi.org/10.1016/j.fgb.2025.104005openalex-snapshot
Nearly telomere-to-telomere genome assembly of the L. edodes diploid genome
inferred← citeshttps://doi.org/10.1016/j.foodchem.2025.144739openalex-snapshot
Proteomics and physiologic analysis reveal different response strategies to cadmium stress in Lentinula edodes
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2025.147032openalex-snapshot
Genome-wide identification and expression profiles of the superoxide dismutase (SOD) genes in Lentinula edodes
inferred← citeshttps://doi.org/10.1093/g3journal/jkad102openalex-snapshot
Chromosome-level assembly of Dictyophora rubrovolvata genome using third-generation DNA sequencing and Hi-C analysis
inferred← citeshttps://doi.org/10.1099/mgen.0.001218openalex-snapshot
Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryotic Laccaria trichodermophora strains by hybrid genome assembly
inferred← citeshttps://doi.org/10.1111/jse.13188openalex-snapshot
Pangenome reveals large‐scale gene loss as a key strategy for adaptive evolution in Agaricus bisporus
inferred← citeshttps://doi.org/10.2139/ssrn.5054473openalex-snapshot
Proteomics And Physiologic Analysis Reveal Different Response Strategies to Cadmium Stress in Lentinula Edodes
inferred← citeshttps://doi.org/10.3389/fmicb.2025.1522075openalex-snapshot
Two sexually compatible monokaryons from a heterokaryotic Lentinula edodes strain respond differently to heat stress
inferred← citeshttps://doi.org/10.3389/fmicb.2026.1669303openalex-snapshot
Chromosome-scale genome assembly of Naematelia sinensis (Jin Er mushroom) offers new insights into the distinct mating-type genomes feature and genome evolution
inferred← citeshttps://doi.org/10.3390/horticulturae12040424openalex-snapshot
A Molecular Marker System Based on Whole-Genome Sequencing for Mating Type Identification in Major Chinese Cultivars of Lentinula edodes
inferred← citeshttps://doi.org/10.3390/ijms27177744openalex-snapshot
Multi-Omics Analysis Reveals Molecular Networks and Key Pathways Associated with Cysteine- and Methionine-Mediated Biosynthesis of Sulfur-Containing Flavor Metabolites in Lentinula edodes
inferred← citeshttps://doi.org/10.3390/jof10090602openalex-snapshot
Telomere-to-Telomere Haplotype-Resolved Genomes of Agrocybe chaxingu Reveals Unique Genetic Features and Developmental Insights
inferred← citeshttps://doi.org/10.3390/jof11010062openalex-snapshot
Chromosome-Level Genome Assembly and Annotation of the Highly Heterozygous Phallus echinovolvatus Provide New Insights into Its Genetics
inferred← citeshttps://doi.org/10.3390/jof11020122openalex-snapshot
Comparative Genomic Analysis of Two Monokaryons of Auricularia heimuer Hei29
inferred← citeshttps://doi.org/10.3390/jof12050328openalex-snapshot
Identification of Candidate Genes Associated with the Pileus-Deficient Phenotype in Lentinula edodes Through Comparative Genomic and Transcriptomic Analyses
inferred← citeshttps://doi.org/10.3390/jof8050496openalex-snapshot
Correction: Gao et al. Haplotype-Resolved Genome Analyses Reveal Genetically Distinct Nuclei within a Commercial Cultivar of Lentinula edodes. J. Fungi 2022, 8, 167
inferred← citeshttps://doi.org/10.3390/jof8060581openalex-snapshot
Pan-Genomes Provide Insights into the Genetic Basis of Auricularia heimuer Domestication
inferred← citeshttps://doi.org/10.3390/jof9100959openalex-snapshot
Genetic and Molecular Evidence of a Tetrapolar Mating System in the Edible Mushroom Grifola frondosa
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