ArticleGenomics, proteomics & bioinformatics2020
Genome Assembly and Pathway Analysis of Edible Mushroom Agrocybe cylindracea.
Article in Genomics, proteomics & bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 32 citations in OpenAlex.
- Genome and Comparative Transcriptome Analysis of Growth and Developmental Changes in the Pileus of theJournal of fungi (Basel, Switzerland) · 2026Article
- Hybrid Genome Assembly and Annotation of the Basidiomycete FungusInternational journal of molecular sciences · 2026Article
- Systematic study ofIMA fungus · 2026Article
- The Influence of the Divergent Substrate on Physicochemical Properties and Metabolite Profiling ofJournal of fungi (Basel, Switzerland) · 2025Article
- Cylindracin, a Cys-rich protein expressed in the fruiting body of Cyclocybe cylindracea, inhibits growth of filamentous fungi but not yeasts or bacteria.FEBS open bio · 2024Article
- Telomere-to-Telomere Haplotype-Resolved Genomes ofJournal of fungi (Basel, Switzerland) · 2024Article
- Integrative Analysis of Transcriptome and Metabolome Sheds Light on Flavonoid Biosynthesis in the Fruiting Body ofJournal of fungi (Basel, Switzerland) · 2024Article
- Chromosome-Level Assembly and Comparative Genomic Analysis ofJournal of fungi (Basel, Switzerland) · 2024Article
- Whole Genome Sequence of an Edible MushroomJournal of fungi (Basel, Switzerland) · 2023Article
- Complete genome sequences and comparative secretomic analysis for the industrially cultivated edible mushroomFrontiers in microbiology · 2023Article
- Genome, transcriptome, and metabolome analyses provide new insights into the resource development in an edible fungusFrontiers in microbiology · 2023Article
- First genome assembly and annotation ofFrontiers in cellular and infection microbiology · 2023Article
- Whole Genome Sequence of an Edible MushroomJournal of fungi (Basel, Switzerland) · 2022Article
- Beneficial bacterial-Frontiers in microbiology · 2022Article
- Whole-genome sequence of a high-temperature edible mushroomFrontiers in microbiology · 2022Article
- Metabolomics Analysis ofFrontiers in nutrition · 2022Article
- Whole Genome Sequencing and Annotation ofJournal of fungi (Basel, Switzerland) · 2021Article
- Whole-genome assembly of Ganoderma leucocontextum (Ganodermataceae, Fungi) discovered from the Tibetan Plateau of China.G3 (Bethesda, Md.) · 2021Article
- Macrosynteny analysis between Lentinula edodes and Lentinula novae-zelandiae reveals signals of domestication in Lentinula edodes.Scientific reports · 2021Article
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Agrocybe cylindracea, an edible mushroom, is widely cultivated for its abundance of nutrients and flavor, and many of its metabolites are reported to have beneficial roles, such as medicinal effects on tumors and chronical illnesses. However, the lack of genomic information has hindered further molecular studies on this fungus. Here, we present a genome assembly of A. cylindracea together with comparative genomics and pathway analyses of Agaricales species. The draft, generated from both next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing platforms to overcome high genetic heterozygosity, is composed of a 56.5 Mb sequence and 15,384 predicted genes. This mushroom possesses a complex reproductive system, including tetrapolar heterothallic and secondary homothallic mechanisms, and harbors several hydrolases and peptidases for gradual and effective degradation of various carbon sources. Our pathway analysis reveals complex processes involved in the biosynthesis of polysaccharides and other active substances, including B vitamins, unsaturated fatty acids, and N-acetylglucosamine. RNA-seq data show that A. cylindracea stipes tend to synthesize carbohydrate for carbon sequestration and energy storage, whereas pilei are more active in carbon utilization and unsaturated fatty acid biosynthesis. These results reflect diverse functions of the two anatomical structures of the fruiting body. Our comprehensive genomic and transcriptomic data, as well as preliminary comparative analyses, provide insights into the molecular details of the medicinal effects in terms of active compounds and nutrient components.
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