A-WINGS: an integrated genome database for Pleurocybella porrigens (Angel’s wing oyster mushroom, Sugihiratake)

Yamamoto, Nobuto; Suzuki, Tomohiro; Kobayashi, Mariko; Dohra, Hideo; Sasaki, Yohei; Hirai, Hirofumi; Yokoyama, Koji; Kawagishi, Hirokazu; Yano, Kentarô

doi:10.1186/1756-0500-7-866

Cited by 8 publications

(2 citation statements)

References 19 publications

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“…‘BLAST Search’ allows users to search for homologous nucleotide or amino acid sequences from the genome assembly or coding sequences. ‘GO Tree View’ is a graphical search tool for genes with Gene Ontology annotations 32 . It allows interactive gene searches by browsing unspecified GO terms.…”

Section: Resultsmentioning

confidence: 99%

Genome sequence analysis of the fairy ring-forming fungus Lepista sordida and gene candidates for interaction with plants

Takano

Yamamoto

Suzuki

et al. 2019

Sci Rep

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Circular patterns called “fairy rings” in fields are a natural phenomenon that arises through the interaction between basidiomycete fungi and plants. Acceleration or inhibition of plant vegetative growth and the formation of mushroom fruiting bodies are both commonly observed when fairy rings form. The gene of an enzyme involved in the biosynthesis of these regulators was recently isolated in the fairy ring-forming fungus, Lepista sordida . To identify other genes involved in L. sordida fairy ring formation, we used previously generated sequence data to produce a more complete draft genome sequence for this species. Finally, we predicted the metabolic pathways of the plant growth regulators and 29 candidate enzyme-coding genes involved in fairy-ring formation based on gene annotations. Comparisons of protein coding genes among basidiomycete fungi revealed two nitric oxide synthase gene candidates that were uniquely encoded in genomes of fairy ring-forming fungi. These results provide a basis for the discovery of genes involved in fairy ring formation and for understanding the mechanisms involved in the interaction between fungi and plants. We also constructed a new web database F-RINGS ( http://bioinf.mind.meiji.ac.jp/f-rings/ ) to provide the comprehensive genomic information for L. sordida .

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Section: Resultsmentioning

confidence: 99%

Genome sequence analysis of the fairy ring-forming fungus Lepista sordida and gene candidates for interaction with plants

Takano

Yamamoto

Suzuki

et al. 2019

Sci Rep

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“…Three data matrices were generated for different purposes. The first matrix (Matrix I) comprised single-copy ortholog genes from 141 genomes of representatives of Agaricales and outgroups, including 126 publicly available genomes downloaded from A-WINGS (Yamamoto et al 2014 ), the Joint Genome Institute (JGI), and the National Center for Biotechnology Information (NCBI), and 15 genomes generated in the present study. These were used to establish the framework of suborders and the phylogenetic positions of Sarcomyxaceae and Tricholomopsis within Agaricales .…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic and taxonomic updates of Agaricales , with an emphasis on Tricholomopsis

Wang,

Cai,

Hao

et al. 2023

Mycology

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The order Agaricales was divided into eight suborders. However, the phylogenetic relationships among some suborders are largely unresolved, and the phylogenetic positions and delimitations of some taxa, such as Sarcomyxaceae and Tricholomopsis , remain unsettled. In this study, sequence data of 38 genomes were generated through genome skimming on an Illumina sequencing system. To anchor the systematic position of Sarcomyxaceae and Tricholomopsis , a phylogenetic analysis based on 555 single-copy orthologous genes from the aforementioned genomes and 126 publicly accessible genomes was performed. The results fully supported the clustering of Tricholomopsis with Phyllotopsis and Pleurocybella within Phyllotopsidaceae, which formed a divergent monophyletic major lineage together with Pterulaceae , Radulomycetaceae , and Macrotyphula in Agaricales . The analysis also revealed that Sarcomyxaceae formed a unique major clade. Therefore, two new suborders, Phyllotopsidineae and Sarcomyxineae , are proposed for the two major lineages. Analyses of 450 single-copy orthologous genes and four loci suggested that Tricholomopsis consisted of at least four clades. Tricholomopsis is subsequently subdivided into four distinct sections. Seventeen Tricholomopsis species in China, including six new species, are reported. Conoloma is established to accommodate T. mucronata . The substrate preference of Tricholomopsis species and the transitions of the pileate ornamentations among the species within the genus are discussed.

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A compendium of generic names of agarics and Agaricales

Kalichman

Kirk

Matheny

2020

TAXON

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Agarics (gilled mushrooms) and the order Agaricales include some of the best‐known and most charismatic fungi. However, neither group has had its constituent genera exhaustively compiled in a modern phylogenetic context. To provide that framework, we identified and analyzed 1383 names of genera of agarics (regardless of taxonomic placement) and the Agaricales (regardless of morphology), compiling various data for each name. Including 590 accepted names, the other 793 listed with reasons explaining their disuse, this compendium is intended to be comprehensive at present and phylogenetically up‐to‐date. Data we gathered included type species, continents from which type species were described, accepted synonyms of those species, current family placements, gross macromorphological categories, and sequenced loci (for type specimens, type species, and each genus as a whole). Index Fungorum provided a basis for the data, but much was manually confirmed, augmented, or corrected based on recent literature. Among accepted gilled genera, 82% belonged to the Agaricales; among accepted genera of Agaricales, 67% were gilled. Based on automated searches of GenBank and MycoCosm, 7% of generic names had DNA sequences of their type specimens, 68% had sequences of their type species, and 87% had sequences representing their genus. This leaves an estimated 103 accepted genera entirely lacking molecular data. Some subsets of genera have been sequenced relatively thoroughly (e.g., nidularioid genera and genera described from Europe); others relatively poorly (e.g., cyphelloid genera and genera described from Africa and tropical Asia). We also list nomenclaturally threatened and taxonomically doubtful genus and family names.

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A-WINGS: an integrated genome database for Pleurocybella porrigens (Angel’s wing oyster mushroom, Sugihiratake)

Cited by 8 publications

References 19 publications

Genome sequence analysis of the fairy ring-forming fungus Lepista sordida and gene candidates for interaction with plants

Genome sequence analysis of the fairy ring-forming fungus Lepista sordida and gene candidates for interaction with plants

Phylogenetic and taxonomic updates of Agaricales , with an emphasis on Tricholomopsis

A compendium of generic names of agarics and Agaricales

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