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Journal Articles Proceedings of the National Academy of Sciences of the United States of America Year : 2023

A global phylogenomic analysis of the shiitake genus Lentinula

Sean Sierra-Patev
  • Function : Author
Byoungnam Min
Miguel Naranjo-Ortiz
  • Function : Author
Brian Looney
  • Function : Author
Zachary Konkel
Jason Slot
Yuichi Sakamoto
  • Function : Author
Jacob Steenwyk
Antonis Rokas
Juan Carro
Susana Camarero
Patricia Ferreira
Gonzalo Molpeceres
Francisco Ruiz-Dueñas
Ana Serrano
  • Function : Author
Bernard Henrissat
  • Function : Author
Karen Hughes
Juan Mata
Noemia Kazue Ishikawa
Ruby Vargas-Isla
Shuji Ushijima
  • Function : Author
Chris Smith
  • Function : Author
John Donoghue
Steven Ahrendt
  • Function : Author
William Andreopoulos
Guifen He
  • Function : Author
Kurt Labutti
Anna Lipzen
Vivian Ng
Robert Riley
Laura Sandor
  • Function : Author
Kerrie Barry
  • Function : Author
Angel Martínez
Yang Xiao
John Gibbons
Kazuhisa Terashima
  • Function : Author
Igor Grigoriev
David Hibbett


Lentinula is a broadly distributed group of fungi that contains the cultivated shiitake mushroom, L. edodes . We sequenced 24 genomes representing eight described species and several unnamed lineages of Lentinula from 15 countries on four continents. Lentinula comprises four major clades that arose in the Oligocene, three in the Americas and one in Asia–Australasia. To expand sampling of shiitake mushrooms, we assembled 60 genomes of L. edodes from China that were previously published as raw Illumina reads and added them to our dataset. Lentinula edodes sensu lato (s. lat.) contains three lineages that may warrant recognition as species, one including a single isolate from Nepal that is the sister group to the rest of L. edodes s. lat., a second with 20 cultivars and 12 wild isolates from China, Japan, Korea, and the Russian Far East, and a third with 28 wild isolates from China, Thailand, and Vietnam. Two additional lineages in China have arisen by hybridization among the second and third groups. Genes encoding cysteine sulfoxide lyase ( lecsl ) and γ-glutamyl transpeptidase ( leggt ), which are implicated in biosynthesis of the organosulfur flavor compound lenthionine, have diversified in Lentinula . Paralogs of both genes that are unique to Lentinula ( lecsl 3 and leggt 5b) are coordinately up-regulated in fruiting bodies of L. edodes . The pangenome of L. edodes s. lat. contains 20,308 groups of orthologous genes, but only 6,438 orthogroups (32%) are shared among all strains, whereas 3,444 orthogroups (17%) are found only in wild populations, which should be targeted for conservation.

Dates and versions

hal-04144610 , version 1 (28-06-2023)



Sean Sierra-Patev, Byoungnam Min, Miguel Naranjo-Ortiz, Brian Looney, Zachary Konkel, et al.. A global phylogenomic analysis of the shiitake genus Lentinula. Proceedings of the National Academy of Sciences of the United States of America, 2023, 120 (10), pp.e2214076120. ⟨10.1073/pnas.2214076120⟩. ⟨hal-04144610⟩
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