A global phylogenomic analysis of the shiitake genus Lentinula
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- Biology Department, Clark University, Worcester, MA 01610
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Plant Pathology, Ohio State University, Columbus, OH 43210
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235
- Centro de Investigaciones Biológicas “Margarita Salas,” Consejo Superior de Investigaciones Científicas, Madrid E-28040, Spain
- Department of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, 50009 Zaragoza, Spain, Institute of Biocomputation and Physics of Complex Systems, University of Zaragoza, 50018 Zaragoza, Spain
- DTU Bioengineering, Technical University of Denmark 2800, Kgs. Lyngby, Denmark, Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Université 13288, Marseille, France, INRAE, UMR 1163, Biodiversité et Biotechnologie Fongiques 13009, Marseille, France
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996
- Department of Biology, University of South Alabama, Mobile, AL 36688
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Petrópolis, Manaus AM 69067-375, Brazil
- The Tottori Mycological Institute, Japan Kinoko Research Center Foundation, Tottori 689-1125, Japan
- Manaaki Whenua - Landcare Research, Auckland 1072, New Zealand
- Northwest Mycological Consultants, Corvallis, OR 97330
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Department of Food Science, University of Massachusetts, Amherst, MA 01003
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720
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.
- Research Organization:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
- Sponsoring Organization:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); National Science Foundation (NSF)
- Grant/Contract Number:
- 0000238431; BIO2017-86559-R; PID2019-103901GB-I00; AC02-05CH11231; DEB-1456588
- OSTI ID:
- 1958920
- Alternate ID(s):
- OSTI ID: 2229314
- Journal Information:
- Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Vol. 120 Journal Issue: 10; ISSN 0027-8424
- Publisher:
- Proceedings of the National Academy of SciencesCopyright Statement
- Country of Publication:
- United States
- Language:
- English
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