Christopher L. Schardl, University of Kentucky
Carolyn A. Young, The Samuel Roberts Noble Foundation
Uljana Hesse, University of Kentucky
Stefan G. Amyotte, University of KentuckyFollow
Kalina Andreeva, University of Kentucky
Patrick J. Calie, Eastern Kentucky University
Damien J. Fleetwood, University of Auckland, New Zealand
David C. Haws, University of KentuckyFollow
Neil Moore, University of KentuckyFollow
Birgitt Oeser, University of Muenster, Germany
Daniel G. Panaccione, West Virginia University
Kathryn K. Schweri, University of Kentucky
Christine R. Voisey, AgResearch, New Zealand
Mark L. Farman, University of KentuckyFollow
Jerzy W. Jaromczyk, University of KentuckyFollow
Bruce A. Roe, University of Oklahoma Norman Campus
Donal M. O'Sullivan, National Institute of Agricultural Botany, United Kingdom
Barry Scott, Massey University, New Zealand
Paul Tudzynski, University of Muenster, Germany
Zhiqiang An, University of Texas Health Science Center at Houston
Elissaveta G. Arnaoudova, University of KentuckyFollow
Charles T. Bullock, University of KentuckyFollow
Nikki D. Charlton, The Samuel Roberts Noble Foundation
Li Chen, University of KentuckyFollow
Murray Cox, Massey University, New Zealand
Randy D. Dinkins, Agricultural Research Service
Simona Florea, University of KentuckyFollow
Anthony E. Glenn, Agricultural Research Service
Anna Gordon, National Institute of Agricultural Botany, United Kingdom
Ulrich Güldener, Helmholtz Zentrum München (GmbH), Germany
Daniel R. Harris, University of KentuckyFollow
Walter Hollin, University of KentuckyFollow
Jolanta Jaromczyk, University of KentuckyFollow
Richard D. Johnson, AgResearch, New Zealand
Anar K. Khan, Invermay Agricultural Centre, New Zealand
Eckhard Leistner, Universitaet Bonn, Germany
Adrian Leuchtmann, Institute of Integrative Biology, Switzerland
Chunjie Li, Lanzhou University, China
JinGe Liu, University of KentuckyFollow
Jinze Liu, University of KentuckyFollow
Miao Liu, University of Kentucky
Wade Mace, AgResearch, New Zealand
Caroline Machado, University of KentuckyFollow
Padmaja Nagabhyru, University of KentuckyFollow
Juan Pan, University of KentuckyFollow
Jan Schmid, Massey University, New Zealand
Koya Sugawara, National Agriculture and Food Research Organization (NARO), Japan
Ulrike Steiner, Universitaet Bonn, Germany
Johanna E. Takach, The Samuel Roberts Noble Foundation
Eiji Tanaka, Ishikawa Prefectural University, Japan
Jennifer S. Webb, University of KentuckyFollow
Ella V. Wilson, University of Kentucky
Jennifer L. Wiseman, University of Kentucky
Ruriko Yoshida, University of KentuckyFollow
Zheng Zeng, University of KentuckyFollow


The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some-including the infamous ergot alkaloids-have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses.

Document Type


Publication Date


Notes/Citation Information

Published in PLoS Genetics, v. 9, no. 2, e1003323.

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Digital Object Identifier (DOI) (3962 kB)
Supporting documents