Christopher L. Schardl, University of Kentucky
Carolyn A. Young, The Samuel Roberts Noble Foundation
Uljana Hesse, University of Kentucky
Stefan G. Amyotte, University of Kentucky
Kalina Andreeva, University of Kentucky
Patrick J. Calie, Eastern Kentucky University
Damien J. Fleetwood, University of Auckland
David C. Haws, University of Kentucky
Neil Moore, University of Kentucky
Birgitt Oeser, University of Muenster
Daniel G. Panaccione, West Virginia University
Kathryn K. Schweri, University of Kentucky
Christine R. Voisey, Grasslands Research Centre
Mark L. Farman, University of Kentucky
Jerzy W. Jaromczyk, University of Kentucky
Bruce A. Roe, University of Oklahoma
Donal M. O'Sullivan, National Institute of Agricultural Botany
Barry Scott, Massey University
Paul Tudzynski, University of Muenster
Zhiqiang An, University of Texas at Austin
Elissaveta G. Arnaoudova, University of Kentucky
Charles T. Bullock, University of Kentucky
Nikki D. Charlton, The Samuel Roberts Noble Foundation
Li Chen, University of Kentucky
Murray Cox, Massey University
Randy D. Dinkins, United States Department of Agriculture Agricultural Research Service
Simona Florea, University of Kentucky
Anar K. Khan, Invermay Agricultural Centre
Eckhard Leistner, Universitaet Bonn
Adrian Leuchtmann, ETH Zürich
Chunjie Li, Lanzhou University
JinGe Liu, University of Kentucky
Jinze Liu, University of Kentucky
Miao Liu, University of Kentucky
Wade Mace, Grasslands Research Centre
Caroline Machado, University of Kentucky
Ella V. Wilson, University of Kentucky
Jennifer L. Wiseman, University of Kentucky
Ruriko Yoshida, University of Kentucky
Zheng Zheng, University of Kentucky

Document Type


Publication Date



Davis College of Agriculture, Natural Resources and Design


Division of Plant and Soil Sciences


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.

Source Citation

Schardl, C. L., Young, C. A., Hesse, U., Amyotte, S. G., Andreeva, K., Calie, P. J., … Zeng, Z. (2013). Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci. PLoS Genetics, 9(2), e1003323.


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