IMA Fungus 11(1): e33899, doi: 10.1186/s43008-020-00040-0

RIP mutated ITS genes in populations of Ophiocordyceps sinensis and their implications for molecular systematics

Yi Li^‡, Yi-Jian Yao^§, Ke Wang^|, Hai-Jun Wu^|, Rui-Heng Yang^¶, Yu-Jing Yan^#, Kathryn E. Bushley^¤, David L. Hawksworth^«, Zujian Wu^», Yi-Jian Yao^|

‡ Yangzhou University, College of Food Science and Engineering, Yangzhou, China§ Institute Of Microbiology, Chinese Academy of Sciences, Beijing, China| State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China¶ Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai, China# University of Copenhagen, Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, Copenhagen, Denmark¤ University of Minnesota, Department of Plant and Microbial Biology, St Paul« Universidad Complutense de Madrid, Departamento de Biología Vegetal II, Facultad de Farmacia, Madrid, Spain» Fujian Agriculture and Forestry University, Department of Plant Protection, Fuzhou, China

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Citation: Li Y, Yao Y-J, Wang K, Wu H-J, Yang R-H, Yan Y-J, Bushley KE, Hawksworth DL, Wu Z, Yao Y-J (2020) RIP mutated ITS genes in populations of Ophiocordyceps sinensis and their implications for molecular systematics. IMA Fungus 11(1): e33899. https://doi.org/10.1186/s43008-020-00040-0

Abstract

Different hypotheses have been proposed to interpret the observed unusual ITS (internal transcribed spacer) sequences in Ophiocordyceps sinensis. The coexistence of diverged ITS paralogs in a single genome was previously shown by amplifying the ITS region from mono-ascospore isolates using specific primers designed for different ITS paralog groups. Among those paralogs, are AT-biased ITS sequences which were hypothesized to result from repeat-induced point mutation (RIP). This is a process that detects and mutates repetitive DNA and frequently leads to epigenetic silencing, and these mutations have been interpreted as pseudogenes. Here we investigate the occurrence and frequency of ITS pseudogenes in populations of O. sinensis using large-scale sampling, and discusses the implications of ITS pseudogenes for fungal phylogenetic and evolutionary studies. Our results demonstrate a wide distribution of ITS pseudogenes amongst different geographic populations, and indicate how ITS pseudogenes can contribute to the reconstruction of the evolutionary history of the species.

Keywords

Caterpillar fungus, Cordyceps sinensis, ITS pseudogene, Haplotype, Phylogeny