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

Yi-Jian Yao,Kathryn E Bushley,Hai-Jun Wu,Yi Li,Rui-Heng Yang,Zujian Wu,David L Hawksworth,Yu-Jing Yan,Lan Jiang,Ke Wang

doi: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.

Highlights

The nuclear ribosome DNA is considered a classic example of concerted evolution in most eukaryotes (Nei and Rooney 2005; Ganley and Kobayashi 2007; Stage and Eickbush 2007)
Amplification, identification and geographic distribution of internal transcribed spacer (ITS) pseudogenes A total of 268 ITS sequences were obtained from the 147 individuals of O. sinensis, among which 123 were
Since the divergences in functional copies of the ITS were assumed to be correlated with species diversification in O. sinensis (Jiao 2010; Zhang et al 2009), our results suggest that ITS pseudogenes could have emerged either before or after a new functional ITS haplotype was generated and homogenized

Summary

Introduction

The nuclear ribosome DNA (nrDNA) is considered a classic example of concerted evolution in most eukaryotes (Nei and Rooney 2005; Ganley and Kobayashi 2007; Stage and Eickbush 2007). As one of the most popular components of nrDNA, the internal transcribed spacer (ITS) generally appears to evolve through concerted evolution, and has been widely used in species identifications and phylogenetic studies of diverse organisms (e.g. Buckler and Holtsford 1996; Denman et al 2000; Hřibová et al 2011; Rouland-Lefevre et al 2002). It has been selected as the universal fungal DNA barcode (Schoch et al 2012). Variations in the ITS among individuals of this species were first identified by Kinjo and Zang (2001), and the polymorphisms have been variously interpreted as genetic divergences (Kinjo and Zang 2001), different genotypes (Zhu et al 2010), cryptic species (Stensrud et al 2007), or potentially other species (Xiao et al 2009)

Methods

Discussion

Conclusion