RIP mutated ITS genes in populations of Ophiocordyceps sinensis and their implications for molecular systematics
- PDF / 2,578,155 Bytes
- 10 Pages / 595.276 x 790.866 pts Page_size
- 104 Downloads / 192 Views
IMA Fungus
RESEARCH
Open Access
RIP mutated ITS genes in populations of Ophiocordyceps sinensis and their implications for molecular systematics Yi Li1,2,3†, Lan Jiang3,4†, Ke Wang3,5, Hai-Jun Wu3, Rui-Heng Yang6, Yu-Jing Yan7, Kathryn E. Bushley8, David L. Hawksworth9,10,11,12, Zujian Wu1* and Yi-Jian Yao3*
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
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 thus 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 also been selected as the universal fungal DNA barcode (Schoch et al. 2012). However, intra-genomic ITS * Correspondence: [email protected]; [email protected] † Yi Li and Lan Jiang contributed equally to this work. 1 Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China 3 State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China Full list of author information is available at the end of the article
polymorphisms, indicating potential escapes from concerted evolution, have long been reported in fungi (e.g. O’Donnell and Cigelnik 1997; Wang and Yao 2005). As one kind of intra-genomic polymorphisms, ITS pseudogenes are one category of such polymorphisms, and these have been reported in a variety of fungal species, including Colletotrichum graminicola, Cordyceps militaris, Epichloë spp., Laetiporus spp., Leptosphaeria maculans, Neurospora crassa, and Ophiocordyceps sinensis (Lindner and Banik 2011; Li et al. 20
Data Loading...
