title: Internal transcribed spacer (ITS) evolution in populations of the hyperparasitic European mistletoe pathogen fungus, Sphaeropsis visci (Botryosphaeriaceae): The utility of ITS2 secondary structures.
abstract: We investigated patterns of nucleotide polymorphism in the internal transcribed spacer (ITS) region for Sphaeropsis visci, a hyperparasitic fungus that causes the leaf spot disease of the hemiparasite European mistletoe (Viscum album). Samples of S. visci were obtained from Hungary covering all major infected forest areas. For obtaining PCR products we used a fast and efficient direct PCR approach based on a high fidelity DNA polymerase. A total of 140 ITS sequences were subjected to an array of complementary sequence analyses, which included analyses of secondary structure stability, nucleotide polymorphism patterns, GC content, and presence of conserved motifs. Analysed sequences exhibited features of functional rRNAs. Overall, polymorphism was observed within less conserved motifs, such as loops and bulges, or, alternatively, as non-canonical G-U pairs within conserved regions of double stranded helices. The secondary structure of ITS2 provides new opportunities for obtaining further valuable information, which could be used in phylogenetic analyses, or at population level as demonstrated in our study. This is due to additional information provided by secondary structures and their models. The combined score matrix was used with the methods implemented in the programme 4SALE. Besides the pseudoprotein coding method of 4SALE, the molecular morphometric character coding also has potential for gaining further information for phylogenetic analyses based on the geometric features of the sub-structural elements of the ITS2 RNA transcript.
authors.affiliation: Botany Unit, Finnish Museum of Natural History, University of Helsinki, PO Box 7, Helsinki FI-00014, Finland. Electronic address: peter.poczai@gmail.com.
authors.forename: Péter
authors.initials: P
authors.lastname: Poczai
authors.affiliation: Plant Biology, Department of Biosciences, PO Box 65, FI-00014, University of Helsinki, Finland. Electronic address: ildikovarga@hotmail.hu.
authors.forename: Ildikó
authors.initials: I
authors.lastname: Varga
authors.affiliation: Plant Biology, Department of Biosciences, PO Box 65, FI-00014, University of Helsinki, Finland. Electronic address: jaakko.hyvonen@helsinki.fi.
authors.forename: Jaakko
authors.initials: J
authors.lastname: Hyvönen
mesh_terms: D001203:Ascomycota / Q000145:classification* / Q000235:genetics*; D001483:Base Sequence; D021903:DNA, Ribosomal Spacer; D019143:Evolution, Molecular; D014784:Mistletoe / Q000382:microbiology; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011544:Pseudogenes; D012331:RNA, Fungal / Q000737:chemistry* / Q000235:genetics; D012335:RNA, Ribosomal / Q000737:chemistry* / Q000235:genetics; D011995:Recombination, Genetic
chemical_list: D021903:DNA, Ribosomal Spacer; D012331:RNA, Fungal; D012335:RNA, Ribosomal
keywords: Ascomycetes; Hyperparasitism; Internal transcribed spacer (ITS); Parasitic plants; Viscum album