Browsing by Subject "RIBOSOMAL DNA"

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  • Spirin, Viacheslav; Malysheva, Vera; Roberts, Peter; Trichies, Gérard; Savchenko, Anton; Larsson, Karl-Henrik (2019)
    Morphological and DNA data show that effused representatives of the Auriculariales (Basidiomycota) with sphaeropedunculate basidia belong to eleven genera of which seven are dealt with in this study. Among them, Myxarium is the largest genus containing 21 accepted species of which nine are reintroduced below and five are described as new. Protodontia is limited to three species only, P. subgelatinosa (the generic type) and two newly described species from Africa. Protoacia is a new monotypic genus for P. delicata, sp. nov., widely distributed on coniferous hosts in Eurasia. Myxariellum is erected for two new species with smooth hymenophore from northwestern North America while Gelacantha is introduced for G. pura, a new species with hydnoid hymenophore from Caucasus. Our data do not confirm the present synonymy of Sebacina sphaerospora with Tremella glaira, and these species are placed in two separate genera - Hydrophana, gen. nov., and Ofella, gen. nov., respectively. A key to European Myxarium and similar-looking species is included.
  • Korhonen, Aku; Seelan, Jaya Seelan Sathiya; Miettinen, Otto (2018)
    We propose a taxonomic revision of the two closely related white-rot polypore species, Skeletocutis nivea (Jungh.) Jean Keller and S. ochroalba Niemela (Incrustoporiaceae, Basidiomycota), based on phylogenetic analyses of nuclear ribosomal internal transcribed spacer (ITS) and translation elongation factor EF-1 alpha sequences. We show that prevailing morphological species concepts of S. nivea and S. ochroalba are non-monophyletic and we delineate new species boundaries based on phylogenetic inference. We recognise eleven species within the prevailing species concept of S. nivea (S. calida sp. nov., S. coprosmae comb. nov., S. futilis sp. nov., S. impervia sp. nov., S. ipuletii sp. nov., S. lepida sp. nov., S. nemonzlis sp. nov., S. nivea sensu typi, S. semipileata comb. nov., S. unguina sp. nov. and S. yuchengii sp. nov.) and assign new sequenced epitypes for S. nivea and S. semipileata. The traditional concept of S. ochroalba comprises two independent lineages embedded within the S. nivea species complex. The Eurasian conifer-dwelling species S. cummata sp. nov. is recognised as separate from the North American S. ochroalba sensu stricto. Despite comprehensive microscopic examination, the majority of the recognised species are left without stable diagnostic character combinations that would enable species identification based solely on morphology and ecology.
  • Heino, Sarika; Fang, Shentong; Lähde, Marianne; Högström, Jenny; Nassiri, Sina; Campbell, Andrew; Flanagan, Dustin; Raven, Alexander; Hodder, Michael; Nasreddin, Nadia; Xue, Hai-Hui; Delorenzi, Mauro; Leedham, Simon; Petrova, Tatiana; Sansom, Owen; Alitalo, Kari (2021)
    Somatic mutations in APC or CTNNB1 genes lead to aberrant Wnt signaling and colorectal cancer (CRC) initiation and progression via-catenin-T cell factor/lymphoid enhancer binding factor TCF/LEF transcription factors. We found that Lef1 was expressed exclusively in Apc-mutant, Wnt ligand-independent tumors, but not in ligand-dependent, serrated tumors. To analyze Lef1 function in tumor development, we conditionally deleted Lef1 in intestinal stem cells of Apc(fl/fl) mice or broadly from the entire intestinal epithelium of Apc(fl/fl) or Apc(Min/+) mice. Loss of Lef1 markedly increased tumor initiation and tumor cell proliferation, reduced the expression of several Wnt antagonists, and increased Myc proto-oncogene expression and formation of ectopic crypts in Apc-mutant adenomas. Our results uncover a previously unknown negative feedback mechanism in CRC, in which ectopic Lef1 expression suppresses intestinal tumorigenesis by restricting adenoma cell dedifferentiation to a crypt-progenitor phenotype and by reducing the formation of cancer stem cell niches.
  • Chronopoulou, Myrsini; Salonen, Iines; Bird, Clare; Reichart, Gert-Jan; Koho, Karoliina (2019)
    Foraminifera are ubiquitous marine protists with an important role in the benthic carbon cycle. However, morphological observations often fail to resolve their exact taxonomic placement and there is a lack of field studies on their particular trophic preferences. Here, we propose the application of metabarcoding as a tool for the elucidation of the in situ feeding behavior of benthic foraminifera, while also allowing the correct taxonomic assignment of the feeder, using the V9 region of the 18S (small subunit; SSU) rRNA gene. Living foraminiferal specimens were collected from two intertidal mudflats of the Wadden Sea and DNA was extracted from foraminiferal individuals and from the surrounding sediments. Molecular analysis allowed us to confirm that our foraminiferal specimens belong to three genetic types: Ammonia sp. T6, Elphidium sp. S5 and Haynesina sp. S16. Foraminiferal intracellular eukaryote communities reflected to an extent those of the surrounding sediments but at different relative abundances. Unlike sediment eukaryote communities, which were largely determined by the sampling site, foraminiferal intracellular eukaryote communities were driven by foraminiferal species, followed by sediment depth. Our data suggests that Ammonia sp. T6 can predate on metazoan classes, whereas Elphidium sp. S5 and Haynesina sp. S16 are more likely to ingest diatoms. These observations, alongside the use of metabarcoding in similar ecological studies, significantly contribute to our overall understanding of the ecological roles of these protists in intertidal benthic environments and their position and function in the benthic food webs.
  • Cizkova, Jana; Hribova, Eva; Christelova, Pavla; Van den Houwe, Ines; Häkkinen, Markku; Roux, Nicolas; Swennen, Rony; Dolezel, Jaroslav (2015)
    The production of bananas is threatened by rapid spreading of various diseases and adverse environmental conditions. The preservation and characterization of banana diversity is essential for the purposes of crop improvement. The world's largest banana germplasm collection maintained at the Bioversity International Transit Centre (ITC) in Belgium is continuously expanded by new accessions of edible cultivars and wild species. Detailed morphological and molecular characterization of the accessions is necessary for efficient management of the collection and utilization of banana diversity. In this work, nuclear DNA content and genomic distribution of 45S and 5S rDNA were examined in 21 diploid accessions recently added to ITC collection, representing both sections of the genus Musa. 2C DNA content in the section Musa ranged from 1.217 to 1.315 pg. Species belonging to section Callimusa had 2C DNA contents ranging from 1.390 to 1.772 pg. While the number of 45S rDNA loci was conserved in the section Musa, it was highly variable in Callimusa species. 5S rRNA gene clusters were found on two to eight chromosomes per diploid cell. The accessions were genotyped using a set of 19 microsatellite markers to establish their relationships with the remaining accessions held at ITC. Genetic diversity done by SSR genotyping platform was extended by phylogenetic analysis of ITS region. ITS sequence data supported the clustering obtained by SSR analysis for most of the accessions. High level of nucleotide diversity and presence of more than two types of ITS sequences in eight wild diploids pointed to their origin by hybridization of different genotypes. This study significantly expands the number of wild Musa species where nuclear genome size and genomic distribution of rDNA loci is known. SSR genotyping identified Musa species that are closely related to the previously characterized accessions and provided data to aid in their classification. Sequence analysis of ITS region provided further information about evolutionary relationships between individual accessions and suggested that some of analyzed accessions were interspecific hybrids and/or backcross progeny.
  • Pino-Bodas, R.; Zhurbenko, M. P.; Stenroos, S. (2017)
    Though most of the lichenicolous fungi belong to the Ascomycetes, their phylogenetic placement based on molecular data is lacking for numerous species. In this study the phylogenetic placement of 19 species of lichenicolous fungi was determined using four loci (LSU rDNA, SSU rDNA, ITS rDNA and mtSSU). The phylogenetic analyses revealed that the studied lichenicolous fungi are widespread across the phylogeny of Lecanoromycetes. One species is placed in Acarosporales, Sarcogyne sphaerospora; five species in Dactylosporaceae, Dactylospora ahtii, D. deminuta, D. glaucoides, D. parasitica and Dactylospora sp.; four species belong to Lecanorales, Lichenosticta alcicorniaria, Epicladonia simplex, E. stenospora and Scutula epiblastematica. The genus Epicladonia is polyphyletic and the type E. sandstedei belongs to Leotiomycetes. Phaeopyxis punctum and Bachmanniomyces uncialicola form a well supported clade in the Ostropomycetidae. Epigloea soleiformis is related to Arthrorhaphis and Anzina. Four species are placed in Ostropales, Corticifraga peltigerae, Cryptodiscus epicladonia, C. galaninae and C. cladoniicola comb. nov. (= Lettauia cladoniicola). Three new species are described, Dactylospora ahtii, Cryptodiscus epicladonia and C. galaninae.
  • Rikkinen, Jouko; Beimforde, Christina; Seyfullah, Leyla; Perrichot, Vincent; Schmidt, Kerstin; Schmidt, Alexander (2016)
    A novel species of ascomycetes is described from resin of Araucaria humboldtensis on Mont Humboldt in New Caledonia. The fungus is placed in the new genus Resinogalea Rikkinen & A.R. Schmidt, with the species name R. humboldtensis Rikkinen & A.R. Schmidt. It has only been found growing on semi-hardened resin flows on branches of its endemic and endangered conifer host. The morphology and anatomy of the new fungus are compared with those of ecologically similar taxa, including Bruceomyces castoris. The new family Bruceomycetaceae Rikkinen & A.R. Schmidt is described to accommodate Resinogalea and Bruceomyces.
  • Viner, Ilya; Kokaeva, Lyudmila; Spirin, Viacheslav; Miettinen, Otto (2021)
    Modern taxonomic studies of Agaricomycetes rely on the integrative analyses of morphology, environmental data, geographic distribution, and usually several DNA loci. However, sampling and selection of DNA loci for the analyses are commonly shallow. In this study, we suggest minimal numbers of necessary specimens to sample and DNA loci to analyze in order to prevent inadequate taxonomic decisions in species groups with minor morphological and genealogical differences. We sampled four unlinked nuclear DNA gene regions (nuc rDNA ITS1-5.8S-ITS2, gh63, rpb2, and tef1) to revise the systematics of a common wood-decaying species Basidioradulum radula (Hymenochaetales) on an intercontinental set of specimens collected in the Northern Hemisphere. The DNA loci analyzed violate the genealogical concordance phylogenetic species recognition principles, thus confirming a single-species interpretation. We conclude that Hyphodontia syringae is a younger synonym of B. radula.
  • Hirvonen, Katariina; Laivuori, Hannele; Lahti, Jari; Strandberg, Timo; Eriksson, Johan G.; Hackman, Peter (2017)
    Background: Sirtuin-6 (SIRT6) is involved in various crucial cellular pathways, being a key regulator of telomere structure, DNA repair, metabolism, transcriptional control and the NF-kappa B pathway. Sirt6 knock-out mice have been reported to develop typical features of aging and senescence at the age of 2-3 weeks and die within 4 weeks. The aim of this study was to investigate whether sequence variations of SIRT6 are associated with aging and longevity in Finnish men. Methods: The sample of this study consisted of 43 longer-living and healthy males and 92 male control subjects who have died of natural causes at an average age of 66,6 (+/- 4,1) years and who belonged to the Helsinki Birth Cohort Study (HBCS). Single nucleotide polymorphisms (SNPs) in the exons and their surroundings of the SIRT6 were studied using direct PCR sequencing. Results: The SNP rs117385980 (C > T), situated 23 bases downstream of the exon 2 exon/intron border was found in heterozygous form in 1/43 longer-living healthy men (Minor allele frequency (MAF) 0,0116) and in 9/92 controls (MAF 0,0489). To replicate this finding, we studied a group of 63 healthy men at an average age of 83 years from the Helsinki Businessmen Study (HBS)-cohort. The heterozygosity of the same SNP was seen in 2/63 men from the HBS-cohort (MAF 0,0159). Fisher exact test was performed in our two combined study samples. The P-value for all samples combined was 0.07 and the odds ratio 3.53 (95% confidence interval 0.96-13.4). Conclusions: These results suggest an inverse association between the T allele of rs117385980 and longevity. The result needs to be confirmed in a larger study. It remains to be determined whether rs117385980 itself has an effect or if it is a mere genetic marker for some other yet undiscovered sequence variant causing a functional effect.
  • Spirin, Viacheslav; Malysheva, Vera; Mendes-Alvarenga, Renato Lucio; Kotiranta, Heikki; Larsson, Karl-Henrik (2020)
    To date, Basidiodendron luteogriseum, the generic type of Basidiodendron (Auriculariales, Basidiomycota) has been treated as a synonym of B. eyrei. Our data show they are not conspecific. The identity of other members of the B. eyrei complex, i.e., B. deminutum and B. grandinioides, is clarified based on morphological and DNA data, and 10 new species are described from Eurasia, as well as from North and South America.
  • Spirin, Viacheslav; Malysheva, Vera; Haelewaters, Danny; Larsson, Karl-Henrik (2019)
    Stypella vermiformis is a heterobasidiomycete producing minute gelatinous basidiocarps on rotten wood of conifers in the Northern Hemisphere. In the current literature, Stypella papillata, the genus type of Stypella (described from Brazil), is treated as a taxonomic synonym of S. vermiformis. In the present paper, we revise the type material of S. papillata and a number of specimens addressed to S. vermiformis. As a result, the presumed synonymy of S. papillata and S. vermiformis is rejected and the genus Stypella is restricted to the single species S. papillata. Morphological and molecular phylogenetic studies of specimens from the Northern Hemisphere corresponding to the current concept of S. vermiformis uncovered three species from two newly described genera. S. vermiformis s.str. is distributed in temperate Europe and has small-sized basidia and basidiospores, and it is placed in a new genus, Mycostilla. Another genus, Stypellopsis, is created for two other species, the North American Stypellopsis farlowii, comb. nov., and the North European Stypellopsis hyperborea, sp. nov. Basidia and basidiospores of Stypellopsis spp. are larger than in Mycostilla vermiformis but other morphological characters are very similar. In addition, Spiculogloea minuta (Spiculogloeomycetes, Pucciniomycotina) is reported as new to Norway, parasitising basidiocarps of M. vermiformis and Tulasnella spp.
  • Suija, Ave; Kaasalainen, Ulla Susanna; Kirika, Paul; Rikkinen, Jouko Kalevi (2018)
    During lichenological explorations of tropical montane forests in Kenya, a remarkable new lichenicolous fungus was repeatedly found growing on thalli of the epiphytic tripartite cyanolichen Crocodia cf. clathrata. Molecular phylogenetic analyses placed the fungus within Gomphillaceae (Ostropales, Lecanoromycetes), a family mainly of lichen-symbiotic species in the tropics. The anatomical features (unitunicate, non-amyloid asci and simple, septate paraphyses) as well as the hemiangiocarpic ascoma development confirm its taxonomic affinity. DNA sequence data showed the closest relationship was with Gyalidea fritzei, followed by Corticifraga peltigerae. A monotypic genus, Taitaia, is introduced to incorporate a single species, T. aurea. The new fungus is characterized by aggregated ascomata with yellow margins and salmon red discs developing from a single base.