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  • Sanli, Kemal, et al. (författare)
  • Metagenomic Sequencing of Marine Periphyton: Taxonomic and Functional Insights into Biofilm Communities
  • 2015
  • Ingår i: Frontiers in Microbiology. - 1664-302X. ; 6:1192
  • Tidskriftsartikel (refereegranskat)abstract
    • Periphyton communities are complex phototrophic, multispecies biofilms that develop on surfaces in aquatic environments. These communities harbor a large diversity of organisms comprising viruses, bacteria, algae, fungi, protozoans and metazoans. However, thus far the total biodiversity of periphyton has not been described. In this study, we use metagenomics to characterize periphyton communities from the marine environment of the Swedish west coast. Although we found approximately ten times more eukaryotic rRNA marker gene sequences compared to prokaryotic, the whole metagenome-based similarity searches showed that bacteria constitute the most abundant phyla in these biofilms. We show that marine periphyton encompass a range of heterotrophic and phototrophic organisms. Heterotrophic bacteria, including the majority of proteobacterial clades and Bacteroidetes, and eukaryotic macro-invertebrates were found to dominate periphyton. The phototrophic groups comprise Cyanobacteria and the alpha-proteobacterial genus Roseobacter, followed by different micro- and macro-algae. We also assess the metabolic pathways that predispose these communities to an attached lifestyle. Functional indicators of the biofilm form of life in periphyton involve genes coding for enzymes that catalyze the production and degradation of extracellular polymeric substances, mainly in the form of complex sugars such as starch and glycogen-like meshes together with chitin. Genes for 278 different transporter proteins were detected in the metagenome, constituting the most abundant protein complexes. Finally, genes encoding enzymes that participate in anaerobic pathways, such as denitrification and methanogenesis, were detected suggesting the presence of anaerobic or low-oxygen micro-zones within the biofilms.
  • Alm Rosenblad, Magnus, 1957-, et al. (författare)
  • Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)
  • 2016
  • Ingår i: MycoKeys. - 1314-4057 .- 1314-4049. ; 13, s. 21-33
  • Tidskriftsartikel (refereegranskat)abstract
    • During a routine scan for Signal Recognition Particle (SRP) RNAs in eukaryotic sequences, we surprisingly found in silico evidence in GenBank for a 265-base long SRP RNA sequence in the ITS1 region of a total of 11 fully identified species in three ectomycorrhizal genera of the Basidiomycota (Fungi): Astraeus, Russula, and Lactarius. To rule out sequence artifacts, one specimen from a species indicated to have the SRP RNA-containing ITS region in each of these genera was ordered and re-sequenced. Sequences identical to the corresponding GenBank entries were recovered, or in the case of a non-original but conspecific specimen differed by three bases, showing that these species indeed have an SRP RNA sequence incorporated into their ITS1 region. Other than the ribosomal genes, this is the first known case of non-coding RNAs in the eukaryotic ITS region, and it may assist in the examination of other types of insertions in fungal genomes.
  • Tedersoo, Leho, et al. (författare)
  • Novel soil-inhabiting clades fill gaps in the fungal tree of life
  • 2017
  • Ingår i: Microbiome. - 2049-2618. ; 5
  • Tidskriftsartikel (refereegranskat)abstract
    • Background - Fungi are a diverse eukaryotic group of degraders, pathogens, and symbionts, with many lineages known only from DNA sequences in soil, sediments, air, and water. Results - We provide rough phylogenetic placement and principal niche analysis for >40 previously unrecognized fungal groups at the order and class level from global soil samples based on combined 18S (nSSU) and 28S (nLSU) rRNA gene sequences. Especially, Rozellomycota (Cryptomycota), Zygomycota s.lat, Ascomycota, and Basidiomycota are rich in novel fungal lineages, most of which exhibit distinct preferences for climate and soil pH. Conclusions - This study uncovers the great phylogenetic richness of previously unrecognized order- to phylum-level fungal lineages. Most of these rare groups are distributed in different ecosystems of the world but exhibit distinct ecological preferences for climate or soil pH. Across the fungal kingdom, tropical and non-tropical habitats are equally likely to harbor novel groups. We advocate that a combination of traditional and high-throughput sequencing methods enable efficient recovery and phylogenetic placement of such unknown taxonomic groups.
  • Sigvald, Roland, et al. (författare)
  • Molecular identification of bloodmeals and species composition in Culicoides biting midges
  • 2013
  • Ingår i: Medical and Veterinary Entomology. - Wiley: 12 months. - 0269-283X .- 1365-2915. ; 27, s. 104-112
  • Tidskriftsartikel (refereegranskat)abstract
    • Investigations of host preferences in haematophagous insects, including Culicoides biting midges (Diptera: Ceratopogonidae), are critical in order to assess transmission routes of vector-borne diseases. In this study, we collected and morphologically identified 164 blood-engorged Culicoides females caught in both light traps and permanent 12-m high suction traps during 20082010 in Sweden. Molecular analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene in the biting midges was performed to verify species classification, discern phylogenetic relationships and uncover possible cryptic species. Bloodmeal analysis using universal vertebrate cytochrome b primers revealed a clear distinction in host selection between mammalophilic and ornithophilic Culicoides species. Host sequences found matches in horse (n = 59), sheep (n = 39), cattle (n = 26), Eurasian elk (n = 1) and 10 different bird species (n = 18). We identified 15 Culicoides species previously recorded in Scandinavia and four additional species haplotypes that were distinctly different from the described species. All ornithophilic individuals (n = 23) were caught exclusively in the suction traps, as were, interestingly, almost all mammalophilic species (n = 41), indicating that many biting midge species may be able to cover long distances after completing a bloodmeal. These results add new information on the composition of Culicoides species and their host preferences and their potential long-distance dispersal while blood-engorged.
  • Alström, Per (författare)
  • Mitochondrial phylogeny of the Eurasian/African reed warbler complex (Acrocephalus, Aves). Disagreement between morphological and molecular evidence and cryptic divergence: A case for resurrecting Calamoherpe ambigua Brehm 1857
  • 2016
  • Ingår i: Molecular Phylogenetics and Evolution. - Elsevier. - 1055-7903 .- 1095-9513. ; 102, s. 30-44
  • Tidskriftsartikel (refereegranskat)abstract
    • A tree based on the mitochondrial cyt b gene for 278 samples from throughout the range of the Eurasian Reed Warbler <em>Acrocephalus scirpaceus</em> - African Reed Warbler <em>A. baeticatus </em>complex shows well supported geographically structured divergence for eight distinct lineages. The phylogenetic structuring together with the clarification of priority, provided by sequence data from seven type specimens, suggests that both taxonomy and distribution boundaries are in need of revision. The Iberian and Moroccan populations form a well-supported Glade, and we propose that these are treated as taxonomically distinct, under the name <em>ambiguus</em> (Brehm, 1857). We propose that the names <em>scirpaceus</em>, <em>fuscus</em>, <em>avicenniae</em>, <em>ambiguus</em>, <em>minor</em>, <em>cinnamomeus</em>, <em>hallae</em> and <em>baeticatus</em> are used for the well supported clades in the complex, which we recommend to treat as one polytypic species, <em>A. scirpaceus</em>, pending studies of gene flow and assortative mating in the contact zones.
  • Alström, Per (författare)
  • Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves: Alaudidae)
  • 2016
  • Ingår i: Molecular Phylogenetics and Evolution. - Elsevier. - 1055-7903 .- 1095-9513. ; 102, s. 233-245
  • Tidskriftsartikel (refereegranskat)abstract
    • The avian genus <em>Calandrella</em> (larks) was recently suggested to be non-monophyletic, and was divided into two genera, of which <em>Calandrella</em> sensu stricto comprises 4-5 species in Eurasia and Africa. We analysed mitochondrial cytochrome b (cytb) and nuclear Restriction-site Associated DNA (RAD) sequences from all species, and for cytb we studied 21 of the 22 recognised subspecies, with the aim to clarify the phylogenetic relationships within the genus and to compare large-scale nuclear sequence patterns with a widely used mitochondrial marker. Cytb indicated deep splits among the currently recognised species, although it failed to support the interrelationships among most of these. It also revealed unexpected deep divergences within <em>C. brachydactyla</em>, <em>C. blanfordi/C erlangeri</em>, <em>C. cinerea</em>, and <em>C. acutirostris</em>. It also suggested that both <em>C. brachydactyla</em> and <em>C. blanfordi</em>, as presently circumscribed, are paraphyletic. In contrast, most of the many subspecies of <em>C brachydactyla</em> and <em>C. cinerea</em> were unsupported by cytb, although two populations of <em>C. cinerea</em> were found to be genetically distinct. The RAD data corroborated the cytb tree (for the smaller number of taxa analysed) and recovered strongly supported interspecific relationships. However, coalescence analyses of the RAD data, analysed in SNAPP both with and without an outgroup, received equally strong support for two conflicting topologies. We suggest that the tree rooted with an outgroup - which is not recommended for SNAPP - is more trustworthy, and suggest that the reliability of analyses performed without any outgroup species should be thoroughly evaluated. We also demonstrate that degraded museum samples can be phylogenetically informative in RAD analyses following careful bioinformatic treatment. We note that the genus <em>Calandrella</em> is in need of taxonomic revision.
  • Alström, Per (författare)
  • Phylogenetic position of the Wallcreeper Tichodroma muraria
  • 2016
  • Ingår i: Journal of Ornithology. - Springer Science Business Media. - 2193-7192 .- 2193-7206. ; 157, s. 913-918
  • Tidskriftsartikel (refereegranskat)abstract
    • The Wallcreeper <em>Tichodroma muraria</em> is usually placed in a monotypic family or subfamily within the superfamily Certhioidea, with assumed close relationships to <em>Certhia</em> (treecreepers), <em>Sitta</em> (nuthatches) and <em>Salpornis</em> (spotted creepers). Previous studies have suggested that <em>Tichodroma</em> is most closely related to <em>Sitta</em>, alternatively to <em>Salpornis</em>. We analysed the relationships of <em>Tichodroma</em> using two mitochondrial and five nuclear loci. The tree based on concatenated sequences strongly supported a sister relationship between <em>Tichodroma</em> and <em>Sitta</em>, as well as between <em>Salpornis</em> and <em>Certhia</em>. However, species tree analysis (MP-EST) was unable to resolve these relationships, and although the concatenation tree remains the best hypothesis, more data are needed to corroborate this.
  • Alström, Per (författare)
  • The Rusty-tailed Flycatcher (Muscicapa ruficauda; Ayes: Muscicapidae) is a member of the genus Ficedula
  • 2016
  • Ingår i: Molecular Phylogenetics and Evolution. - Elsevier. - 1055-7903 .- 1095-9513. ; 102, s. 56-61
  • Tidskriftsartikel (refereegranskat)abstract
    • The phylogenetic relationships of the avian family Muscicapidae (Old World chats and flycatchers) have historically been enigmatic and remain an active area of study. Widespread instances of non-monophyly resulting from misleading morphological and behavioral similarities have merited numerous taxonomic revisions to the group. Here we report one such instance with regard to the Rusty-tailed Flycatcher <em>Muscicapa ruficauda</em>, which has recently been placed in the newly proposed monotypic genus <em>Ripleyia</em>, due to inferred sister relationship to the genus <em>Muscicapa</em> and related genera (Voelker et al., 2016a). This name was later replaced by <em>Ripleyornis</em>, as it was realized that <em>Ripleyia</em> is a junior homonym of a genus of Mollusca (Voelker et al., 2016b). Using a Bayesian phylogenetic assessment of the Muscicapidae with near-complete taxon sampling of the genus <em>Ficedula</em> for five loci, along with an acoustic comparison of <em>M. ruficauda</em> to a subset of other flycatcher species, we show that this species should be reassigned to the genus <em>Ficedula</em> and accordingly that the names <em>Ripleyia</em> and <em>Ripleyornis</em> are both junior synonyms of <em>Ficedula</em>.<br />
  • Hallenberg, Nils, 1947-, et al. (författare)
  • Pseudolagarobasidium (Basidiomycota): on the reinstatement of a genus of parasitic, saprophytic, and endophytic resupinate fungi
  • 2008
  • Ingår i: Botany. - 1916-2804. ; 86:11, s. 1319-1325
  • Tidskriftsartikel (refereegranskat)abstract
    • The small resupinate genus Pseudolagarobasidium (Polyporales, Basidiomycota) presently comprises less than five species, all of which were described from tropical to subtropical regions, and two of which are root parasites on leguminous trees. The genus has recently been synonymized with Radulodon on morphological grounds, and the present study evaluates this proposal in a molecular context. Pseudolagarobasidium was found to constitute a well supported, monophyletic group excluding Radulodon and this synonymy is rejected. The ecological range of the genus spans saprotrophy to parasitism, and this study presents evidence that at least one lineage in Pseudolagarobasidium is endophytic in the cacao tree (Theobroma cacao L.). Key words: Polyporales, Radulodon, phylogeny, plant interactions. Résumé: Le Pseudolagarobasidium (Polyporales, Basidiomycota) constitue un genre de petits champignons résupinés qui comporte actuellement cinq espèces, toutes décrites à partir de régions tropicales ou subtropicales, incluant deux espèces parasites des racines d'arbres de la famille des légumineuses. On en a récemment établi la synonymie avec le genre Radulodon sur la base morphologique, mais les auteurs utilisent ici l'approche moléculaire. On constate que le genre Pseudolagarobasidium constitue un groupe monophylétique robuste excluant les Radulodon ce qui conduit au rejet de cette synonymie. L'amplitude écologique du genre va du saprophytisme au parasitisme, et on présente des preuves qu'au moins une lignée est un endophyte du cacaoyer (Theobroma cacao L.). Mots-clés : Polyporales, Radulon, phylogénie, interactions végétales.
  • Subhash, Santhilal, 1987-, et al. (författare)
  • Sperm Originated Chromatin Imprints and LincRNAs in Organismal Development and Cancer
  • 2020
  • Ingår i: iScience. - 2589-0042. ; 23:6
  • Tidskriftsartikel (refereegranskat)abstract
    • Importance of sperm-derived transcripts and chromatin imprints in organismal development is poorly investigated. Here using an integrative approach, we show that human sperm transcripts are equally important as oocyte. Sperm-specific and sperm-oocyte common transcripts carry distinct chromatin structures at their promoters correlating with corresponding transcript levels in sperm. Interestingly, sperm-specific H3K4me3 patterns at the lincRNA promoters are not maintained in the germ layers and somatic tissues. However, bivalent chromatin at the sperm-specific protein-coding gene promoters is maintained throughout the development. Sperm-specific transcripts reach their peak expression during zygotic genome activation, whereas sperm-oocyte common transcripts are present during early preimplantation development but decline at the onset of zygotic genome activation. Additionally, there is an inverse correlation between sperm-specific and sperm-oocyte lincRNAs throughout the development. Sperm-lincRNAs also show aberrant activation in tumors. Overall, our observations indicate that sperm transcripts carrying chromatin imprints may play an important role in human development and cancer.
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