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  • 1
    In: Scientific Reports, 2018, Vol.8
    Description: A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
    Keywords: Author Correction
    ISSN: Scientific Reports
    E-ISSN: 2045-2322
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  • 2
    In: Molecular Ecology, January 2015, Vol.24(1), pp.235-248
    Description: Micro‐organisms associated with plants and animals affect host fitness, shape community structure and influence ecosystem properties. Climate change is expected to influence microbial communities, but their reactions are not well understood. Host‐associated micro‐organisms are influenced by the climate reactions of their hosts, which may undergo range shifts due to climatic niche tracking, or may be actively relocated to mitigate the effects of climate change. We used a common‐garden experiment and metabarcoding to examine the effect of host relocation and high‐latitude warming on the complex fungal endophytic microbiome associated with leaves of an ecologically dominant boreal forest tree ( L.). We also considered the potential effects of poplar genetic identity in defining the reactions of the microbiome to the treatments. The relocation of hosts to the north increased the diversity of the microbiome and influenced its structure, with results indicating enemy release from plausible pathogens. High‐latitude warming decreased microbiome diversity in comparison with natural northern conditions. The warming also caused structural changes, which made the fungal communities distinct in comparison with both low‐latitude and high‐latitude natural communities, and increased the abundance of plausible pathogens. The reactions of the microbiome to relocation and warming were strongly dependent on host genetic identity. This suggests that climate change effects on host–microbiome systems may be mediated by the interaction of environmental factors and the population genetic processes of the hosts.
    Keywords: Climate Change ; Community Genetics ; Enemy Release ; Metabarcoding ; Micro‐Organism Biogeography ; Plant–Fungal Interactions
    ISSN: 0962-1083
    E-ISSN: 1365-294X
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  • 3
    Language: English
    In: PLoS ONE, 01 January 2017, Vol.12(7), p.e0180284
    Description: Pertusarialean lichens include more than 300 species belonging to several independent phylogenetic lineages. Only some of these phylogenetic clades have been comprehensively sampled for molecular data, and formally described as genera. Here we present a taxonomic treatment of a group of pertusarialean lichens formerly known as "Pertusaria amara-group", "Monomurata-group", or "Variolaria-group", which includes widespread and well-known taxa such as P. amara, P. albescens, or P. ophthalmiza. We generated a 6-locus data set with 79 OTUs representing 75 species. The distinction of the Variolaria clade is supported and consequently, the resurrection of the genus Lepra is followed. Thirty-five new combinations into Lepra are proposed and the new species Lepra austropacifica is described from mangroves in the South Pacific. Lepra is circumscribed to include species with disciform ascomata, a weakly to non-amyloid hymenial gel, strongly amyloid asci without clear apical amyloid structures, containing 1 or 2, single-layered, thin-walled ascospores. Chlorinated xanthones are not present, but thamnolic and picrolichenic acids occur frequently, as well as orcinol depsides. Seventy-one species are accepted in the genus. Although the distinction of the genus from Pertusaria is strongly supported, the relationships of Lepra remain unresolved and the genus is tentatively placed in Pertusariales incertae sedis.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 4
    Language: English
    In: Molecular Phylogenetics and Evolution, July 2014, Vol.76, pp.202-210
    Description: The accurate assessment of species boundaries in symbiotic systems is a prerequisite for the study of speciation, co-evolution and selectivity. Many studies have shown the high genetic diversity of green algae from the genus , the most common photobiont of lichen-forming fungi. However, the phylogenetic relationships, and the amount of cryptic diversity of these algae are still poorly understood, and an adequate species concept for trebouxiophycean algae is still missing. In this study we used a multifaceted approach based on coalescence (GMYC, STEM) and phylogenetic relationships to assess species boundaries in the trebouxioid photobionts of the lichen-forming fungus . We further investigated whether putative species of found in are shared with other lichen-forming fungi. We found that is associated with at least five species of and most of them are shared with other lichen-forming fungi, showing different patterns of species-to-species and species-to-community interactions. We also show that one of the putative species is found exclusively in association with and is restricted to thalli from localities with Mediterranean microclimate. We suggest that the species delimitation method presented in this study is a promising tool to address species boundaries within the heterogeneous genus .
    Keywords: Terrestrial Green Algae ; Cryptic Species ; Environmental Specialization ; Photobiont Sharing ; Lasallia Pustulata ; Biology
    ISSN: 1055-7903
    E-ISSN: 1095-9513
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  • 5
    Language: English
    In: Journal of Biotechnology, December 2013, Vol.168(4), pp.589-600
    Description: MicroRNAs (miRNAs) are promising targets for cell engineering through modulation of crucial cellular pathways. An effective introduction of miRNAs into the cell is a prerequisite to reliably study microRNA function. Previously, non-viral delivery of nucleic acids has been demonstrated to be cell type as well as culture medium dependent. Due to their importance for biopharmaceutical research and manufacturing, Chinese hamster ovary (CHO) and Cevec's Amniocyte Production (CAP) cells were used as host cell lines to investigate transfection reagents with respect to successful delivery of small non-coding RNAs (ncRNAs) and their ability to allow for biological activity of miRNAs and small interfering RNAs (siRNAs) within the cell. In the present study, we screened numerous transfection reagents for their suitability to successfully deliver miRNA mimics into CHO DG44 and CAP cells. Our investigation revealed that the determination of transfection efficiency for a given transfection reagent alone is not sufficient to draw conclusions about its ability to maintain the functionality of the miRNA. We could show that independent from high transfection rates observed for several reagents only one was suitable for efficient introduction of functional miRNA mimics into cells cultured in complex protein production media. We provide evidence for the functionality of transferred ncRNAs by demonstrating siRNA-mediated changes in protein levels and cellular phenotype as well as decreased ( ) transcript levels by its upstream miR-1 regulator. Furthermore, the process could be shown to be scalable which has important implications for biotechnological applications.
    Keywords: Microrna ; Transfection ; Cho ; CAP ; Screenfect A ; Engineering
    ISSN: 0168-1656
    E-ISSN: 1873-4863
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  • 6
    Language: English
    In: Sci Rep, 2017, Vol.7(1), pp.14881-14881
    Description: The metagenome skimming approach, i.e. low coverage shotgun sequencing of multi-species assemblages and subsequent reconstruction of individual genomes, is increasingly used for in-depth genomic characterization of ecological communities. This approach is a promising tool for reconstructing genomes of facultative symbionts, such as lichen-forming fungi, from metagenomic reads. However, no study has so far tested accuracy and completeness of assemblies based on metagenomic sequences compared to assemblies based on pure culture strains of lichenized fungi. Here we assembled the genomes of Evernia prunastri and Pseudevernia furfuracea based on metagenomic sequences derived from whole lichen thalli. We extracted fungal contigs using two different taxonomic binning methods, and performed gene prediction on the fungal contig subsets. We then assessed quality and completeness of the metagenome-based assemblies using genome assemblies as reference which are based on pure culture strains of the two fungal species. Our comparison showed that we were able to reconstruct fungal genomes from uncultured lichen thalli, and also cover most of the gene space (86–90%). Metagenome skimming will facilitate genome mining, comparative (phylo)genomics, and population genetics of lichen-forming fungi by circumventing the time-consuming, sometimes unfeasible, step of aposymbiotic cultivation.
    Keywords: Biology;
    ISSN: 2045-2322
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  • 7
    Language: English
    In: PLoS ONE, 01 January 2015, Vol.10(5), p.e0124625
    Description: Species recognition in lichen-forming fungi has been a challenge because of unsettled species concepts, few taxonomically relevant traits, and limitations of traditionally used morphological and chemical characters for identifying closely related species. Here we analyze species diversity in the cosmopolitan genus Protoparmelia s.l. The ~25 described species in this group occur across diverse habitats from the boreal-arctic/alpine to the tropics, but their relationship to each other remains unexplored. In this study, we inferred the phylogeny of 18 species currently assigned to this genus based on 160 specimens and six markers: mtSSU, nuLSU, ITS, RPB1, MCM7, and TSR1. We assessed the circumscription of species-level lineages in Protoparmelia s. str. using two coalescent-based species delimitation methods--BP&P and spedeSTEM. Our results suggest the presence of a tropical and an extra-tropical lineage, and eleven previously unrecognized distinct species-level lineages in Protoparmelia s. str. Several cryptic lineages were discovered as compared to phenotype-based species delimitation. Many of the putative species are supported by geographic evidence.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 8
    Language: English
    In: Fungal Ecology, April 2013, Vol.6(2), pp.141-151
    Description: To facilitate marker selection in sequence-based studies on genetic diversity and symbiont selectivity in lichens we conducted a comparison of eight molecular markers in the lichen-forming fungus and its trebouxioid photobiont. We compared mtSSU rDNA, mtLSU rDNA, , (mycobiont) and nrITS rDNA, , psbJ-L intergenic spacer, (photobiont) of 45 individuals from European populations of . Mycobiont and photobiont loci had congruent phylogenetic signals. Based on the results of this study we recommend the use of and (mycobiont), and nrITS rDNA and (photobiont). In this specific study system we found no sequence variability in the mycobiont loci , nrITS rDNA, , and , which we sequenced for a subset of individuals. We had limited success amplifying (mycobiont), actin and chloroplast LSU rDNA (photobiont), however, we do not rule out that these loci could be valuable markers in other species.
    Keywords: Adaptation ; Barcoding ; Genetic Diversity ; Lasallia Pustulata ; Lichen ; Mycobiont ; Photobiont ; Phylogeny ; Population Biology ; Selectivity ; Trebouxia ; Botany
    ISSN: 1754-5048
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  • 9
    Language: English
    In: Scientific reports, 05 June 2018, Vol.8(1), pp.8624
    Description: The implementation of HTS (high-throughput sequencing) approaches is rapidly changing our understanding of the lichen symbiosis, by uncovering high bacterial and fungal diversity, which is often host-specific. Recently, HTS methods revealed the presence of multiple photobionts inside a single thallus in several lichen species. This differs from Sanger technology, which typically yields a single, unambiguous algal sequence per individual. Here we compared HTS and Sanger methods for estimating the diversity of green algal symbionts within lichen thalli using 240 lichen individuals belonging to two species of lichen-forming fungi. According to HTS data, Sanger technology consistently yielded the most abundant photobiont sequence in the sample. However, if the second most abundant photobiont exceeded 30% of the total HTS reads in a sample, Sanger sequencing generally failed. Our results suggest that most lichen individuals in the two analyzed species, Lasallia hispanica and L. pustulata, indeed contain a single, predominant green algal photobiont. We conclude that Sanger sequencing is a valid approach to detect the dominant photobionts in lichen individuals and populations. We discuss which research areas in lichen ecology and evolution will continue to benefit from Sanger sequencing, and which areas will profit from HTS approaches to assessing symbiont diversity.
    Keywords: Chlorophyta -- Classification ; DNA Barcoding, Taxonomic -- Methods ; High-Throughput Nucleotide Sequencing -- Methods ; Lichens -- Growth & Development ; Metagenomics -- Methods ; Sequence Analysis, DNA -- Methods
    E-ISSN: 2045-2322
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  • 10
    Language: English
    In: Fungal Ecology, October 2013, Vol.6(5), pp.466-470
    Keywords: Botany
    ISSN: 1754-5048
    Source: ScienceDirect Journals (Elsevier)
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