Photobiont associations in co-occurring umbilicate lichens with contrasting modes of reproduction in coastal Norway

2016 ◽  
Vol 48 (5) ◽  
pp. 545-557 ◽  
Author(s):  
Geir HESTMARK ◽  
François LUTZONI ◽  
Jolanta MIADLIKOWSKA
Keyword(s):  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Sampling Site ◽  
Internal Transcribed Spacer Region ◽  
Phylogenetic Placement ◽  
Lichen Symbiosis ◽  
Lasallia Pustulata ◽  
Green Algal ◽  
Coastal Cliffs ◽  
Algal Genus

AbstractThe identity and phylogenetic placement of photobionts associated with two lichen-forming fungi, Umbilicaria spodochroa and Lasallia pustulata were examined. These lichens commonly grow together in high abundance on coastal cliffs in Norway, Sweden and Finland. The mycobiont of U. spodochroa reproduces sexually through ascospores, and must find a suitable algal partner in the environment to re-establish the lichen symbiosis. Lasallia pustulata reproduces mainly vegetatively using symbiotic propagules (isidia) containing both symbiotic partners (photobiont and mycobiont). Based on DNA sequences of the internal transcribed spacer region (ITS) we detected seven haplotypes of the green-algal genus Trebouxia in 19 pairs of adjacent thalli of U. spodochroa and L. pustulata from five coastal localities in Norway. As expected, U. spodochroa associated with a higher diversity of photobionts (seven haplotypes) than the mostly asexually reproducing L. pustulata (four haplotypes). The latter was associated with the same haplotype in 15 of the 19 thalli sampled. Nine of the lichen pairs examined share the same algal haplotype, supporting the hypothesis that the mycobiont of U. spodochroa might associate with the photobiont ‘pirated’ from the abundant isidia produced by L. pustulata that are often scattered on the cliff surfaces. Up to six haplotypes of Trebouxia were found within a single sampling site, indicating a low level of specificity of both mycobionts for their algal partner. Most photobiont strains associated with species of Umbilicaria and Lasallia, including samples from this study, represent phylogenetically closely related taxa of Trebouxia grouped within a small number of main clades (Trebouxia sp., T. simplex/T. jamesii, and T. incrustata+T. gigantea). Three of the photobiont haplotypes were found only in U. spodochroa thalli.

Species boundaries and phylogenetic relationships within the green algal genus Codium (Bryopsidales) based on plastid DNA sequences

2007 ◽  
Vol 44 (1) ◽  
pp. 240-254 ◽  
Author(s):  
Heroen Verbruggen ◽  
Frederik Leliaert ◽  
Christine A. Maggs ◽  
Satoshi Shimada ◽  
Tom Schils ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Plastid Dna ◽  
Species Boundaries ◽  
Green Algal ◽  
Algal Genus

Kamalia indica, a new genus and species belonging to Diaporthales (Ascomycota, Fungi) described based on morphology and molecular phylogeny

Phytotaxa ◽  
2019 ◽  
Vol 425 (4) ◽  
pp. 233-243
Author(s):  
SHIWALI RANA ◽  
SANJAY KUMAR SINGH
Keyword(s):  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
New Genus ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Type Specimen ◽  
Morphological Description ◽  
Fungal Culture ◽  
Internal Transcribed Spacer Region

A fungal taxa isolated from leaf spots of Mallotus philippensis from Kangra district of North-Western Himalayan region of India is established as a new genus based on morphological characters of asexual-morphs, cultural characteristics and phylogenetic analyses of the partial nuclear ribosomal 28S large subunit (LSU) and internal transcribed spacer (ITS) rDNA sequence data. The generic placement of the genus has been determined based on DNA sequences from authenticated isolates. The present taxon has turned out to be distinct, showing nearly 90% identity with other known genera in Diaporthales based on nrDNA internal transcribed spacer region. The morphological description is provided for the new taxa and compared with the similar taxa belonging to the order Diaporthales. The culture was found to show heavy sporulation in all kind of media. The type specimen and ex type culture have been deposited in the Ajrekar Mycological Herbarium (AMH) and National Fungal Culture Collection of India (NFCCI-WDCM 932), respectively.

scholarly journals Phylogenetic Trees of Aecial-Stage Rust Fungus, Puccinia paederiae (Dietel) Gorlenko Causing Gall on Paederia linearis Hook f.

2017 ◽  
Vol 15 (10) ◽  
pp. 739-752
Author(s):  
Wuttiwat JITJAK ◽  
Niwat SANOAMUANG
Keyword(s):  
Bayesian Methods ◽  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Rust Fungus ◽  
Large Subunit ◽  
Molecular Data ◽  
Small Subunit ◽  
Phylogenetic Study ◽  
Internal Transcribed Spacer Region

A rust fungus, Puccinia paederiae (Dietel) Gorlenko causing galls on the stem of the skunk vine (Paederia linearis Hook. f. var. linealis and P. linealis var. palida (Craib) Puff) was collected for phylogenetic study as no molecular data was exclusively available for this fungus. Three regions of ribosomal DNA sequences, small subunit (SSU), large subunit (LSU) and internal transcribed spacer region 1 (ITS1) were employed. The results of maximum parsimony and Bayesian methods suggested that among the trees with these sequences, this fungus was nested in Pucciniaceae clades and Puccinia species with supportive statistical values. This is the first report on the phylogenetic analysis using multiple genes of the rust, P. paederiae.

scholarly journals The Lichens’ Microbiota, Still a Mystery?

2021 ◽  
Vol 12 ◽  
Author(s):  
Maria Grimm ◽  
Martin Grube ◽  
Ulf Schiefelbein ◽  
Daniela Zühlke ◽  
Jörg Bernhardt ◽  
...  
Keyword(s):  
Higher Plants ◽  
Sampling Site ◽  
Protective Layer ◽  
Global Scale ◽  
Core Microbiome ◽  
Lichen Symbiosis ◽  
Green Algal ◽  
Wide Range ◽  
Terrestrial Habitats ◽  
Ecological Continuity

Lichens represent self-supporting symbioses, which occur in a wide range of terrestrial habitats and which contribute significantly to mineral cycling and energy flow at a global scale. Lichens usually grow much slower than higher plants. Nevertheless, lichens can contribute substantially to biomass production. This review focuses on the lichen symbiosis in general and especially on the model species Lobaria pulmonaria L. Hoffm., which is a large foliose lichen that occurs worldwide on tree trunks in undisturbed forests with long ecological continuity. In comparison to many other lichens, L. pulmonaria is less tolerant to desiccation and highly sensitive to air pollution. The name-giving mycobiont (belonging to the Ascomycota), provides a protective layer covering a layer of the green-algal photobiont (Dictyochloropsis reticulata) and interspersed cyanobacterial cell clusters (Nostoc spec.). Recently performed metaproteome analyses confirm the partition of functions in lichen partnerships. The ample functional diversity of the mycobiont contrasts the predominant function of the photobiont in production (and secretion) of energy-rich carbohydrates, and the cyanobiont’s contribution by nitrogen fixation. In addition, high throughput and state-of-the-art metagenomics and community fingerprinting, metatranscriptomics, and MS-based metaproteomics identify the bacterial community present on L. pulmonaria as a surprisingly abundant and structurally integrated element of the lichen symbiosis. Comparative metaproteome analyses of lichens from different sampling sites suggest the presence of a relatively stable core microbiome and a sampling site-specific portion of the microbiome. Moreover, these studies indicate how the microbiota may contribute to the symbiotic system, to improve its health, growth and fitness.

Gymnopus barbipes and G. dysodes, new records for Pakistan

Mycotaxon ◽  
2020 ◽  
Vol 135 (1) ◽  
pp. 203-212
Author(s):  
Malka Saba ◽  
Junaid Khan ◽  
Samina Sarwar ◽  
Hassan Sher ◽  
Abdul Nasir Khalid
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
New Records ◽  
Phylogenetic Analyses ◽  
Internal Transcribed Spacer Region

Morphological and phylogenetic analyses were conducted to identify Gymnopus species collected in Pakistan during 2013–14. Phylogenetic analysis was performed using internal transcribed spacer region (ITS) of ribosomal DNA sequences. Among the collected taxa, we identified Gymnopus barbipes and G. dysodes, represent new records for Pakistan. Their detailed descriptions and illustrations are also provided.

scholarly journals Molecular phylogenetic analyses of Drakaeinae: Diurideae (Orchidaceae) based on DNA sequences of the internal transcribed spacer region

2014 ◽  
Vol 27 (1) ◽  
pp. 3 ◽  
Author(s):  
Joseph T. Miller ◽  
Mark A. Clements
Keyword(s):  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Internal Transcribed Spacer Region ◽  
Orchid Species ◽  
Weak Support ◽  
Separate Genus ◽  
Rdna Sequences ◽  
Molecular Phylogenetic ◽  
Taxonomic Summary

Results of the analysis of rDNA sequences based on 55 collections representative of 32 Drakaeinae orchid species and outgroups supported the monophyly of the subtribe, with weak support for the inclusion of Spiculaea, and revealed six strongly supported monophyletic, well defined morphological groups. Caleana is monophyletic. Chiloglottis s.lat. is monophyletic when Simpliglottis and Myrmechila are included. Our results also suggested that the segregate genus Phoringopsis is better treated as part of Arthrochilus.There is sufficient molecular and morphological support for recognition of the leafless, mycroheterotrophic Thynninorchis to be maintained as a separate genus. A taxonomic summary is provided, including reassignment of taxa at generic ranks and new combinations for Caleana alcockii (Hopper & A.P.Br.) M.A.Clem., Caleana brockmanii (Hopper & A.P.Br.) M.A.Clem., Caleana disjuncta (D.L.Jones) M.A.Clem., Caleana dixonii (Hopper & A.P.Br.) M.A.Clem., Caleana gracilicordata (Hopper & A.P.Br.) M.A.Clem., Caleana granitica (Hopper & A.P.Br.) M.A.Clem., Caleana hortiorum (Hopper & A.P.Br.) M.A.Clem., Caleana lyonsii (Hopper & A.P.Br.) M.A.Clem., Caleana parvula (Hopper & A.P.Br.) M.A.Clem., Caleana terminalis (Hopper & A.P.Br.) M.A.Clem. and Caleana triens (Hopper & A.P.Br.) M.A.Clem.

scholarly journals The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0253772
Author(s):  
Rosa E. Prahl ◽  
Shahjahan Khan ◽  
Ravinesh C. Deo
Keyword(s):  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Its Region ◽  
Growth Conditions ◽  
Genetic Distances ◽  
Its Sequences ◽  
Internal Transcribed Spacer Region ◽  
Culture Characteristics

Many fungi require specific growth conditions before they can be identified. Direct environmental DNA sequencing is advantageous, although for some taxa, specific primers need to be used for successful amplification of molecular markers. The internal transcribed spacer region is the preferred DNA barcode for fungi. However, inter- and intra-specific distances in ITS sequences highly vary among some fungal groups; consequently, it is not a solely reliable tool for species delineation. Ampelomyces, mycoparasites of the fungal phytopathogen order Erysiphales, can have ITS genetic differences up to 15%; this may lead to misidentification with other closely related unknown fungi. Indeed, Ampelomyces were initially misidentified as other pycnidial mycoparasites, but subsequent research showed that they differ in pycnidia morphology and culture characteristics. We investigated whether the ITS2 nucleotide content and secondary structure was different between Ampelomyces ITS2 sequences and those unrelated to this genus. To this end, we retrieved all ITS sequences referred to as Ampelomyces from the GenBank database. This analysis revealed that fungal ITS environmental DNA sequences are still being deposited in the database under the name Ampelomyces, but they do not belong to this genus. We also detected variations in the conserved hybridization model of the ITS2 proximal 5.8S and 28S stem from two Ampelomyces strains. Moreover, we suggested for the first time that pseudogenes form in the ITS region of this mycoparasite. A phylogenetic analysis based on ITS2 sequences-structures grouped the environmental sequences of putative Ampelomyces into a different clade from the Ampelomyces-containing clades. Indeed, when conducting ITS2 analysis, resolution of genetic distances between Ampelomyces and those putative Ampelomyces improved. Each clade represented a distinct consensus ITS2 S2, which suggested that different pre-ribosomal RNA (pre-rRNA) processes occur across different lineages. This study recommends the use of ITS2 S2s as an important tool to analyse environmental sequencing and unveiling the underlying evolutionary processes.

scholarly journals Green-algal photobiont diversity (Trebouxia spp.) in representatives of Teloschistaceae (Lecanoromycetes, lichen-forming ascomycetes)

2014 ◽  
Vol 46 (2) ◽  
pp. 189-212 ◽  
Author(s):  
Shyam NYATI ◽  
Sandra SCHERRER ◽  
Silke WERTH ◽  
Rosmarie HONEGGER
Keyword(s):  
Environmental Conditions ◽  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Geographical Location ◽  
Distribution Patterns ◽  
Bootstrap Support ◽  
Internal Transcribed Spacer Region ◽  
Sterile Culture ◽  
Green Algal ◽  
Xanthoria Parietina

AbstractThe green algal photobionts of 12 Xanthoria, seven Xanthomendoza, two Teloschistes species and Josefpoeltia parva (all Teloschistaceae) were analyzed. Xanthoria parietina was sampled on four continents. More than 300 photobiont isolates were brought into sterile culture. The nuclear ribosomal internal transcribed spacer region (nrITS; 101 sequences) and the large subunit of the RuBiSco gene (rbcL; 54 sequences) of either whole lichen DNA or photobiont isolates were phylogenetically analyzed. ITS and rbcL phylogenies were congruent, although some subclades had low bootstrap support. Trebouxia arboricola,T. decolorans and closely related, unnamed Trebouxia species, all belonging to clade A, were found as photobionts of Xanthoria species. Xanthomendoza species associated with either T. decolorans (clade A), T. impressa, T. gelatinosa (clade I) or with an unnamed Trebouxia species. Trebouxia gelatinosa genotypes (clade I) were the photobionts of Teloschistes chrysophthalmus,T. hosseusianus and Josefpoeltia parva. Only weak correlations between distribution patterns of algal genotypes and environmental conditions or geographical location were observed.

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