Secondary structure prediction of ITS rRNA region and molecular phylogeny: an integrated approach for the precise speciation of Muscodor species

Kapoor, Neha; Gambhir, Lokesh; Saxena, Sanjai

doi:10.1007/s13213-018-1381-8

Cited by 8 publications

(8 citation statements)

References 48 publications

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“…Q. phakopsoricola also presents an unpaired uracil in helix II, instead of a U-U mismatch, which is known for some fungi (Glass et al 2013). The observed pattern of the secondary structure of the ITS molecule of Q. phakopsoricola is similar to the pattern of secondary structures of functional ITS2 known in other fungi (Freire et al 2012;Glass et al 2013;Rampersad 2014;Kapoor et al 2018).…”

Section: Morphology and Taxonomic Identitysupporting

confidence: 68%

“…In the 5.8S gene (M1, M2, M3), at least three motifs are conserved among angiosperms (Harpke and Peterson 2008) and the same or slightly modified sequence strings occur in fungi. In total, across all three regions, a single substitution change is reported in Colletotrichum (Rampersad 2014), two in Induratia ("Muscodor", Kapoor et al 2018), three in Batrachochytrium dendrobatidis Longcore, Pessier & D.K. Nichols (Glass et al 2013), and four in Phakopsora (Freire et al 2012) and Conidiobolus (Glass et al 2013).…”

Section: Morphology and Taxonomic Identitymentioning

confidence: 99%

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Nucleotide composition bias of rDNA sequences as a source of phylogenetic artifacts in Basidiomycota—a case of a new lineage of a uredinicolous Ramularia-like anamorph with affinities to Ustilaginomycotina

et al. 2021

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A Ramularia-like hyphomycete was discovered on uredinia of Phakopsora ampelopsidis on leaves of wild Ampelopsis brevipedunculata and cultivated Parthenocissus tricuspidata in several cities in Taiwan. The micromorphology of this fungicolous fungus is similar to that of species of the genus Ramularia which are mostly plant parasites but some species grow on rust fungi. Analyses of SSU and LSU rDNA and RPB2 gene sequence data and of ultrastructural features observed by scanning and transmission electron microscopy revealed that the fungus represents a novel lineage within the Ustilaginomycotina. The name Quasiramularia phakopsoricola is proposed for this new species in a new genus, a new family, and a new order. Sequence data obtained for ITS1, 5.8S, and ITS2 rDNA, however, did not match to any known fungal lineage. Bioinformatics analyses showed that these sequence data are extremely GC poor, but most probably do not represent a pseudogene. Extreme deviations of GC content can be observed in several lineages of Basidiomycota. Such variations affect the results of phylogenetic analyses and are an important source of artifacts.

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Section: Morphology and Taxonomic Identitysupporting

confidence: 68%

Section: Morphology and Taxonomic Identitymentioning

confidence: 99%

Nucleotide composition bias of rDNA sequences as a source of phylogenetic artifacts in Basidiomycota—a case of a new lineage of a uredinicolous Ramularia-like anamorph with affinities to Ustilaginomycotina

et al. 2021

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“…Undeniably, ITS2 secondary structure plays a critical part in rRNA processing and formation of functional 60S subunit. Despite considerable variation in its nucleotide sequences, a typical eukaryotic ITS2 secondary structure (also known as four-helix or ring-pin model) consists of four helices that are maintained through several common and shared structure motifs including internal loops, hairpin loops, and bulges (Schultz et al, 2005;Kapoor et al, 2018). These structure motifs impart stability to the ITS2 structure and are reportedly susceptible to polymorphisms that further give rise to non-canonical G-U pairs within the conserved regions of double-stranded helices (Cote and Peculis, 2001;Freire et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

Isolation and Characterization of an Endophytic Fungus Colletotrichum coccodes Producing Tyrosol From Houttuynia cordata Thunb. Using ITS2 RNA Secondary Structure and Molecular Docking Study

Talukdar

Padhi

Kumar

et al. 2021

Front. Bioeng. Biotechnol.

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An endophytic fungus isolated from healthy leaf tissues of Houttuynia cordata Thunb., an ethnomedicinal plant of North East India, showed a considerable amount of antimicrobial activity. The ethyl acetate extract of the fungal culture filtrates displayed promising antimicrobial activity against a panel of clinically significant pathogens including Candida albicans, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. Bioassay guided purification of the organic extract using column and thin layer chromatography yielded a pure homogenous compound which was identified using spectroscopic methods (essentially by 1H NMR and MS) as tyrosol, a well-known phenylethanoid present in several natural sources. Besides, molecular docking studies against tyrosyl tRNA synthetases (TyrRS) of S. aureus (PDB ID: 1JIL) and E. coli (PDB ID: 1VBM), and CYP45014α-lanosterol demethylase (CYP51) of C. albicans (PDB ID: 5FSA) revealed tyrosol has a strong binding affinity with the enzyme active site residues. The fungus was identified as Colletotrichum sp. and characterized by its genomic ITS rDNA and ITS2 sequences. Phylogenetic analyses showed clustering of our isolate with Colletotrichum coccodes. Species of Colletotrichum are also reported to be plant pathogens. Therefore, to confirm the endophytic lifestyle of the isolate, ITS2 RNA secondary structure study was undertaken. The result indicated our isolate exhibited differences in the folding pattern as well as in motif structures when compared to those of pathogenic C. coccodes. The findings indicated that endophytic fungi harboring H. cordata could be explored as a potent source of antimicrobial agents.

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“…C. cicadae was cultured in a 28°C incubator for 5 days and the colony morphology was observed. DNA extraction, PCR amplification, fragment purification, and sequencing were conducted as previously reported ( 17 ). The obtained sequences were compared by BLAST and the phylogenetic tree was constructed using MEGA-X.…”

Section: Methodsmentioning

confidence: 99%

Optimisation of the production of a selenium-enriched polysaccharide from Cordyceps cicadae S1 and its structure and antioxidant activity

Zhuansun

Liu

et al. 2022

Front. Nutr.

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The fermentation medium of a newly identified Cordyceps cicadae S1 was optimized by response surface methodology, with the optimal medium containing sucrose (80 g/L), yeast powder (60 g/L), KH2PO4 (5 g/L), MgSO4·7H2O (1 g/L) and Na2SeO3 (0. 1 g/L). Under these conditions, the extracellular polysaccharide yield was 8.09 g/L. A novel selenium-enriched polysaccharide (PACI-1) was isolated from Cordyceps cicadae, purified and identified as a homofructose polysaccharide with a low average molecular weight of 9.95 × 103 Da. The fine structure of PACI-1 was analyzed using NMR, CD, and AFM. Additionally, the in vitro antioxidant results showed that the PACI-1 had stronger antioxidant capacity than natural polysaccharides. These results provided a candidate strain for producing selenium polysaccharide and a new polysaccharide from C. cicadae, which showed good antioxidant activity.

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Secondary structure prediction of ITS rRNA region and molecular phylogeny: an integrated approach for the precise speciation of Muscodor species

Cited by 8 publications

References 48 publications

Nucleotide composition bias of rDNA sequences as a source of phylogenetic artifacts in Basidiomycota—a case of a new lineage of a uredinicolous Ramularia-like anamorph with affinities to Ustilaginomycotina

Nucleotide composition bias of rDNA sequences as a source of phylogenetic artifacts in Basidiomycota—a case of a new lineage of a uredinicolous Ramularia-like anamorph with affinities to Ustilaginomycotina

Isolation and Characterization of an Endophytic Fungus Colletotrichum coccodes Producing Tyrosol From Houttuynia cordata Thunb. Using ITS2 RNA Secondary Structure and Molecular Docking Study

Optimisation of the production of a selenium-enriched polysaccharide from Cordyceps cicadae S1 and its structure and antioxidant activity

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