ITS2 RNA secondary structure analysis reveals close affinity between endophytic and pathogenic fungi: A case study in Fusarium species

Padhi, Srichandan; Panda, Mrunmaya Kumar; Das, Devaranjan; Tayung, Kumananda

doi:10.1007/s13213-015-1142-x

Cited by 12 publications

(6 citation statements)

References 34 publications

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“…Furthermore, a comparison of ITS2 secondary structure features revealed close affinity among pathogenic and endophytic C. coccodes including significant differences in the folding pattern and motif structures. Similar observations have also been put forth by several studies (Padhi and Tayung, 2013;Padhi et al, 2016) which suggested ITS2 structure could be used as a phylogenetic marker to establish similarities and variations between different lifestyles of the same species. The EtOAc-derived organic extract which showed promising activity in inhibiting the growth of test pathogens was further purified to yield a potent phenolic compound identified to be tyrosol based on its NMR and ESIMS spectra.…”

Section: Discussionsupporting

confidence: 81%

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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Section: Discussionsupporting

confidence: 81%

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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“…Sequence variations led to the differences in the folding pattern as a result of which five distinct patterns were recognized in this study. However the helical patterns of the structures observed were similar to those described for fungi, plant-parasitic nematodes and many other eukaryotes [33,103,109,110]. The ITS2 sequence-secondary structure based phylogenetic tree was highly congruent with the ITS2 sequence and the full length of ITS rDNA sequence based phylogenetic tree topology at the species level.…”

Section: Discussionsupporting

confidence: 71%

“…Based on these rationales, ITS2 molecular morphometrics was employed in this study to delimit the FEF. The secondary structure of the ITS2 regions was predicted using the widely reported Mfold program with default conditions as described in erstwhile reports [33,102,103].…”

Section: Discussionmentioning

confidence: 99%

Internal transcribed spacer 2 (ITS2) molecular morphometric analysis based species delimitation of foliar endophytic fungi from Aglaia elaeagnoidea, Flacourtia inermis and Premna serratifolia

et al. 2019

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Molecular morphometrics is an emerging third dimensional aspect of fungal species delimitation. They have been demonstrated to be more informative than conventional barcoding methods. Hence in this study, foliar endophytic fungal (FEF) assemblages in three Magnoliopsida plants were delimited using nuclear ribosomal internal transcribed spacer 2 (ITS2) sequence—secondary structural features based phylogenetic analysis, also known as molecular morphometrics. A total of 392 FEF isolates were obtained from the Aglaia elaeagnoidea , Flacourtia inermis , and Premna serratifolia leaves and grouped into 98 morphotypes. Among these host plants, P . serratifolia showed the maximum percentage of colonization frequency. Representatives of each morphotype was sequenced and subjected to further molecular characterization. The results revealed that morphotypes were belonged to the phylum of Ascomycota, distributed over two classes (Sordariomycetes (68.59%) and Dothideomycetes (31.41%)), 6 orders and 19 genera. Based on compensatory base changes (CBC) analysis and absolute identity of ITS2 structure, 21, 20 and 23 species were recognized from A . elaeagnoidea , F . inermis , and P . serratifolia respectively. Diversity indices were higher in A . elaeagnoidea , despite it accounted for a modest 16.8% of total isolates recorded in this study. The genus Colletotrichum was predominant in A . elaeagnoidea (39%) and P . serratifolia (48%). Similarly, Diaporthe (43%) was dominant in F . inermis . Several host-specific species were also observed. This study concludes that these plants host diverse species of Ascomycota. To the best of our knowledge, this is the first detailed report on FEF diversity from these plants. Also, the inclusion of ITS2 secondary structure information along with the sequence provides a further dimension to resolve the inherent problems in identification of fungal species.

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“…Our results show large differences in pathogenicity among the three Cryphonectria species included in the study. Differences in lifestyles among congeneric species were previously reported in other fungal genera, including Alternaria (Thomma, 2003), Diaporthe (Gomes et al, 2013), andFusarium (Kuldau andYates, 2000;Padhi et al, 2016). Although the Asian species C. parasitica is an aggressive pathogen on non-Asian Castanea species (Rigling and Prospero, 2018), C. japonica, which is also native to Asia, is likely not pathogenic on European chestnut, nor S1 on European beech and pedunculate oak.…”

Section: Discussionmentioning

confidence: 77%

Testing the Pathogenic Potential of Cryphonectria parasitica and Related Species on Three Common European Fagaceae

Dennert

Rigling

Meyer

et al. 2020

Front. For. Glob. Change

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Invasions by non-native pathogens represent a major threat to managed and natural ecosystems worldwide. Although necessary for adopting preventive strategies, the identification of invasive species before they are introduced is particularly difficult. Indeed, most pathogenic species that have become established in the last decades were first described only after they became invasive. To prevent further biological invasions, not only the early identification of potential new invasive plant pathogens is crucial, but also the assessment of their potential host range. In this study, we determined the pathogenicity and the saprotrophic ability of three Cryphonectria species toward three potential hosts in the family Fagaceae. For this, seedlings and dormant stems of European chestnut (Castanea sativa), pedunculate oak (Quercus robur) and European beech (Fagus sylvatica) were inoculated with different genotypes of C. parasitica (Asian species, invasive in Europe), C. naterciae (European species), and C. japonica (Asian species, not present in Europe). Lesion growth was measured and mortality assessed for 4 months. The highest damage was caused by C. parasitica on European chestnut, while C. japonica and C. naterciae induced significantly smaller lesions on this host species. All three Cryphonectria species did not grow saprophytically on F. sylvatica and Q. robur, but successfully colonized dormant stems of C. sativa. In the context of biological invasions, our study shows that the Asian C. japonica most likely represents a much less severe threat than C. parasitica for the tested European host species. Nonetheless, the ability of C. naterciae and C. japonica to saprotrophically colonize fresh chestnut wood may suggest that they could become established in chestnut forests and eventually infect weakened chestnut trees or other hosts not tested in this study.

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ITS2 RNA secondary structure analysis reveals close affinity between endophytic and pathogenic fungi: A case study in Fusarium species

Cited by 12 publications

References 34 publications

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

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

Internal transcribed spacer 2 (ITS2) molecular morphometric analysis based species delimitation of foliar endophytic fungi from Aglaia elaeagnoidea, Flacourtia inermis and Premna serratifolia

Testing the Pathogenic Potential of Cryphonectria parasitica and Related Species on Three Common European Fagaceae

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