Evaluation of ITS2 molecular morphometrics effectiveness in species delimitation of Ascomycota – A pilot study

Sundaresan, N.; Sahu, Amit Kumar; Jagan, Enthai Ganeshan; Pandi, Mohan

doi:10.1016/j.funbio.2019.05.002

Cited by 7 publications

(5 citation statements)

References 63 publications

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“…Subsequently, the secondary structure of ITS2 was determined using Homology Modelling (HM) of the ITS2 (Internal Transcribed Spacer 2 Ribosomal RNA Database) Workbench ( ) access date 18 May 2021, with a default setting at 75% threshold for helix transfer similarity. A gap open penalty of 20 and a gap extension penalty of 4 were used for the transfer helices [ 65 , 66 ].…”

Section: Methodsmentioning

confidence: 99%

Specification and DNA Barcoding of Thai Traditional Remedy for Chronic Kidney Disease: Pikad Tri-phol-sa-mut-than

Thariwong

Intharuksa

Sirisa-ard

et al. 2021

Plants

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The Pikad Tri-phol-sa-mut-than (TS) remedy, a Thai traditional medicine, is officially recorded in Tamra Paetsart Sonkrau Chabub Anurak for its capabilities in treating kidney deficiency. TS remedy is composed of three fruit species—Aegle marmelos (L.) Corrêa., Coriandrum sativum L., and Morinda citrifolia L.—in an equal part by weight. The quality of the raw material is one of the essential factors that can affect the effectiveness and safety of treatment by herbal remedy. The pharmacognostic evaluation and DNA barcode of the three fruit species and TS remedy were performed in this study to authenticate them from contamination, and to provide the scientific database for further uses. Macroscopic and microscopic examination, chemical profile by TLC, and DNA barcoding were employed to positively identify the raw materials bought from the herbal market, especially the powder form. Consequently, the outcomes of this investigation can be used to develop an essential and effective tool for the authentication of crude drugs and herbal remedies.

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Section: Methodsmentioning

confidence: 99%

Specification and DNA Barcoding of Thai Traditional Remedy for Chronic Kidney Disease: Pikad Tri-phol-sa-mut-than

Thariwong

Intharuksa

Sirisa-ard

et al. 2021

Plants

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“…Ref. [47] explored the utility of ITS2 molecular morphometrics for delineating Ascomycota species, emphasizing the effectiveness of this approach in elucidating fungal species boundaries and potentially easing challenges associated with molecular characterization. Integration of secondary structure information with primary sequencing data significantly enhances species identification within plant genera and sheds light on their evolutionary history.…”

Section: Discussionmentioning

confidence: 99%

Endophytic Fungal Diversity in Hardwickia binata: Bridging the Gap between Traditional and Modern Techniques

Joe Xavier Sneha,

Thangavel,

Mani

et al. 2024

Microbiology Research

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Endophytic fungus is crucial for maintaining plant health and defense mechanisms, acting as protective barriers against pathogens, and producing medicinally beneficial bioactive compounds. Genome sequencing and metagenomics have significantly enhanced the understanding of fungal diversity and metabolic capabilities, enabling the identification of new genes and substances. Traditional culture-dependent methods have been complemented by culture-independent techniques, offering a more comprehensive view of fungal diversity. Using both culture-dependent and culture-independent techniques, the present research investigation explored the diversity of endophytic fungi encountered in the foliage of Hardwickia binata. The study examined the topographical characteristics and nutritional content of soil samples collected from the locality of the selected plant sample, H. binata, to better comprehend the effects on the plant’s growth. The balanced nutrient constituted approximately a pH of 7.2, which suggested an alkaline nature and promoted plant development. The ratio of nitrogen, phosphorous, and potassium remained 3:1:1. A total of 25 fungal isolates, categorized into 17 morphotypes, were obtained using the culture-dependent approach; Curvularia and Nigrospora emerged as the most common genera. Furthermore, the prediction of the ITS2 secondary structure supports the identification of species, highlighting a wide variety of fungal species present in H. binata. The culture-independent approach generated 69,570 high-quality sequences, identifying 269 Operational Taxonomic Units (OTUs). The dominant Ascomycota phylum, along with various genera, indicated a rich fungal community associated with H. binata. This study advances the understanding of the endophytic fungus communities that are associated with H. binata and the nature of soil ecology. The findings emphasize the significance of holistic techniques in the study of microbial dynamics within plant systems as well as their implications for ecosystem management and plant health.

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“…We take these results as independent support for the proposed species list (Table 4), but it is admissible that part of those twelve LSU-only clades might be considered for merging with others, especially as the respective ITS sequences become known. We wanted to explore the possible utility of RNA secondary structure reconstructions as a new level of phylogenetic support, as has been done in a variety of contexts (Zhuang and Liu 2012;Kapoor et al 2018;Sundaresan et al 2019). Our use of RNAalifold (Bernhart et al 2008) aimed at verifying, within the framework of the collected sequences, whether the taxonomic results from the onedimensional (sequence-only) analyses could be reinforced by working with the secondary structures.…”

Section: Discussionmentioning

confidence: 99%

Charting Taxa inAmanitaSectionAmidella(Basidiomycota:Amanitaceae)

Oliveira,

Arraiano-Castilho

2024

Preprint

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Species determination in the Amidella clade is notoriously difficult, because of the relative dearth of field characters and the rather common occurrence of homoplasies. This results in a substantial number of misnamed and unnamed collections, a misapprehension of the geographic range of known species, and a gross underestimation of the number of species it contains. To assess the diversity that should be considered as part of Amidella, DNA sequences available for this group were retrieved in public nucleotide databases, using a combination of approaches to achieve a comprehensive representation. Phylogenetic analysis based on the aligned ITS sequences, consistently with the results from other molecular markers (nLSU, RPB2, TEF1, BTUB), suggests five major clades: one containing the type species Amanita volvata, another for Amanita ponderosa and allies, a third one (roughly half of all species) with Amanita lepiotoides, and two others without valid species yet. Consensus rRNA folding structures were obtained for these clades, maintaining their congruence and separation from neighbouring congeneric clades. At species level, around 78 clades were delimited, of which only up to 17 can be assigned a valid name, with a few more corresponding to provisional taxa listed in the amanitaceae.org website. Two further species without assigned sequences might correspond to the proposed clades. The current evidence suggests a rather narrow geographic range for most of these clades. This study provides a phylogeny-arranged outlook of the worldwide distribution of Amidella species, and a framework for designing clade-specific molecular markers to assist in identification.

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Evaluation of ITS2 molecular morphometrics effectiveness in species delimitation of Ascomycota – A pilot study

Cited by 7 publications

References 63 publications

Specification and DNA Barcoding of Thai Traditional Remedy for Chronic Kidney Disease: Pikad Tri-phol-sa-mut-than

Specification and DNA Barcoding of Thai Traditional Remedy for Chronic Kidney Disease: Pikad Tri-phol-sa-mut-than

Endophytic Fungal Diversity in Hardwickia binata: Bridging the Gap between Traditional and Modern Techniques

Charting Taxa inAmanitaSectionAmidella(Basidiomycota:Amanitaceae)

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