Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates

Gautam, Ajay Kumar; Verma, Rajnish Kumar; Avasthi, Shubhi; Sushma, .; Bohra, Yogita; Devadatha, Bandarupalli; Niranjan, Mekala; Suwannarach, Nakarin

doi:10.3390/jof8030226

Cited by 30 publications

(14 citation statements)

References 485 publications

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“…Ancestor state reconstruction currently requires inferring phenotypes of ancestral species using observations from present-day species [ 55 , 56 ]. As new classical and molecular methods for identifying fungi continue to develop [ 57 ], ancestor state reconstruction analysis of fungal taxonomy is at the forefront of a new trend [ 8 , 58 , 59 , 60 ]. Future studies on species diversity and evolution of Phyllachora species require more extensive sampling and high-quality molecular data.…”

Section: Discussionmentioning

confidence: 99%

Taxonomy, Phylogenetic and Ancestral Area Reconstruction in Phyllachora, with Four Novel Species from Northwestern China

et al. 2022

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The members of Phyllachora are biotrophic, obligate plant parasitic fungi featuring a high degree of host specificity. This genus also features a high degree of species richness and worldwide distribution. In this study, four species occurring on leaf and stem of two different species of grass were collected from Shanxi and Shaanxi Provinces, China. Based on morphological analysis, multigene (combined data set of LSU, SSU, and ITS) phylogenetic analyses (maximum likelihood and Bayesian analysis), and host relationship, we introduce herein four new taxa of Phyllachora. Ancestral area reconstruction analysis showed that the ancestral area of Phyllachora occurred in Latin America about 194 Mya. Novel taxa are compared with the related Phyllachora species. Detailed descriptions, illustrations, and notes are provided for each species.

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Section: Discussionmentioning

confidence: 99%

Taxonomy, Phylogenetic and Ancestral Area Reconstruction in Phyllachora, with Four Novel Species from Northwestern China

et al. 2022

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“…Due to the lack of molecular studies, many genera or species need to be recollected and epitypified, to place them in their correct taxonomic position. The combination of traditional and modern methods is an important approach and is a demand of our time to understand fungi (rust fungi) more precisely [56,57]. As the molecular phylogeny is carried out, the taxonomic ambiguities of all these species will be resolved.…”

Section: Discussionmentioning

confidence: 99%

A Comprehensive Account of the Rust Genus Skierka (Skierkaceae)

Balkrishna

Gautam

Avasthi

et al. 2022

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The rust genus Skierka belonging to the phylum Basidiomycota was described in 1900 by Raciborski with Skierka canarii as the type species. The published literature on this rust genus reveals its ambiguity in taxonomic placement. It was challenging to taxonomically delineate and precisely identify each species within this genus due to the species sharing some common characteristics. The latest studies based on morphology taxonomy and molecular characteristics, however, have solved this puzzle now and placed this genus in its new family Skierkaceae. To understand all about the genus Skierka, this compilation was carried out to unveil the general characteristics, history, diversity, distribution, ecology, morphology and molecular taxonomy of different species of Skierka. After exploring 14 species of Skierka, it was observed that this genus is distributed in seven plant families in 19 countries all over the world. The genus appears to be well-represented in Asian and South American counties. This rust has not been reported from any European countries to date. The morpho-taxonomy of all species is well studied, but molecular analyses are still required. Only two species of the genus namely S. robusta and S. diploglottidis were identified based molecular analyses. Therefore, further studies should be focused on epitypifying the taxa that are too old and updating their taxonomy based on molecular, biochemical, and physiological aspects along with morphological characteristics. Multiple analytical methods should be considered when dealing with multi-locus datasets. This will increase our understanding of the diversity, distribution, and identification of these rust fungi.

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“…These molecular tools include restriction fragment length polymorphisms (RFLP), random amplified polymorphic DNA markers (RAPD), sequence analysis of ribosomal DNA, microsatellite markers and coding sequence variation phylogenetic markers [3], [14]. Gautam et al [15] pointed out more recently DNAbased methods in taxonomy, particularly rRNA sequences or rDNA, strain-specific fluorescent oligonucleotides, and the polymerase chain reaction (PCR). Each of these methods has specific applications and advantages [16].…”

Section: Handelmentioning

confidence: 99%

Genetic Diversity of Trichoderma and Hypocrea lixii Iraqi Strains by Using Random Amplified Polymorphic DNA (RAPD) Technique

Handel

2023

Iraqi Journal of Science

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As the diversity and characteristics of Trichoderma species are difficult to determine using morphological methods, henceforth molecular tools are crucial. This study utilized random amplified polymorphic DNA (RAPD) technique to investigate the genetic diversity of Trichoderma with sexual phase Hypocrea and to identify similarities and differences in the phylogenetic tree. Nine Iraqi Trichoderma strains (four strains of T. atroviride, one strain of Hypocrea lixii, two strains of T. gamsii and two strains of T. longibriantium) were examined in this research. The genomic DNA of each species was extracted and amplified with each of the five primers. 197 bands were obtained by using five oligodeoxynucleotide primers of which 98.47% were polymorphic and about 1.52% were monomorphic. When primers OPA4, OPA8, and OPA10 were used, the genetic variability was about 100%. Whereas, after using primers OPA7 and OPA5, the obtained genetic variability was 95.7% and 92.6% respectively. Gel images of the RAPD were processed with photo-cap program which detected the bands of isolates based on the ladder. The detected bands were then clustered based on the Jaccard method in Past software that showed T. atroviride, T. gamsii, Hypocrea lixii, and T. longibrachiatum isolates were grouped as clades and lineages. Although all strains belonged to the same species and group in one clade, they differed in size and number of bands. The Jaccard cluster analysis showed that the three isolates of T. atroviride were closely related to each other, while the four isolates of T. atroviride in one cluster were same as Hypocrea lixii, the isolates of T. gamsii and two strains of T. longibrachiatum formed one cluster. Thus, the high reliability of RAPD markers could be applied to identify Trichoderma species and create genetic maps instead of other DNA-based methods which are not only costly but time-consuming too.

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Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates

Cited by 30 publications

References 485 publications

Taxonomy, Phylogenetic and Ancestral Area Reconstruction in Phyllachora, with Four Novel Species from Northwestern China

Taxonomy, Phylogenetic and Ancestral Area Reconstruction in Phyllachora, with Four Novel Species from Northwestern China

A Comprehensive Account of the Rust Genus Skierka (Skierkaceae)

Genetic Diversity of Trichoderma and Hypocrea lixii Iraqi Strains by Using Random Amplified Polymorphic DNA (RAPD) Technique

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