AFLP Analysis of <i>Trichoderma</i> spp. from India Compared with Sequence and Morphological‐based Diagnostics

Buhariwalla, Hutokshi K.; Srilakshmi, P.; Kannan, S.; Kanchi, R. S.; Chandra, Sanjeev; Satyaprasad, K.; Waliyar, F; Thakur, R. P.; Crouch, Jonathan H.

doi:10.1111/j.1439-0434.2005.00989.x

Cited by 9 publications

(4 citation statements)

References 45 publications

(70 reference statements)

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“…To overcome this problem amplified fragment length polymorphism (AFLP), the amplification of repetitive sequence-based PCR (rep PCR), and random amplified polymorphic DNA (RAPD) are recommended. However, these techniques have been used primarily for eukaryotic organisms (De Curtis et al 2004;Buhariwalla et al 2005). AFLP, rep PCR, and RAPD have been used for fingerprinting microorganisms.…”

Section: Molecular Monitoring Methodsmentioning

confidence: 99%

Rhizosphere and Root Colonization by Bacterial Inoculants and Their Monitoring Methods: A Critical Area in PGPR Research

Ahmad

Husain²,

Ahmad³

2011

Microbes and Microbial Technology

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Roots serve a multitude of functions in plants including anchorage, acquisition of nutrients and water, and production of exudates with growth regulatory properties. The root-soil interface, or rhizosphere, is the site of greatest biological and chemical activity within the soil matrix. Plant growth-promoting rhizobacteria (PGPR) are known to influence plant health by controlling plant pathogens or via direct enhancement of plant development in the laboratory and in greenhouse experiments. Unfortunately, however, results in the field have been less consistent. The colonization of roots by inoculated bacteria is an important step in the interaction between beneficial bacteria and the host plant. However, colonization is a complex phenomenon influenced by many biotic and abiotic parameters, some of which are only now apparent. Monitoring fate and metabolic activity of microbial inoculants as well as their impact on rhizosphere and soil microbial communities are needed to guarantee safe and reliable application, independent of whether they are genetically modified or not. The first and most crucial prerequisite for effective use of PGPRs is that strain identity and activity are continuously confirmed. A combination of both classical and molecular techniques must be perfected for more effective monitoring of inoculants strain (both genetically modified and unmodified) after release into the soil. Recent developments in techniques for studying rhizobacterial communities and detection and tracking systems of inoculated bacteria are important in future application and assessment of effectiveness and consistent performance of microbial inoculants in crop production and protection.

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Section: Molecular Monitoring Methodsmentioning

confidence: 99%

Rhizosphere and Root Colonization by Bacterial Inoculants and Their Monitoring Methods: A Critical Area in PGPR Research

Ahmad

Husain²,

Ahmad³

2011

Microbes and Microbial Technology

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“…There are abundant reports of molecular genotyping techniques applied to fungal biocontrol agents available in the literature. One of the most attractive methods, however, due to its ability to efficiently generate large numbers of markers at low cost which are amenable to automated fluorescence-based scoring is AFLP (amplification fragment length polymorphism), which has been used to identify and differentiate closely related species of Trichoderma [24].…”

Section: Introductionmentioning

confidence: 99%

Trichoderma from Brazilian garlic and onion crop soils and description of two new species: Trichoderma azevedoi and Trichoderma peberdyi

et al. 2020

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Fifty four Trichoderma strains were isolated from soil samples collected from garlic and onion crops in eight different sites in Brazil and were identified using phylogenetic analysis based on combined ITS region, tef1-α, cal, act and rpb2 sequences. The genetic variability of the recovered Trichoderma species was analysed by AFLP and their phenotypic variability determined using MALDI-TOF. The strain clusters from both typing techniques coincided with the taxonomic determinations made from phylogenetic analysis. The phylogenetic analysis showed the occurrence of Trichoderma asperellum, Trichoderma asperelloides, Trichoderma afroharzianum, Trichoderma hamatum, Trichoderma lentiforme, Trichoderma koningiopsis, Trichoderma longibrachiatum and Trichoderma erinaceum, in the soil samples. We also identified and describe two new Trichoderma species, both in the harzianum clade of section Pachybasium, which we have named Trichoderma azevedoi sp. nov. and Trichoderma peberdyi sp. nov. The examined strains of both T. azevedoi (three strains) and T. peberdyi (12 strains) display significant genotypic and phenotypic variability, but form monophyletic clades with strong bootstrap and posterior probability support and are morphologically distinct from their respective most closely related species.

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“…High throughput molecular methods could be developed with the help of these bioinformatics tools and the availability of genome sequences, for the characterization of Trichoderma population. Previously, various techniques like RFLP, RAPD and AFLP ( Hermosa et al, 2001 ; Dodd et al, 2004 ; Buhariwalla et al, 2005 ; Naef et al, 2006 ) had been utilized for the genetic characterization of Trichoderma isolates, however, most of these techniques have their own limitations due to their reproducibility problems and were found inadequate in assessing within species diversity.…”

Section: Introductionmentioning

confidence: 99%

A Comprehensive Characterization of Simple Sequence Repeats in the Sequenced Trichoderma Genomes Provides Valuable Resources for Marker Development

et al. 2016

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Members of genus Trichoderma are known worldwide for mycoparasitism. To gain a better insight into the organization and evolution of their genomes, we used an in silico approach to compare the occurrence, relative abundance and density of SSRs in Trichoderma atroviride, T. harzianum, T. reesei, and T. virens. Our analysis revealed that in all the four genome sequences studied, the occurrence, relative abundance, and density of microsatellites varied and was not influenced by genome sizes. The relative abundance and density of SSRs positively correlated with the G + C content of their genomes. The maximum frequency of SSRs was observed in the smallest genome of T. reesei whereas it was least in second smallest genome of T. atroviride. Among different classes of repeats, the tri-nucleotide repeats were abundant in all the genomes and accounts for ∼38%, whereas hexa-nuceotide repeats were the least (∼10.2%). Further evaluation of the conservation of motifs in the transcript sequences shows a 49.5% conservation among all the motifs. In order to study polymorphism in Trichoderma isolates, 12 polymorphic SSR markers were developed. Of the 12 markers, 6 markers are from T. atroviride and remaining 6 belong to T. harzianum. SSR markers were found to be more polymorphic from T. atroviride with an average polymorphism information content value of 0.745 in comparison with T. harzianum (0.615). Twelve polymorphic markers obtained in this study clearly demonstrate the utility of newly developed SSR markers in establishing genetic relationships among different isolates of Trichoderma.

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AFLP Analysis of Trichoderma spp. from India Compared with Sequence and Morphological‐based Diagnostics

Cited by 9 publications

References 45 publications

Rhizosphere and Root Colonization by Bacterial Inoculants and Their Monitoring Methods: A Critical Area in PGPR Research

Rhizosphere and Root Colonization by Bacterial Inoculants and Their Monitoring Methods: A Critical Area in PGPR Research

Trichoderma from Brazilian garlic and onion crop soils and description of two new species: Trichoderma azevedoi and Trichoderma peberdyi

A Comprehensive Characterization of Simple Sequence Repeats in the Sequenced Trichoderma Genomes Provides Valuable Resources for Marker Development

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