Molecular Identification of Trichoderma reesei

Rahimi, Mohammad Javad; Cai, Feng; Grujić, Marica; Chenthamara, Komal; Druzhinina, Irina S.

doi:10.1007/978-1-0716-1048-0_14

Cited by 2 publications

(2 citation statements)

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“…Consequently, the NCBI GenBank contains all these frequently non-overlapping fragments of the tef1 gene, which complicates its use and in particular affects the results of the sequence similarity search. Together, these findings make the tef1 locus insufficient to be used as the only DNA barcode marker for Trichoderma identification at the species level as it was also proposed by Rahimi et al (2020) for the identifiction of T. reesei. The limitations outlined above also reveal that the application of tef1 together with ITS will not allow unambiguous identification of Trichoderma species.…”

Section: Trichoderma Species Can Be Identified Based On ≥ 99% and ≥ 9mentioning

confidence: 99%

“…Consider selecting primer pairs of tef1 that will guarantee the sequencing of the diagnostic region (see example in Table 3, Fig. 9, note other primer pairs listed in Rahimi et al (2020). (6) Use on-line tools and public databases for the preliminary analysis of the obtained DNA barcodes [such as MIST, (Dou et al 2020) or NCBI BLAST, (Ye et al 2006)].…”

Section: Consulting With the Experienced Expertsmentioning

confidence: 99%

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In honor of John Bissett: authoritative guidelines on molecular identification of Trichoderma

2021

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Modern taxonomy has developed towards the establishment of global authoritative lists of species that assume the standardized principles of species recognition, at least in a given taxonomic group. However, in fungi, species delimitation is frequently subjective because it depends on the choice of a species concept and the criteria selected by a taxonomist. Contrary to it, identification of fungal species is expected to be accurate and precise because it should predict the properties that are required for applications or that are relevant in pathology. The industrial and plant-beneficial fungi from the genus Trichoderma (Hypocreales) offer a suitable model to address this collision between species delimitation and species identification. A few decades ago, Trichoderma diversity was limited to a few dozen species. The introduction of molecular evolutionary methods resulted in the exponential expansion of Trichoderma taxonomy, with up to 50 new species recognized per year. Here, we have reviewed the genus-wide taxonomy of Trichoderma and compiled a complete inventory of all Trichoderma species and DNA barcoding material deposited in public databases (the inventory is available at the website of the International Subcommission on Taxonomy of Trichodermawww.trichoderma.info). Among the 375 species with valid names as of July 2020, 361 (96%) have been cultivated in vitro and DNA barcoded. Thus, we have developed a protocol for molecular identification of Trichoderma that requires analysis of the three DNA barcodes (ITS, tef1, and rpb2), and it is supported by online tools that are available on www.trichokey.info. We then used all the whole-genome sequenced (WGS) Trichoderma strains that are available in public databases to provide versatile practical examples of molecular identification, reveal shortcomings, and discuss possible ambiguities. Based on the Trichoderma example, this study shows why the identification of a fungal species is an intricate and laborious task that requires a background in mycology, molecular biological skills, training in molecular evolutionary analysis, and knowledge of taxonomic literature. We provide an in-depth discussion of species concepts that are applied in Trichoderma taxonomy, and conclude that these fungi are particularly suitable for the implementation of a polyphasic approach that was first introduced in Trichoderma taxonomy by John Bissett (1948–2020), whose work inspired the current study. We also propose a regulatory and unifying role of international commissions on the taxonomy of particular fungal groups. An important outcome of this work is the demonstration of an urgent need for cooperation between Trichoderma researchers to get prepared to the efficient use of the upcoming wave of Trichoderma genomic data.

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Section: Trichoderma Species Can Be Identified Based On ≥ 99% and ≥ 9mentioning

confidence: 99%