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ITS and secondary biomarkers in fungi: review on the evolution of their use based on scientific publications

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Abstract

In this review, we investigated the progress in the use of ribosomal DNA internal transcribed spacer (ITS) and other widely used biomarkers for fungal studies. To achieve this goal, qualitative and quantitative large-scale data mining from the literature and sequence-based searches in public databases was performed. Our survey indicates that the most relevant studies for the fungal barcoding area were published between 2012 and 2015. The ITS region was the most used biomarker within our dataset; however, a significant amount of studies have used ITS associated with other biomarkers, especially the 28S and 18S subunits. Despite the undoubted importance and usefulness of ITS, this genomic region cannot be considered a universal genomic marker for fungi. For some taxonomic groups, a conclusive identification at species level is not achieved using ITS and then another biomarker must be associated.

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Acknowledgements

We thank all whom contributed directly or indirectly to this work, especially the CEFET-MG (Centro Federal de Educação Tecnológica de Minas Gerais), and the Graduate Programs of Bioinformatics and Microbiology of the Universidade Federal de Minas Gerais (UFMG).

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Authors and Affiliations

  1. Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), Belo Horizonte, MG, 30480-000, Brazil

    Fernanda Badotti

  2. Department of Microbiology, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil

    Paula Luize Camargos Fonseca, Luiz Marcelo Ribeiro Tomé, Daniel Trindade Nunes & Aristóteles Góes-Neto

  3. Graduate Program in Bioinformatics, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil

    Aristóteles Góes-Neto

  4. Laboratório de Biologia Molecular e Computacional de Fungos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Presidente Antônio Carlos, 6627, Pampulha, Bloco J3 sala 53, Pampulha, Belo Horizonte, MG, 31270-901, Brazil

    Aristóteles Góes-Neto

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  1. Fernanda Badotti
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  2. Paula Luize Camargos Fonseca
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  3. Luiz Marcelo Ribeiro Tomé
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Contributions

FB and PLCF wrote the paper, DTN performed the analyzes and AGN and LMRT contributed in the discussion of the data and revised the writing.

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Correspondence to Aristóteles Góes-Neto.

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Electronic supplementary material

Below is the link to the electronic supplementary material.

Electronic Supplementary Material 1

Pipelines dependencies (databases, programs, scripts) and details of the bioinformatics analyzes. (DOCX 14 kb)

Electronic Supplementary Material 2

Parameters used to build the network representing the bibliographic coupling analyzes. (DOCX 36 kb)

Electronic Supplementary Material 3

Text-mining script developed to identify terms within the analyzed texts. Python Regular Expression (RE) codes were built and tested in appropriate software platform (available in the website regex101.com). Bash grep searches against all PDF extracted texts were conducted for all terms and its main variants. The resultant grep search lists were then used as test string inputs for the online RE test platform. All terms searched in the text-mining process followed by its RE variants utilized for detection are showed. † To make a better representation for RE, space characters were replaced by dot operators: “□”. (DOCX 16 kb)

Electronic Supplementary Material 4

List of the articles analyzed for DNA biomarkers using the sequence-based literature search approach. The literature-mining output table contains the retrieved presence (1) or absence (0) tags for all searched terms. Searches were conducted against Materials and Methods section of each analyzed publication. (PDF 739 kb)

Electronic Supplementary Material 5

Co-occurrence frequency matrix for the biomarkers combinations. (TIFF 3465 kb)

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Badotti, F., Fonseca, P.L.C., Tomé, L.M.R. et al. ITS and secondary biomarkers in fungi: review on the evolution of their use based on scientific publications. Braz. J. Bot 41, 471–479 (2018). https://doi.org/10.1007/s40415-018-0471-y

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