Database establishment for the secondary fungal DNA barcode translational elongation factor 1 alpha (TEF1 alpha)

Wieland Meyer; Laszlo Irinyi; Minh Thuy Vi Hoang; Vincent Robert; Dea Garcia-Hermoso; Marie Desnos-Ollivier; Chompoonek Yurayart; Chi-Ching Tsang; Chun-Yi Lee; Patrick C. Y. Woo; Ivan Mikhailovich Pchelin; Silke Uhrlass; Pietro Nenoff; Ariya Chindamporn; Sharon Chen; Paul D. N. Hebert; Tania C. Sorrell; Catriona Halliday; Ian Arthur; Maria Luiza Moretti; Celia Maria de Almeida Soares; Mauro de Medeiros Muniz; Rosely Maria Zancope-Oliveira; Fundacao Oswaldo Cruz; Analy Salles de Azevedo Melo; Arnaldo L. Colombo; Angela Satie Nishikaku; Marijke Hendrickx; Dirk Stubbe; Anne-Cecile Normand; Renaud Piarroux; Stephane Ranque; Francoise Dromer; Michael Arabatzis; Aristea Velegraki; Gianluigi Cardinali; Laura Rosio Castanon; Maria Lucia Taylor; Conchita Toriello; Sybren de Hoog; Celia Pais; Wilhelm de Beer; Marieka Gryzenhout; Josep Guarro; Jose F. Cano-Lira; Barbara Robbertse; Conrad Schoch

doi:10.1139/gen-2018-0083

Database establishment for the secondary fungal DNA barcode translational elongation factor 1 alpha (TEF1 alpha)

Wieland Meyer, Laszlo Irinyi, Minh Thuy Vi Hoang, Vincent Robert, Dea Garcia-Hermoso, Marie Desnos-Ollivier, Chompoonek Yurayart, Chi-Ching Tsang, Chun-Yi Lee, Patrick C. Y. Woo, Ivan Mikhailovich Pchelin, Silke Uhrlass, Pietro Nenoff, Ariya Chindamporn, Sharon Chen, Paul D. N. Hebert, Tania C. Sorrell, Catriona Halliday, Ian Arthur, Maria Luiza MorettiCelia Maria de Almeida Soares, Mauro de Medeiros Muniz, Rosely Maria Zancope-Oliveira, Fundacao Oswaldo Cruz, Analy Salles de Azevedo Melo, Arnaldo L. Colombo, Angela Satie Nishikaku, Marijke Hendrickx, Dirk Stubbe, Anne-Cecile Normand, Renaud Piarroux, Stephane Ranque, Francoise Dromer, Michael Arabatzis, Aristea Velegraki, Gianluigi Cardinali, Laura Rosio Castanon, Maria Lucia Taylor, Conchita Toriello, Sybren de Hoog, Celia Pais, Wilhelm de Beer, Marieka Gryzenhout, Josep Guarro, Jose F. Cano-Lira, Barbara Robbertse, Conrad Schoch

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

40 Citations (Scopus)

Abstract

With new or emerging fungal infections, human/animal fungal pathogens are a growing threat worldwide. Current diagnostic tools are slow, non-specific at the species and subspecies levels, and require specific morphological expertise to accurately identify pathogens from pure cultures. DNA barcodes are easily amplified, universal, short species-specific DNA sequences, which enable rapid identification by comparison with a well-curated reference sequence collection. The primary fungal DNA barcode, ITS region, was introduced in 2012 and is now routinely used in diagnostic laboratories. However, the ITS region only accurately identifies around 75% of all medically relevant fungal species, which has prompted the development of a secondary barcode to increase the resolution power and suitability of DNA barcoding for fungal disease diagnostics. The translational elongation factor 1α (TEF1α) was selected in 2015 as a secondary fungal DNA barcode, but has not been implemented into practice, due to the absence of a reference database. Here, we have established a quality-controlled reference database for the secondary barcode which together with the ISHAM-ITS database, forms the "ISHAM BARCODE DATABASE", available online at: http://its.mycologylab.org/. We encourage the mycology community for active contributions. The application of a dual DNA barcoding system enables accurate identification of all clinically important fungal pathogens.

Original language	English
Pages (from-to)	160-169
Journal	Genome
Volume	62
Issue number	3
Early online date	22 Nov 2018
DOIs	https://doi.org/10.1139/gen-2018-0083 https://doi.org/10.1139/gen-2018-0083
Publication status	Published - Mar 2019

Keywords

fungal DNA barcoding
secondary fungal DNA barcode database
translational elongation factor 1 alpha

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Meyer, W., Irinyi, L., Minh Thuy Vi Hoang, Robert, V., Garcia-Hermoso, D., Desnos-Ollivier, M., Yurayart, C., Tsang, C.-C., Lee, C.-Y., Woo, P. C. Y., Pchelin, I. M., Uhrlass, S., Nenoff, P., Chindamporn, A., Chen, S., Hebert, P. D. N., Sorrell, T. C., Halliday, C., Arthur, I., ... Schoch, C. (2019). Database establishment for the secondary fungal DNA barcode translational elongation factor 1 alpha (TEF1 alpha). Genome, 62(3), 160-169. https://doi.org/10.1139/gen-2018-0083, https://doi.org/10.1139/gen-2018-0083

@article{a34808647e104ca59f201f543cff43b5,

title = "Database establishment for the secondary fungal DNA barcode translational elongation factor 1 alpha (TEF1 alpha)",

abstract = "With new or emerging fungal infections, human/animal fungal pathogens are a growing threat worldwide. Current diagnostic tools are slow, non-specific at the species and subspecies levels, and require specific morphological expertise to accurately identify pathogens from pure cultures. DNA barcodes are easily amplified, universal, short species-specific DNA sequences, which enable rapid identification by comparison with a well-curated reference sequence collection. The primary fungal DNA barcode, ITS region, was introduced in 2012 and is now routinely used in diagnostic laboratories. However, the ITS region only accurately identifies around 75% of all medically relevant fungal species, which has prompted the development of a secondary barcode to increase the resolution power and suitability of DNA barcoding for fungal disease diagnostics. The translational elongation factor 1α (TEF1α) was selected in 2015 as a secondary fungal DNA barcode, but has not been implemented into practice, due to the absence of a reference database. Here, we have established a quality-controlled reference database for the secondary barcode which together with the ISHAM-ITS database, forms the {"}ISHAM BARCODE DATABASE{"}, available online at: http://its.mycologylab.org/. We encourage the mycology community for active contributions. The application of a dual DNA barcoding system enables accurate identification of all clinically important fungal pathogens.",

keywords = "fungal DNA barcoding, secondary fungal DNA barcode database, translational elongation factor 1 alpha",

author = "Wieland Meyer and Laszlo Irinyi and {Minh Thuy Vi Hoang} and Vincent Robert and Dea Garcia-Hermoso and Marie Desnos-Ollivier and Chompoonek Yurayart and Chi-Ching Tsang and Chun-Yi Lee and Woo, {Patrick C. Y.} and Pchelin, {Ivan Mikhailovich} and Silke Uhrlass and Pietro Nenoff and Ariya Chindamporn and Sharon Chen and Hebert, {Paul D. N.} and Sorrell, {Tania C.} and Catriona Halliday and Ian Arthur and Moretti, {Maria Luiza} and {de Almeida Soares}, {Celia Maria} and Muniz, {Mauro de Medeiros} and Zancope-Oliveira, {Rosely Maria} and Cruz, {Fundacao Oswaldo} and Melo, {Analy Salles de Azevedo} and Colombo, {Arnaldo L.} and Nishikaku, {Angela Satie} and Marijke Hendrickx and Dirk Stubbe and Anne-Cecile Normand and Renaud Piarroux and Stephane Ranque and Francoise Dromer and Michael Arabatzis and Aristea Velegraki and Gianluigi Cardinali and Castanon, {Laura Rosio} and Taylor, {Maria Lucia} and Conchita Toriello and {de Hoog}, Sybren and Celia Pais and {de Beer}, Wilhelm and Marieka Gryzenhout and Josep Guarro and Cano-Lira, {Jose F.} and Barbara Robbertse and Conrad Schoch",

year = "2019",

month = mar,

doi = "10.1139/gen-2018-0083",

language = "English",

volume = "62",

pages = "160--169",

journal = "Genome",

issn = "0831-2796",

publisher = "National Research Council of Canada",

number = "3",

}

Meyer, W, Irinyi, L, Minh Thuy Vi Hoang, , Robert, V, Garcia-Hermoso, D, Desnos-Ollivier, M, Yurayart, C, Tsang, C-C, Lee, C-Y, Woo, PCY, Pchelin, IM, Uhrlass, S, Nenoff, P, Chindamporn, A, Chen, S, Hebert, PDN, Sorrell, TC, Halliday, C, Arthur, I, Moretti, ML, de Almeida Soares, CM, Muniz, MDM, Zancope-Oliveira, RM, Cruz, FO, Melo, ASDA, Colombo, AL, Nishikaku, AS, Hendrickx, M, Stubbe, D, Normand, A-C, Piarroux, R, Ranque, S, Dromer, F, Arabatzis, M, Velegraki, A, Cardinali, G, Castanon, LR, Taylor, ML, Toriello, C, de Hoog, S, Pais, C, de Beer, W, Gryzenhout, M, Guarro, J, Cano-Lira, JF, Robbertse, B & Schoch, C 2019, 'Database establishment for the secondary fungal DNA barcode translational elongation factor 1 alpha (TEF1 alpha)', Genome, vol. 62, no. 3, pp. 160-169. https://doi.org/10.1139/gen-2018-0083, https://doi.org/10.1139/gen-2018-0083

TY - JOUR

T1 - Database establishment for the secondary fungal DNA barcode translational elongation factor 1 alpha (TEF1 alpha)

AU - Meyer, Wieland

AU - Irinyi, Laszlo

AU - Minh Thuy Vi Hoang,

AU - Robert, Vincent

AU - Garcia-Hermoso, Dea

AU - Desnos-Ollivier, Marie

AU - Yurayart, Chompoonek

AU - Tsang, Chi-Ching

AU - Lee, Chun-Yi

AU - Woo, Patrick C. Y.

AU - Pchelin, Ivan Mikhailovich

AU - Uhrlass, Silke

AU - Nenoff, Pietro

AU - Chindamporn, Ariya

AU - Chen, Sharon

AU - Hebert, Paul D. N.

AU - Sorrell, Tania C.

AU - Halliday, Catriona

AU - Arthur, Ian

AU - Moretti, Maria Luiza

AU - de Almeida Soares, Celia Maria

AU - Muniz, Mauro de Medeiros

AU - Zancope-Oliveira, Rosely Maria

AU - Cruz, Fundacao Oswaldo

AU - Melo, Analy Salles de Azevedo

AU - Colombo, Arnaldo L.

AU - Nishikaku, Angela Satie

AU - Hendrickx, Marijke

AU - Stubbe, Dirk

AU - Normand, Anne-Cecile

AU - Piarroux, Renaud

AU - Ranque, Stephane

AU - Dromer, Francoise

AU - Arabatzis, Michael

AU - Velegraki, Aristea

AU - Cardinali, Gianluigi

AU - Castanon, Laura Rosio

AU - Taylor, Maria Lucia

AU - Toriello, Conchita

AU - de Hoog, Sybren

AU - Pais, Celia

AU - de Beer, Wilhelm

AU - Gryzenhout, Marieka

AU - Guarro, Josep

AU - Cano-Lira, Jose F.

AU - Robbertse, Barbara

AU - Schoch, Conrad

PY - 2019/3

Y1 - 2019/3

N2 - With new or emerging fungal infections, human/animal fungal pathogens are a growing threat worldwide. Current diagnostic tools are slow, non-specific at the species and subspecies levels, and require specific morphological expertise to accurately identify pathogens from pure cultures. DNA barcodes are easily amplified, universal, short species-specific DNA sequences, which enable rapid identification by comparison with a well-curated reference sequence collection. The primary fungal DNA barcode, ITS region, was introduced in 2012 and is now routinely used in diagnostic laboratories. However, the ITS region only accurately identifies around 75% of all medically relevant fungal species, which has prompted the development of a secondary barcode to increase the resolution power and suitability of DNA barcoding for fungal disease diagnostics. The translational elongation factor 1α (TEF1α) was selected in 2015 as a secondary fungal DNA barcode, but has not been implemented into practice, due to the absence of a reference database. Here, we have established a quality-controlled reference database for the secondary barcode which together with the ISHAM-ITS database, forms the "ISHAM BARCODE DATABASE", available online at: http://its.mycologylab.org/. We encourage the mycology community for active contributions. The application of a dual DNA barcoding system enables accurate identification of all clinically important fungal pathogens.

AB - With new or emerging fungal infections, human/animal fungal pathogens are a growing threat worldwide. Current diagnostic tools are slow, non-specific at the species and subspecies levels, and require specific morphological expertise to accurately identify pathogens from pure cultures. DNA barcodes are easily amplified, universal, short species-specific DNA sequences, which enable rapid identification by comparison with a well-curated reference sequence collection. The primary fungal DNA barcode, ITS region, was introduced in 2012 and is now routinely used in diagnostic laboratories. However, the ITS region only accurately identifies around 75% of all medically relevant fungal species, which has prompted the development of a secondary barcode to increase the resolution power and suitability of DNA barcoding for fungal disease diagnostics. The translational elongation factor 1α (TEF1α) was selected in 2015 as a secondary fungal DNA barcode, but has not been implemented into practice, due to the absence of a reference database. Here, we have established a quality-controlled reference database for the secondary barcode which together with the ISHAM-ITS database, forms the "ISHAM BARCODE DATABASE", available online at: http://its.mycologylab.org/. We encourage the mycology community for active contributions. The application of a dual DNA barcoding system enables accurate identification of all clinically important fungal pathogens.

KW - fungal DNA barcoding

KW - secondary fungal DNA barcode database

KW - translational elongation factor 1 alpha

U2 - 10.1139/gen-2018-0083

DO - 10.1139/gen-2018-0083

M3 - Article

C2 - 30465691

SN - 0831-2796

VL - 62

SP - 160

EP - 169

JO - Genome

JF - Genome

IS - 3

ER -

Database establishment for the secondary fungal DNA barcode translational elongation factor 1 alpha (TEF1 alpha)

Abstract

Keywords

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