Semi-automated sequence curation for reliable reference datasets in ITS2 vascular plant DNA (meta-) barcoding

Andreia Quaresma; Markus J. Ankenbrand; Carlos Ariel Yadró Garcia; José Rufino; Mónica Honrado; Joana Amaral; Robert Brodschneider; Valters Brusbardis; Kristina Gratzer; Fani Hatjina; Ole Kilpinen; Marco Pietropaoli; I. Roessink; Jozef van der Steen; Flemming Vejsnaes; Maria Alice Pinto; Alexander Keller

doi:10.1038/s41597-024-02962-5

Semi-automated sequence curation for reliable reference datasets in ITS2 vascular plant DNA (meta-) barcoding

Andreia Quaresma, Markus J. Ankenbrand, Carlos Ariel Yadró Garcia, José Rufino, Mónica Honrado, Joana Amaral, Robert Brodschneider, Valters Brusbardis, Kristina Gratzer, Fani Hatjina, Ole Kilpinen, Marco Pietropaoli, I. Roessink, Jozef van der Steen, Flemming Vejsnaes, Maria Alice Pinto, Alexander Keller^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

6 Citations (Scopus)

Abstract

One of the most critical steps for accurate taxonomic identification in DNA (meta)-barcoding is to have an accurate DNA reference sequence dataset for the marker of choice. Therefore, developing such a dataset has been a long-term ambition, especially in the Viridiplantae kingdom. Typically, reference datasets are constructed with sequences downloaded from general public databases, which can carry taxonomic and other relevant errors. Herein, we constructed a curated (i) global dataset, (ii) European crop dataset, and (iii) 27 datasets for the EU countries for the ITS2 barcoding marker of vascular plants. To that end, we first developed a pipeline script that entails (i) an automated curation stage comprising five filters, (ii) manual taxonomic correction for misclassified taxa, and (iii) manual addition of newly sequenced species. The pipeline allows easy updating of the curated datasets. With this approach, 13% of the sequences, corresponding to 7% of species originally imported from GenBank, were discarded. Further, 259 sequences were manually added to the curated global dataset, which now comprises 307,977 sequences of 111,382 plant species.

Original language	English
Article number	129
Journal	Scientific Data
Volume	11
DOIs	https://doi.org/10.1038/s41597-024-02962-5
Publication status	Published - 25 Jan 2024

Keywords

Sequence curation
ITS2 vascular plant DNA
meta barcoding

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10.1038/s41597-024-02962-5Licence: CC BY

https://edepot.wur.nl/647669Licence: CC BY

ITS2 Global database
Quaresma, A. (Creator), Amaral, J. (Creator), Brodschneider, R. (Creator), Brusbardis, V. (Creator), Gratzer, K. (Creator), Hatjina, F. (Creator), Honrado, M. (Creator), Kilpinen, O. (Creator), Pietropaoli, M. (Creator), Roessink, I. (Creator), Rufino, J. (Creator), van der Steen, J. (Creator), Vejsnaes, F. (Creator), Yadró Garcia, C. A. (Creator), Pinto, M. A. (Creator) & Keller, A. (Creator), Instituto Politécnico de Bragança, 24 May 2023
DOI: 10.5281/zenodo.7968518
Dataset
ITS2 Crop database
Quaresma, A. (Creator), Amaral, J. (Creator), Brodschneider, R. (Creator), Brusbardis, V. (Creator), Gratzer, K. (Creator), Hatjina, F. (Creator), Honrado, M. (Creator), Kilpinen, O. (Creator), Pietropaoli, M. (Creator), Roessink, I. (Creator), Rufino, J. (Creator), van der Steen, J. (Creator), Vejsnaes, F. (Creator), Yadró Garcia, C. A. (Creator), Pinto, M. A. (Creator) & Keller, A. (Creator), Instituto Politécnico de Bragança, 25 May 2023
DOI: 10.5281/zenodo.7969939
Dataset
ITS2 European countries
Quaresma, A. (Creator), Amaral, J. (Creator), Brodschneider, R. (Creator), Brusbardis, V. (Creator), Gratzer, K. (Creator), Hatjina, F. (Creator), Honrado, M. (Creator), Kilpinen, O. (Creator), Pietropaoli, M. (Creator), Roessink, I. (Creator), Rufino, J. (Creator), van der Steen, J. (Creator), Vejsnaes, F. (Creator), Yadró Garcia, C. A. (Creator), Pinto, M. A. (Creator) & Keller, A. (Creator), Instituto Politécnico de Bragança, 25 May 2023
DOI: 10.5281/zenodo.7970045
Dataset

Cite this

Quaresma, A., Ankenbrand, M. J., Yadró Garcia, C. A., Rufino, J., Honrado, M., Amaral, J., Brodschneider, R., Brusbardis, V., Gratzer, K., Hatjina, F., Kilpinen, O., Pietropaoli, M., Roessink, I., van der Steen, J., Vejsnaes, F., Pinto, M. A., & Keller, A. (2024). Semi-automated sequence curation for reliable reference datasets in ITS2 vascular plant DNA (meta-) barcoding. Scientific Data, 11, Article 129. https://doi.org/10.1038/s41597-024-02962-5

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abstract = "One of the most critical steps for accurate taxonomic identification in DNA (meta)-barcoding is to have an accurate DNA reference sequence dataset for the marker of choice. Therefore, developing such a dataset has been a long-term ambition, especially in the Viridiplantae kingdom. Typically, reference datasets are constructed with sequences downloaded from general public databases, which can carry taxonomic and other relevant errors. Herein, we constructed a curated (i) global dataset, (ii) European crop dataset, and (iii) 27 datasets for the EU countries for the ITS2 barcoding marker of vascular plants. To that end, we first developed a pipeline script that entails (i) an automated curation stage comprising five filters, (ii) manual taxonomic correction for misclassified taxa, and (iii) manual addition of newly sequenced species. The pipeline allows easy updating of the curated datasets. With this approach, 13% of the sequences, corresponding to 7% of species originally imported from GenBank, were discarded. Further, 259 sequences were manually added to the curated global dataset, which now comprises 307,977 sequences of 111,382 plant species.",

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Quaresma, A, Ankenbrand, MJ, Yadró Garcia, CA, Rufino, J, Honrado, M, Amaral, J, Brodschneider, R, Brusbardis, V, Gratzer, K, Hatjina, F, Kilpinen, O, Pietropaoli, M, Roessink, I, van der Steen, J, Vejsnaes, F, Pinto, MA & Keller, A 2024, 'Semi-automated sequence curation for reliable reference datasets in ITS2 vascular plant DNA (meta-) barcoding', Scientific Data, vol. 11, 129. https://doi.org/10.1038/s41597-024-02962-5

TY - JOUR

T1 - Semi-automated sequence curation for reliable reference datasets in ITS2 vascular plant DNA (meta-) barcoding

AU - Quaresma, Andreia

AU - Ankenbrand, Markus J.

AU - Yadró Garcia, Carlos Ariel

AU - Rufino, José

AU - Honrado, Mónica

AU - Amaral, Joana

AU - Brodschneider, Robert

AU - Brusbardis, Valters

AU - Gratzer, Kristina

AU - Hatjina, Fani

AU - Kilpinen, Ole

AU - Pietropaoli, Marco

AU - Roessink, I.

AU - van der Steen, Jozef

AU - Vejsnaes, Flemming

AU - Pinto, Maria Alice

AU - Keller, Alexander

PY - 2024/1/25

Y1 - 2024/1/25

N2 - One of the most critical steps for accurate taxonomic identification in DNA (meta)-barcoding is to have an accurate DNA reference sequence dataset for the marker of choice. Therefore, developing such a dataset has been a long-term ambition, especially in the Viridiplantae kingdom. Typically, reference datasets are constructed with sequences downloaded from general public databases, which can carry taxonomic and other relevant errors. Herein, we constructed a curated (i) global dataset, (ii) European crop dataset, and (iii) 27 datasets for the EU countries for the ITS2 barcoding marker of vascular plants. To that end, we first developed a pipeline script that entails (i) an automated curation stage comprising five filters, (ii) manual taxonomic correction for misclassified taxa, and (iii) manual addition of newly sequenced species. The pipeline allows easy updating of the curated datasets. With this approach, 13% of the sequences, corresponding to 7% of species originally imported from GenBank, were discarded. Further, 259 sequences were manually added to the curated global dataset, which now comprises 307,977 sequences of 111,382 plant species.

AB - One of the most critical steps for accurate taxonomic identification in DNA (meta)-barcoding is to have an accurate DNA reference sequence dataset for the marker of choice. Therefore, developing such a dataset has been a long-term ambition, especially in the Viridiplantae kingdom. Typically, reference datasets are constructed with sequences downloaded from general public databases, which can carry taxonomic and other relevant errors. Herein, we constructed a curated (i) global dataset, (ii) European crop dataset, and (iii) 27 datasets for the EU countries for the ITS2 barcoding marker of vascular plants. To that end, we first developed a pipeline script that entails (i) an automated curation stage comprising five filters, (ii) manual taxonomic correction for misclassified taxa, and (iii) manual addition of newly sequenced species. The pipeline allows easy updating of the curated datasets. With this approach, 13% of the sequences, corresponding to 7% of species originally imported from GenBank, were discarded. Further, 259 sequences were manually added to the curated global dataset, which now comprises 307,977 sequences of 111,382 plant species.

KW - Sequence curation

KW - ITS2 vascular plant DNA

KW - meta barcoding

U2 - 10.1038/s41597-024-02962-5

DO - 10.1038/s41597-024-02962-5

M3 - Article

SN - 2052-4463

VL - 11

JO - Scientific Data

JF - Scientific Data

M1 - 129

ER -

Semi-automated sequence curation for reliable reference datasets in ITS2 vascular plant DNA (meta-) barcoding

Abstract

Keywords

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Datasets

ITS2 Global database

ITS2 Crop database

ITS2 European countries

Cite this