Molecular characterization of Xanthomonas species isolated from Araceae and the development of a triplex TaqMan assay for detection of Xanthomonas phaseoli pv. dieffenbachiae

J.M. van der Wolf; M.C. Krijger; O. Mendes; B. Brankovics; P.J.M. Bonants; Leonie  Didden; Ellis Meekes

doi:10.1007/s10658-022-02466-1

Molecular characterization of Xanthomonas species isolated from Araceae and the development of a triplex TaqMan assay for detection of Xanthomonas phaseoli pv. dieffenbachiae

J.M. van der Wolf^*, M.C. Krijger, O. Mendes, B. Brankovics, P.J.M. Bonants, Leonie Didden, Ellis Meekes

^*Corresponding author for this work

Biointeractions and Plant Health

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

3 Citations (Scopus)

Abstract

In total 58 Xanthomonas strains isolated from Araceae worldwide, together with 13 other phylogenetically-related Xanthomonas strains, were characterized using multilocus sequence analysis based on concatenated sequences of seven single copy orthologous genes, extracted from whole genome sequences. The analysis revealed a monophyletic clade of 48 strains, 44 isolated from Anthurium, identified as X. phaseoli pv. dieffenbachiae (Xpd) confirmed by nucleotide identity analysis. The other strains from aroids were identified as Xanthomonas euvesicatoria (2 strains), X citri (5 strains) and Xanthomonas sacchari (3 strains). Two TaqMan assays were designed for specific detection of Xpd, one targeting sequences of a hypothetical protein and one targeting a type I restriction endonuclease subunit S. The two assays showed similar reaction kinetics and were merged with an assay comprising an amplification and extraction control into a triplex assay. The assay was able to detect minimally 100 copies of a target sequence delivered as a gBlock, 100 fg of genomic DNA and 104 cells per mL in an Anthurium leaf extract.

Original language	English
Pages (from-to)	167-179
Number of pages	13
Journal	European Journal of Plant Pathology
Volume	163
Issue number	1
Early online date	22 Mar 2022
DOIs	https://doi.org/10.1007/s10658-022-02466-1
Publication status	Published - May 2022

Keywords

Xanthomonas axonopodis pv. dieffenbachiae
Multilocus sequence analysis
Whole genome sequencing
Anthurium
Average nucleotide identity
Taxonomy

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10.1007/s10658-022-02466-1Licence: CC BY

https://edepot.wur.nl/566946Licence: CC BY

Molecular characterization of Xanthomonas species pathogenic on Araceae
van der Wolf, J. M. (Creator), Krijger, M. C. (Creator), Mendes, O. (Creator), Brankovics, B. (Creator), Bonants, P. J. M. (Creator), Didden, L. (Creator) & Meekes, E. (Creator), Wageningen University & Research, 4 Apr 2021
https://www.ncbi.nlm.nih.gov/bioproject/716613
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van der Wolf, J. M., Krijger, M. C., Mendes, O., Brankovics, B., Bonants, P. J. M., Didden, L., & Meekes, E. (2022). Molecular characterization of Xanthomonas species isolated from Araceae and the development of a triplex TaqMan assay for detection of Xanthomonas phaseoli pv. dieffenbachiae. European Journal of Plant Pathology, 163(1), 167-179. https://doi.org/10.1007/s10658-022-02466-1

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title = "Molecular characterization of Xanthomonas species isolated from Araceae and the development of a triplex TaqMan assay for detection of Xanthomonas phaseoli pv. dieffenbachiae",

abstract = "In total 58 Xanthomonas strains isolated from Araceae worldwide, together with 13 other phylogenetically-related Xanthomonas strains, were characterized using multilocus sequence analysis based on concatenated sequences of seven single copy orthologous genes, extracted from whole genome sequences. The analysis revealed a monophyletic clade of 48 strains, 44 isolated from Anthurium, identified as X. phaseoli pv. dieffenbachiae (Xpd) confirmed by nucleotide identity analysis. The other strains from aroids were identified as Xanthomonas euvesicatoria (2 strains), X citri (5 strains) and Xanthomonas sacchari (3 strains). Two TaqMan assays were designed for specific detection of Xpd, one targeting sequences of a hypothetical protein and one targeting a type I restriction endonuclease subunit S. The two assays showed similar reaction kinetics and were merged with an assay comprising an amplification and extraction control into a triplex assay. The assay was able to detect minimally 100 copies of a target sequence delivered as a gBlock, 100 fg of genomic DNA and 104 cells per mL in an Anthurium leaf extract.",

keywords = "Xanthomonas axonopodis pv. dieffenbachiae, Multilocus sequence analysis, Whole genome sequencing, Anthurium, Average nucleotide identity, Taxonomy",

author = "{van der Wolf}, J.M. and M.C. Krijger and O. Mendes and B. Brankovics and P.J.M. Bonants and Leonie Didden and Ellis Meekes",

year = "2022",

month = may,

doi = "10.1007/s10658-022-02466-1",

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van der Wolf, JM , Krijger, MC , Mendes, O , Brankovics, B, Bonants, PJM, Didden, L & Meekes, E 2022, 'Molecular characterization of Xanthomonas species isolated from Araceae and the development of a triplex TaqMan assay for detection of Xanthomonas phaseoli pv. dieffenbachiae', European Journal of Plant Pathology, vol. 163, no. 1, pp. 167-179. https://doi.org/10.1007/s10658-022-02466-1

Molecular characterization of Xanthomonas species isolated from Araceae and the development of a triplex TaqMan assay for detection of Xanthomonas phaseoli pv. dieffenbachiae. / van der Wolf, J.M.; Krijger, M.C.; Mendes, O. et al.
In: European Journal of Plant Pathology, Vol. 163, No. 1, 05.2022, p. 167-179.

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

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T1 - Molecular characterization of Xanthomonas species isolated from Araceae and the development of a triplex TaqMan assay for detection of Xanthomonas phaseoli pv. dieffenbachiae

AU - van der Wolf, J.M.

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AU - Mendes, O.

AU - Brankovics, B.

AU - Bonants, P.J.M.

AU - Didden, Leonie

AU - Meekes, Ellis

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N2 - In total 58 Xanthomonas strains isolated from Araceae worldwide, together with 13 other phylogenetically-related Xanthomonas strains, were characterized using multilocus sequence analysis based on concatenated sequences of seven single copy orthologous genes, extracted from whole genome sequences. The analysis revealed a monophyletic clade of 48 strains, 44 isolated from Anthurium, identified as X. phaseoli pv. dieffenbachiae (Xpd) confirmed by nucleotide identity analysis. The other strains from aroids were identified as Xanthomonas euvesicatoria (2 strains), X citri (5 strains) and Xanthomonas sacchari (3 strains). Two TaqMan assays were designed for specific detection of Xpd, one targeting sequences of a hypothetical protein and one targeting a type I restriction endonuclease subunit S. The two assays showed similar reaction kinetics and were merged with an assay comprising an amplification and extraction control into a triplex assay. The assay was able to detect minimally 100 copies of a target sequence delivered as a gBlock, 100 fg of genomic DNA and 104 cells per mL in an Anthurium leaf extract.

AB - In total 58 Xanthomonas strains isolated from Araceae worldwide, together with 13 other phylogenetically-related Xanthomonas strains, were characterized using multilocus sequence analysis based on concatenated sequences of seven single copy orthologous genes, extracted from whole genome sequences. The analysis revealed a monophyletic clade of 48 strains, 44 isolated from Anthurium, identified as X. phaseoli pv. dieffenbachiae (Xpd) confirmed by nucleotide identity analysis. The other strains from aroids were identified as Xanthomonas euvesicatoria (2 strains), X citri (5 strains) and Xanthomonas sacchari (3 strains). Two TaqMan assays were designed for specific detection of Xpd, one targeting sequences of a hypothetical protein and one targeting a type I restriction endonuclease subunit S. The two assays showed similar reaction kinetics and were merged with an assay comprising an amplification and extraction control into a triplex assay. The assay was able to detect minimally 100 copies of a target sequence delivered as a gBlock, 100 fg of genomic DNA and 104 cells per mL in an Anthurium leaf extract.

KW - Xanthomonas axonopodis pv. dieffenbachiae

KW - Multilocus sequence analysis

KW - Whole genome sequencing

KW - Anthurium

KW - Average nucleotide identity

KW - Taxonomy

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DO - 10.1007/s10658-022-02466-1

M3 - Article

SN - 0929-1873

VL - 163

SP - 167

EP - 179

JO - European Journal of Plant Pathology

JF - European Journal of Plant Pathology

IS - 1

ER -

Molecular characterization of Xanthomonas species isolated from Araceae and the development of a triplex TaqMan assay for detection of Xanthomonas phaseoli pv. dieffenbachiae

Abstract

Keywords

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Datasets

Molecular characterization of Xanthomonas species pathogenic on Araceae

Cite this