Differentiation of the Xanthomonas hortorum – Xanthomonas hydrangeae species complex using sensitive and selective LAMP assays

Dia, Nay C.; Cottyn, Bart; Blom, Jochen; Smits, Theo H. M.; Pothier, Joël F.

doi:10.3389/fagro.2022.898778

Please use this identifier to cite or link to this item: https://doi.org/10.21256/zhaw-25178

Full metadata record

DC Field	Value	Language
dc.contributor.author	Dia, Nay C.	-
dc.contributor.author	Cottyn, Bart	-
dc.contributor.author	Blom, Jochen	-
dc.contributor.author	Smits, Theo H. M.	-
dc.contributor.author	Pothier, Joël F.	-
dc.date.accessioned	2022-06-24T14:04:36Z	-
dc.date.available	2022-06-24T14:04:36Z	-
dc.date.issued	2022-06-01	-
dc.identifier.issn	2673-3218	de_CH
dc.identifier.uri	https://digitalcollection.zhaw.ch/handle/11475/25178	-
dc.description	Related publications: https://doi.org/10.1099/ijsem.0.005163, https://doi.org/10.1002/ndr2.12008	de_CH
dc.description.abstract	The seven pathovars of Xanthomonas hortorum and Xanthomonas hydrangeae, referred to as the X. hortorum – X. hydrangeae species complex, cause disease on a multitude of plants, including crops, ornamental and wild plants. Cross-pathogenicity was proven for some of the strains within this species complex. It is thus important to have highly specific and fast diagnostics methods for members of the X. hortorum – X. hydrangeae species complex. A comparative genomic analysis was conducted for representative members within the complex to identify singletons for use as genomic targets for the assays. Seven loop-mediated isothermal amplification (LAMP) diagnostics assays were developed for the detection of six clades within the X. hortorum – X. hydrangeae species complex, in addition to one assay specific for the entire species complex. Primer sets were tested on a set of 62 reference strains. The primer sets amplified their respective targets within 15 minutes. Based on the reference set, all assays had a sensitivity, specificity, and efficiency of 100%. The assays were used on a validation set of 60 strains. According to the LAMP results, out of the 60 strains, 39 strains were assigned to one of the clades within the complex, 9 were assigned to the complex but to yet undefined clades within the complex, and 12 strains were previously misclassified as X. hortorum since their genomic DNA did not yield amplification with any of the assays. The seven genome-based assays are promising for use as diagnostic tools for various members within the X. hortorum – X. hydrangeae species complex, and for assigning new and historical isolates to this complex.	de_CH
dc.language.iso	en	de_CH
dc.publisher	Frontiers Research Foundation	de_CH
dc.relation.ispartof	Frontiers in Agronomy	de_CH
dc.rights	http://creativecommons.org/licenses/by/4.0/	de_CH
dc.subject	Singleton	de_CH
dc.subject	Bacterial leaf spot	de_CH
dc.subject	Diagnostic method	de_CH
dc.subject	Natural infection	de_CH
dc.subject	Hydrangea	de_CH
dc.subject.ddc	572: Biochemie	de_CH
dc.subject.ddc	579: Mikrobiologie	de_CH
dc.title	Differentiation of the Xanthomonas hortorum – Xanthomonas hydrangeae species complex using sensitive and selective LAMP assays	de_CH
dc.type	Beitrag in wissenschaftlicher Zeitschrift	de_CH
dcterms.type	Text	de_CH
zhaw.departement	Life Sciences und Facility Management	de_CH
zhaw.organisationalunit	Institut für Umwelt und Natürliche Ressourcen (IUNR)	de_CH
dc.identifier.doi	10.3389/fagro.2022.898778	de_CH
dc.identifier.doi	10.21256/zhaw-25178	-
zhaw.funding.eu	No	de_CH
zhaw.issue	898778	de_CH
zhaw.originated.zhaw	Yes	de_CH
zhaw.publication.status	publishedVersion	de_CH
zhaw.volume	4	de_CH
zhaw.publication.review	Peer review (Publikation)	de_CH
zhaw.funding.snf	177064	de_CH
zhaw.webfeed	High Performance Computing (HPC)	de_CH
zhaw.webfeed	Umweltgenomik	de_CH
zhaw.funding.zhaw	Xhortomics: Entwicklung von diagnostischen und epidemiologischen Hilfsmitteln für die Xanthomonas hortorum Spezies Gruppe basierend auf OMICs Technologien	de_CH
zhaw.author.additional	No	de_CH
zhaw.display.portrait	Yes	de_CH
Appears in collections:	Publikationen Life Sciences und Facility Management

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Dia, N. C., Cottyn, B., Blom, J., Smits, T. H. M., & Pothier, J. F. (2022). Differentiation of the Xanthomonas hortorum – Xanthomonas hydrangeae species complex using sensitive and selective LAMP assays. Frontiers in Agronomy, 4(898778). https://doi.org/10.3389/fagro.2022.898778

Dia, N.C. et al. (2022) ‘Differentiation of the Xanthomonas hortorum – Xanthomonas hydrangeae species complex using sensitive and selective LAMP assays’, Frontiers in Agronomy, 4(898778). Available at: https://doi.org/10.3389/fagro.2022.898778.

N. C. Dia, B. Cottyn, J. Blom, T. H. M. Smits, and J. F. Pothier, “Differentiation of the Xanthomonas hortorum – Xanthomonas hydrangeae species complex using sensitive and selective LAMP assays,” Frontiers in Agronomy, vol. 4, no. 898778, Jun. 2022, doi: 10.3389/fagro.2022.898778.

DIA, Nay C., Bart COTTYN, Jochen BLOM, Theo H. M. SMITS und Joël F. POTHIER, 2022. Differentiation of the Xanthomonas hortorum – Xanthomonas hydrangeae species complex using sensitive and selective LAMP assays. Frontiers in Agronomy. 1 Juni 2022. Bd. 4, Nr. 898778. DOI 10.3389/fagro.2022.898778

Dia, Nay C., Bart Cottyn, Jochen Blom, Theo H. M. Smits, and Joël F. Pothier. 2022. “Differentiation of the Xanthomonas Hortorum – Xanthomonas Hydrangeae Species Complex Using Sensitive and Selective LAMP Assays.” Frontiers in Agronomy 4 (898778). https://doi.org/10.3389/fagro.2022.898778.

Dia, Nay C., et al. “Differentiation of the Xanthomonas Hortorum – Xanthomonas Hydrangeae Species Complex Using Sensitive and Selective LAMP Assays.” Frontiers in Agronomy, vol. 4, no. 898778, June 2022, https://doi.org/10.3389/fagro.2022.898778.