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American Journal of Potato Research

, Volume 92, Issue 2, pp 218–222 | Cite as

Why Genomics Research on Pectobacterium and Dickeya Makes a Difference

  • Ian TothEmail author
  • Sonia Humphris
  • Emma Campbell
  • Leighton Pritchard
SYMPOSIUM PAPER

Abstract

The genome sequence of Pectobacterium atrosepticum (Pba), one of the most economically damaging bacterial diseases of potato in temperate regions, was published in 2004. Even though, at the time, the number of completely sequenced bacterial genomes numbered only in the low hundreds we were able to use comparative genomics techniques to identify novel regions of DNA that were specific to Pba or only shared with closely related bacteria. Pba was found to contain many genes that were previously undescribed in this group of pathogens but were potentially coding for pathogenicity determinants, some of which appeared to be involved in either triggering or suppressing the plant’s disease resistance processes. Our work since then has employed functional genomics methods to elucidate the ways in which this pathogen interacts with plants and causes disease, and how it has acquired the means to do this. These studies have allowed us to demonstrate a role in pathogenesis for bacterial genes, and to identify potato genes involved in resistance, leading to production of a transgenic potato plant that was fully resistant to the pathogen. Pba genes involved in phenotypes suited to a plant-associated lifestyle were also identified, with roles including attachment to, and colonization of, the roots of both crops and weeds. This understanding has led us to study alternative host plants for Pba in the environment, and the importance of this mode of environmental persistence for pathogen epidemiology and its spread to and between potato crops. Recently, we sequenced 25 strains representing the species range of the related phytopathogenic Dickeya genus (all formerly Erwinia chrysanthemi). Comparative genomic analyses of these sequences enabled application of a novel bioinformatics pipeline for generating diagnostic primers, enabling assays for the soft rot potato pathogens D. dianthicola and D. solani (which are an increasing problem on potato in Europe) as well as other Dickeya species. These assays are currently being validated for molecular diagnostic testing by a number of European plant health laboratories.

Keywords

Genomics Pectobacterium Dickeya 

Resumen

En el 2004 se publicó la secuencia genómica de Pectobacterium atrosepticum (Pba), una de las enfermedades bacterianas de la papa más dañinas económicamente en regiones templadas. Aun así, en ese tiempo, el número de genomas bacterianos secuenciados completamente se numeraba en pocos cientos, pudimos usar técnicas genómicas comparativas para identificar nuevas regiones de DNA que fueran específicas para Pba o solamente compartidas con bacterias estrechamente relacionadas. Se encontró que Pba contenía muchos genes que no habían sido descritos previamente en este grupo de patógenos pero que potencialmente estaban codificando para determinantes de patogenicidad, alguno de los cuales parecía estar involucrado ya fuera en disparar o en suprimir los procesos de resistencia de la planta a la enfermedad. Nuestro trabajo desde entonces ha empleado métodos genómicos funcionales para dilucidar las formas en las cuales este patógeno interactúa con las plantas y causa enfermedad, y como ha adquirido los medios para hacerlo. Estos estudios nos han permitido demostrar un papel en patogénesis para los genes bacteriales, y para identificar los genes de la papa involucrados en resistencia, lo que condujo a la producción de una planta de papa transgénica que fue completamente resistente al patógeno. También se identificaron los genes de Pba involucrados en fenotipos adaptados a un estilo de vida asociado con la planta, con desempeños que incluían adherencia y colonización de raíces de ambos, cultivos y malezas. Este entendimiento nos ha conducido a estudiar plantas hospederas alternantes para Pba en el ambiente, y la importancia de este modo de persistencia en el ambiente para epidemiología del patógeno y su dispersión hacia y entre cultivos de papa. Recientemente secuenciamos 25 cepas representando la amplitud de la especie del género fitopatogénico relacionado Dickeya (todos previamente Erwinia chrysanthemi). Los análisis genómicos comparativos de estas secuencias permitieron la aplicación de un novedoso conducto bioinformático para la generación de iniciadores de diagnóstico, permitiendo ensayos para los patógenos de pudrición suave D. dianthicola y D. solani (que son un problema en aumento en papa en Europa) así como para otras especies de Dickeya. Estos ensayos están siendo validados actualmente para pruebas de diagnóstico molecular por un número de laboratorios europeos de fitosanidad.

Notes

Acknowledgments

The authors are grateful for funding provided by the Rural and Environmental Science and Analytical Services (RESAS) division of the Scottish Government and the Agriculture and Horticulture Development Board (AHDB) through the Potato Council (grants R437 and R475).

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Copyright information

© The Potato Association of America 2015

Authors and Affiliations

  • Ian Toth
    • 1
    Email author
  • Sonia Humphris
    • 1
  • Emma Campbell
    • 1
  • Leighton Pritchard
    • 1
  1. 1.James Hutton InstituteDundeeUK

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