European population of $Pectobacterium\ punjabense$: Genomic diversity, tuber maceration capacity and a detection tool for this rarely occurring potato pathogen

Jeremy Cigna (1, 2) , Angélique Laurent (3, 2) , Malgorzata Waleron (4) , Krzysztof Waleron (4) , Pauline Dewaegeneire (2) , Jan van Der Wolf (5) , Didier Andrivon (3) , Denis Faure (1) , Valérie Hélias (3, 2)

1 I2BC - Institut de Biologie Intégrative de la Cellule
2 FN3PT - Fédération Nationale des Producteurs de Plants de Pomme de Terre
3 IGEPP - Institut de Génétique, Environnement et Protection des Plantes
4 Medical University of Gdańsk
5 WUR - Wageningen University and Research [Wageningen]

Enterobacteria belonging to the and genera are responsible for soft rot and blackleg diseases occurring in many crops around the world. Since 2016, the number of described species has more than doubled. However, some new species, such as , are often poorly characterized, and little is known about their genomic and phenotypic variation. Here, we explored several European culture collections and identified seven strains of All were collected from potato blackleg symptoms, sometimes from a long time ago, i.e., the IFB5596 strain isolated almost 25 years ago. We showed that this species remains rare, with less than 0.24% of strains identified among pectinolytic bacteria present in the surveyed collections. The analysis of the genomic diversity revealed the non-clonal character of species. Furthermore, the strains showed aggressiveness differences. Finally, a qPCR Taqman assay was developed for rapid and specific strain characterization and for use in diagnostic programs.

Mots clés: Pectobacterium punjabense; detection qPCR TaqMan assay; genomic diversity; maceration tuber; soft rot enterobacteria

Domaines: Sciences de l'environnement

Jeremy Cigna, Angélique Laurent, Malgorzata Waleron, Krzysztof Waleron, Pauline Dewaegeneire, et al.. European population of $Pectobacterium\ punjabense$: Genomic diversity, tuber maceration capacity and a detection tool for this rarely occurring potato pathogen. Microorganisms, 2021, 9 (4), pp.781. ⟨10.3390/microorganisms9040781⟩. ⟨hal-03285249⟩