Diversity and phylogeny of Polymyxa spp.

Details

Supervisors

Genard, Margaux ; Legrève, Anne

Faculty

Faculté des bioingénieurs

Degree label

Master [120] : bioingénieur en sciences agronomiques, à finalité spécialisée

Abstract

The Polymyxa genus belongs to the order Plasmodiophorida, which groups together mainly obligate plant endoparasites, capable of causing major damage to crops through direct disease induction or transmission of phytoviruses. Polymyxa spp. are involved in the transmission of over 20 viruses, causing considerable agronomic and economic damage. These parasites produce sporospores that can persist for several years in the environment, while retaining their ability to transmit viruses. Sporosores render many control methods, whether chemical, biological or cultural, ineffective and often unacceptable from an environmental point of view. Furthermore, the longevity of sporosores and the factors influencing the infection process remain poorly understood, complicating the management of these pathogens. The Polymyxa genus comprises two morphologically identical species: Polymyxa graminis and Polymyxa betae. Analyses combining rRNA sequences, host ranges and environmental conditions have enabled us to distinguish five formae speciales within P. graminis: Pg f. sp. temperata, tepida, tropicalis, subtropicalis and colombiana. The contrast observed between the genetic diversity and cases of infection deviating from the host ranges described may suggest the need to re-evaluate current taxonomy. The aim of this study was to explore the diversity of Polymyxa spp. through the sequencing and analysis of genetic markers (SSU rDNA, ITS1-5.8S-ITS2, 28S, L10, RPS5, Btub, eF1α). The aim is to gain a better understanding of the phylogeny of Polymyxa spp. The second objective is to study the viability of Pg sporosores and the parameters likely to optimize reinfection (inoculation method, nutrient solution, pH, watering system, time of inoculation) by testing sporosores over 25 years old. At the end of this study, the actin, glutathione S-transferase and ubiquitin loci were identified as candidate markers for phylogeny and require further testing. The contribution of sequences from numerous isolates has added diversity to the phylogenetic analysis of Polymyxa spp. The 18S marker has been effective in characterizing groupings between special forms. The 28S locus demonstrated superior resolution in defining isolates down to ribotypes. Finally, phylogenetic analysis based on the ITS1-5.8S-ITS2 region proved to be the most accurate marker and confirmed its definition as the preferred character for the phylogeny of Polymyxa spp. The other four markers did not result in consistent phylogenetic analyses and did not clarify the phylogeny of the genus. The tests carried out failed to demonstrate Polymyxa's ability to reinfect roots more than 25 years after the initial infection. Furthermore, none of the parameters studied showed any positive influence on the infection process.