Genetic diversity and molecular variability of ’Candidatus Phytoplasma solani’ based on multilocus sequence typing analysis in tomato plantations of western Turkey

Abstract

‘Candidatus Phytoplasma solani’ (CaPsol) is a very common pathogen in the Euro-Mediterranean regions and has been reported in many countries. Field surveys were conducted in tomato plantations in 2022 to determine the CaPsol infections in the western part of Turkey, which has the highest vegetable production volume. A total of 67 tomato samples, 52 symptomatic and 15 asymptomatic, were collected from four different provinces. A total of thirteen CaPsol strains were identified using molecular techniques from tomato samples. The tuf/stamp/vmp1 genes molecular markers were used to perform molecular and genetic diversity characterizations of these strains. The tuf-b1 genotype and five different stamp genotypes genetically closely related to Eastern European strains were determined in all strains. In addition, these strains showed more than 99% nucleotide sequence similarity with 4 different vmp1 genotypes: V2-TA, V14, V4, and V15. Advanced bioinformatics analyses were performed with stamp (N = 290) and vmp1 (N = 207) strains obtained from this study and GenBank. These analyses showed that the strains for both gene regions descended from two molecular evolutionary ancestors. In order to calculate the genetic distance relationships according to the stamp and vmp1 gene regions, a hierarchical classification was done as geographical and host populations. While these analyses demonstrate the close genetic relationship between Turkish and Eastern European populations, they strongly confirm the importance of the epidemiological cycle between weed, perennial, and insect vectors. Then, molecular variance analyses (AMOVA) were performed on these classified populations. The results indicated high variation for both gene regions but showed that each strain contributed greatly to the CaPsol genetic diversity. Thus, for the first time, multilocus sequence patterns of CaPsol strains obtained from western Turkey were extracted. Extensive genetic analyses have strongly demonstrated the importance of horizontal transmission in the control and epidemiological cycle of CaPsol.