Differentiation of ‘Candidatus Liberibacter asiaticus’ in Saudi Arabia based on tandem repeat variability in genomic locus

Citrus greening, or huanglongbing, is a destructive disease threatening many citrus worldwide, and drastically altering the global dynamics of the citrus industry. The disease is caused by one of several unculturable bacterial species belonging to ‘Candidatus Liberibacter’. The recent availability of complete genome sequences of ‘Candidatus Liberibacter asiaticus’ (CLas) has facilitated comprehensive assessments of genomic variability using a range of approaches, including short tandem repeat analysis. The objective of this study was to evaluate the genetic diversity of CLas populations in Saudi Arabia based on tandem repeat number (TRN) within the CLIBASIA_01645 locus, predicted to encode the bacteriophage C1 repressor protein. Results indicated that the genotype richness of the Saudi Arabian CLas isolates was conserved by 27% based on the TRN locus. Four different genotypes TRN2, TRN3, TRN4, and TRN5 were identified. However, the TRN2 and TRN5 were the most dominant genotypes. All four of the TRN genotypes were associated with CLas-positive mandarin (Citrus reticulata) or sweet orange (C. sinensis) citrus trees. The diversity (H = 0.69) and evenness (H'=0.914) were overall relatively high, with the northern region of Saudi Arabia harboring the highest diversity (0.7) and evenness score (0.9–1.0). Phylogenetic analysis of the CLas-bacteriophage C1 repressor protein of the Saudi Arabian isolates indicated CLas was more closely related to ‘Candidatus Liberibacter africanus’ than to ‘Candidatus Liberibacter americanus’.