Genetic Diversity of the Indian Populations of ‘Candidatus Liberibacter asiaticus’ Based on the Tandem Repeat Variability in a Genomic Locus

Abstract

Citrus huanglongbing (HLB, citrus greening disease) is an extremely destructive disease affecting citrus and causes severe economic loss to the crop yield worldwide. The disease is caused by a phloem-limited, noncultured, gram-negative bacteria Candidatus Liberibacter spp., the widely present and most destructive species being ‘Candidatus Liberibacter asiaticus’. Although the disease has been reported from almost all citrus growing regions of India, knowledge on the molecular variability of the pathogen ‘Ca. L. asiaticus’ populations from different geographical regions and cultivars is limited. In the present study, variability of the Indian ‘Ca. L. asiaticus’ based on the tandem repeats at the genomic locus CLIBASIA_01645 was characterized and categorized into four classes based on the tandem repeat number (TRN); Class I (TRN ≤ 5), Class II (TRN > 5 ≤ 10), Class III (TRN > 10 ≤ 15), and Class IV (TRN > 15). The study revealed that the Indian population of ‘Ca. L. asiaticus’ is more diverse than reported for Florida and Guangdong populations, which showed less diversity. While Florida and Guangdong populations were dominated by a TRN5 and TRN7 genotype, respectively, the Indian ‘Ca. L. asiaticus’ populations with TRN copy numbers 9, 10, 11, 12, and 13 were widely distributed throughout the country. Additionally, TRN2 and TRN17 genotypes were also observed among the Indian ‘Ca. L. asiaticus’ populations. The predominant ‘Ca. L. asiaticus’ genotypes from the northeastern region of India were TRN6 and TRN7 (53.12%) and surprisingly similar to neighboring South China populations. Preliminary results showed absence of preference of citrus cultivars to any specific ‘Ca. L. asiaticus’ genotype.