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.

Genetic Variability Based on Tandem Repeat Numbers in a Genomic Locus of ‘Candidatus Liberibacter asiaticus’ Prevalent in North East India

“…mandarins (Khasi mandarin) were predominantly infected by TRN7 and TRN9 genotypes. In previous study preferential accumulation of TRN5 and TRN9 was reported form mandarins (Ghosh et al, 2015). Sweet oranges in NE region were more frequently infected with CLas of TRN7, whereas preferential accumulation of TRN6 was detected earlier from sweet oranges grown in other parts of India (Ghosh et al, 2015).…”

“…The CLas population previously characterized from the other parts of India (Ghosh et al, 2015) were compared with the strains characterized in the present study in order to have overall picture of its genetic structure. In the NE states of India, where citrus is largely cultivated through seedling propagation but budded plants are less commonly planted, the CLas genotypes of TRN7 were more predominant (23.75% frequency) followed by TRN5 genotypes (15.00% frequency) (Table 2), which indicated that overall infection of class II genotypes of CLas were widely prevalent in the citrus groves of NE India.…”

“…In case if the computed F -value was lower than or equal to the tabular F -value at the 5% level of significance, the differences in the TRN of CLas associated with specific citrus host cultivar was considered non-significant. Based on the genetic variations in the CLI-BASIA_ 01645 locus, the CLas strains were divided into different classes as defined by Ghosh et al (2015) with little modification as: class I, TRN ≤ 5; class II, 5 < TRN ≤ 10; class III, 10 < TRN ≤ 15; class IV, 15 < TRN ≤ 20; and class V, TRN > 20. The population genetic diversity among different populations of CLas were calculated using Nei’s H value as H = 1 − ∑pi 2 , where ‘pi’ referred to as frequency of the allele ‘i’ at the locus (Nei, 1973).…”

“…Greening (“huanglongbing”, HLB) is most destructive disease of citrus causing major economic losses to citrus industry worldwide including India (Ahlawat, 1997; Bové, 2006; Ghosh et al, 2015). From the citrus growing areas of India, the disease was confirmed by transmitting it through Asian citrus psyllid during 1967 (Capoor, 1963; Capoor et al, 1967).…”

“…Tandem repeat number (TRN) variations in the bacterial population are generated through DNA strand slippage (Bichara et al, 2006; Verstrepen et al, 2005) and have role in pathogenic or environmental fitness (Boles et al, 2004). TRN profiling has recently been used for fine genetic resolution of CLas population (Chen et al, 2010; Ghosh et al, 2015; Katoh et al, 2011; Ma et al, 2014). …”