Population Structures of ‘Candidatus Liberibacter asiaticus’ in Southern China

Abstract

Huanglongbing (HLB) is a highly detrimental citrus disease associated with 'Candidatus Liberibacter asiaticus', a nonculturable alpha-proteobacterium. Characterization of the bacterial populations is important for development of disease management strategies. In this study, the 'Ca. L. asiaticus' populations in eight provinces in southern China where HLB is endemic were analyzed based on tandem repeat number (TRN) variations in a previously characterized genomic locus CLIBASIA_01645. Of the 224 HLB samples collected, 175 (78.3%) samples yielded single polymerase chain reaction (PCR) amplicons (the single amplicon group, SAG) and 49 (21.7%) samples produced multiple PCR amplicons (the multiple amplicon group, MAG). Variations in SAG are summarized by Nei's diversity index (H) and ratio of TRN ≤ 10/TRN > 10 genotypes (R10). Variations in the MAG are described by the percentage of occurrence (PMAG). At an orchard-level comparison, the 'Ca. L. asiaticus' population from a Guangdong orchard (n = 24) showed H = 0.50, R10 = 23, and PMAG = 0, significantly different from that of the non-Guangdong orchards in Yunnan (n = 23), H = 0.83, R10 = 2.3, and PMAG = 11.5, and in Hainan (n = 35), H = 0.88, R10 = 1.5, and PMAG = 16.7. In a region-level consideration, the Guangdong 'Ca. L. asiaticus' population (n = 78) was H = 0.77, R10 = 25, and PMAG = 1.3, whereas the non-Guangdong population (n = 84) was H = 0.91, R10 = 1.6, and PMAG = 26.9. Overall, significant differences were observed between the 'Ca. L. asiaticus' population from Guangdong Province and those from the other provinces. A strong aggregation of TRN = 6, 7, and 8 genotypes is characteristic to the 'Ca. L. asiaticus' population in Guangdong. Referenced to genome annotation, we propose that rearrangement of tandem repeats at locus CLIBASIA_01645 could be associated with bacterial environmental adaptation.

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

“…TRN in genomic loci like CLIBASIA_01645 is more precise in genetic differentiation of CLas isolates in comparison to single nucleotide polymorphisms (Katoh et al, 2011). The amplification of CLIBASIA_01645 loci of CLas strains from NEH region in present study revealed that all the strains belonged to single amplicon group (SAG) exhibiting identical electrophoretic profile as reported previously (Chen et al, 2010; Ma et al, 2014). Association of specific TRN class of CLas genotype with specific citrus cultivar has been observed e.g.…”

“…Current study indicated that inter-population TRN distribution in the different citrus groves of India is different. The CLas strains from North East India belonged to SAG as like that of Guangdong and Florida (Chen et al, 2010) unlike that of existence of both SAG and multiple amplicon group reported from Southern China (Ma et al, 2014). …”

“…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). In order to describe the CLas population structure based on TRN10 threshold, the R 10 values were calculated as ratio of TRN ≤ 10 and TRN > 10 genotypes which were stabilized empirically (Chen et al, 2010; Ma et al, 2014). …”

“…Simple sequence repeat or microsatellite markers with variable number of tandem repeats (VNTR) have been widely employed as robust marker in differentiating the bacterial species (Katoh et al, 2011; Lin et al, 2005; Ma et al, 2014). CLIBASIA_ 01645 loci in the CLas genome was identified and used as a sensitive indicator in differentiation of strains (Chen et al, 2010).…”

“…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). …”