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Population Structures of ‘Candidatus Liberibacter asiaticus’ in Southern China

First, second, third, fourth, fifth, and sixth authors: Laboratory of Citrus Huanglongbing Research, Department of Plant Pathology, South China Agricultural University, Guangzhou, P.R. China; and seventh author: Crop Diseases, Pests, and Genetics Research Unit, San Joaquin Valley Agricultural Sciences Center, United States Department of Agriculture-Agricultural Research Service, Parlier, CA.

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 (P_MAG). At an orchard-level comparison, the ‘Ca. L. asiaticus’ population from a Guangdong orchard (n = 24) showed H = 0.50, R₁₀ = 23, and P_MAG = 0, significantly different from that of the non-Guangdong orchards in Yunnan (n = 23), H = 0.83, R₁₀ = 2.3, and P_MAG = 11.5, and in Hainan (n = 35), H = 0.88, R₁₀ = 1.5, and P_MAG = 16.7. In a region-level consideration, the Guangdong ‘Ca. L. asiaticus’ population (n = 78) was H = 0.77, R₁₀ = 25, and P_MAG = 1.3, whereas the non-Guangdong population (n = 84) was H = 0.91, R₁₀ = 1.6, and P_MAG = 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.