Prophage region and short tandem repeats of “ Candidatus Liberibacter asiaticus” reveal significant population structure in China

2020 ◽  
Author(s):  
Yongqin Zheng ◽  
Hongxia Huang ◽  
Zhenhui Huang ◽  
Xiaoling Deng ◽  
Zheng Zheng ◽  
...  
Keyword(s):  
Population Structure ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Candidatus Liberibacter Asiaticus ◽  
Prophage Region ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus ◽  
Short Tandem

scholarly journals Genetic Diversity of ‘Candidatus Liberibacter asiaticus’ Revealed by Short Tandem Repeats and Prophage Typing Indicates Population Homogeneity in Brazil

2019 ◽  
Vol 109 (6) ◽  
pp. 960-971 ◽  
Author(s):  
Priscila Alves da Silva ◽  
Camila Giacomo Fassini ◽  
Laís Simões Sampaio ◽  
Gabriel Dequigiovanni ◽  
Maria Imaculada Zucchi ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Genomic Organization ◽  
The United States ◽  
Candidatus Liberibacter Asiaticus ◽  
Homogeneous Population ◽  
South Central ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus ◽  
Short Tandem

‘Candidatus Liberibacter asiaticus’ is the most common huanglongbing-associated bacteria, being present in Asia, South, Central, and North America. Genomic approaches enabled sequencing of ‘Ca. L. asiaticus’ genomes, allowing for a broader assessment of its genetic variability with the application of polymerase chain reaction (PCR)-based tools such as microsatellite or short tandem repeat (STR) analysis. Although these tools contributed to a detailed analysis of strains from Japan, China, and the United States, Brazilian strains were analyzed in either too few samples with several STRs or in several strains with only a single microsatellite and a single PCR marker. We used 573 ‘Ca. L. asiaticus’ strains, mainly collected from São Paulo State (SPS), in our genetic analyses, employing three STRs and several prophage PCR markers. STR revealed a homogeneous population regardless of sampling year or geographic regions of SPS. Thirty-eight haplotypes were recognized with a predominance of VNTR_005 higher than 10 repeats, with VNTR_002 and VNTR_077 containing 11 and 8 repeats, respectively. This haplotype is indicated as class HE, which comprised 80.28% of strains. Classes HA and HB, predominant in Florida, were not found. A new genomic organization in the junction of prophages SC2 and SC1 is prevalent in Brazilian strains, indicating gene rearrangement and a widespread occurrence of a type 1 prophage as well as the presence of a type 2-like prophage. Our results indicate that ‘Ca. L. asiaticus’ populations are homogeneous and harbor a new genomic organization in prophages type 1 and 2.

scholarly journals Guangdong and Florida Populations of ‘Candidatus Liberibacter asiaticus’ Distinguished by a Genomic Locus with Short Tandem Repeats

2010 ◽  
Vol 100 (6) ◽  
pp. 567-572 ◽  
Author(s):  
J. Chen ◽  
X. Deng ◽  
X. Sun ◽  
D. Jones ◽  
M. Irey ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Candidatus Liberibacter Asiaticus ◽  
Bacterial Strains ◽  
Genomic Locus ◽  
Global Epidemiology ◽  
Geographical Regions ◽  
The World ◽  
Citrus Production ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus

Huanglongbing (HLB) (yellow shoot disease) is a highly destructive disease that threatens citrus production worldwide. The disease was first observed in Guangdong, P.R. China, over 100 years ago, and was found in Florida, United States, in 2005. ‘Candidatus Liberibacter asiaticus’ has been associated with HLB in many citrus-growing regions around the world, including Guangdong and Florida. The global epidemiology of HLB, as well as management of the disease, relies on knowledge of ‘Ca. L. asiaticus’ populations in different geographical regions around the world. In this study, we identified a genetic marker containing small tandem repeats in the genome of ‘Ca. L. asiaticus’ and comparatively analyzed the tandem repeat numbers (TRNs) in ‘Ca. L. asiaticus’ populations from Guangdong and Florida. Analyses of TRNs showed that the bacterial population in Guangdong was different from that in Florida. The Guangdong population consisted predominately of strains with a TRN of 7 (TRN7) at a frequency of 47.6%. The Florida population consisted predominately of strains with a TRN of 5 (TRN5) at a frequency of 84.4%. TRNs ranged from 3 to 16. The apparent absence of TRNs of 9, 10, 11, and 12 separated the bacterial strains into two groups: TRNs < 10 (TRN<10) and TRNs > 10 (TRN>10). In Florida, TRN<10 strains (103/109, or 94.5%) were widely distributed in all HLB-affected counties. TRN>10 strains (6/109, or 5.5%) were found in central Florida. This is the first report documenting the differentiation of ‘Ca. L. asiaticus’ populations between Asia and North America and the possible presence of two differentially distributed genotypes of ‘Ca. L. asiaticus’ in Florida.

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

2015 ◽  
Vol 105 (8) ◽  
pp. 1043-1049 ◽  
Author(s):  
Dilip Kumar Ghosh ◽  
Sumit Bhose ◽  
Manali Motghare ◽  
Ashish Warghane ◽  
Krishanu Mukherjee ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Tandem Repeats ◽  
Economic Loss ◽  
Class Iii ◽  
Candidatus Liberibacter Asiaticus ◽  
Genomic Locus ◽  
Citrus Greening Disease ◽  
Geographical Regions ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus

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.

scholarly journals Population Structures of ‘Candidatus Liberibacter asiaticus’ in Southern China

2014 ◽  
Vol 104 (2) ◽  
pp. 158-162 ◽  
Author(s):  
W. Ma ◽  
M. Liang ◽  
L. Guan ◽  
M. Xu ◽  
X. Wen ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Southern China ◽  
Diversity Index ◽  
Management Strategies ◽  
Candidatus Liberibacter Asiaticus ◽  
Genomic Locus ◽  
Bacterial Populations ◽  
Single Polymerase Chain Reaction ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus

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.

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