Analysis of variable number of tandem repeats of ‘Candidatus Liberibacter asiaticus’ using CLIBASIA_01645 locus
- 1GTU-School of Applied Sciences and Technology (SAST), Gujarat Technological University
- 2Department of Zoology, Gargi College, University of Delhi
Abstract
‘ Candidatus Liberibacter asiaticus’ ( C Las) is a phloem-limited bacterium that causes Huanglongbing (HLB), the devastating citrus greening disease that has led to billions of dollars in losses throughout global citrus production. There is very little epidemiological data available regarding fine-scale molecular variability of C Las populations in different regions of the world or their distribution across various geographical landscapes. Here, we present an assessment of C Las genetic diversity using a hypervariable variable number tandem repeat (VNTR) marker (AGACACA) at the CLIBASIA_01645 locus of 344 genomic sequence data obtained from GenBank from five regions of the world (India-177, China-113, Saudi Arabia-37, Bhutan-10, and Nepal-7). The findings revealed high evolutionary plasticity and non-random distribution of TRN within four distinct classes, significantly deviating from a uniform distribution ( p < 0.05). The analyzed populations were stratified into four distinct classes: Class I (TRN ≤ 5), Class II (TRN > 5 ≤ 10), Class III (TRN > 10 ≤ 15), and Class IV (TRN > 15). The predominant type of subpopulation for all field samples was intermediate variants, with the highest frequencies observed for TRN6 (25%) and TRN7 (17.15%), possibly indicating genomic stability and/or adaptive advantages of specific tandem repeats. On the other hand, lower frequency rare variants (e.g., TRN17, TRN18, and TRN20 at 0.29%) represent some form of continued low frequency micro evolutional replication slippage and corresponding absence of some individual TRs indicates evidence of local purging forces. Crucially, the Indian C Las populations exhibited significantly greater densities of molecular diversity than populations from China, Saudi, Bhutan, and Nepal examined in this study. The distinct TRN signature profiles of these populations’ subpopulations exhibit strong geographic correlation with ecological regions, reinforcing the CLIBASIA_01645 locus as a strong marker for epidemiological surveillance for tracking global strain movement to develop target-specific HLB management programs.
Related
- Bactrocera oleae gut microbiome shows metabolic potential to complement the decline of symbiotic ‘Candidatus Erwinia dacicola’ in artificially-reared flies
- A Saccharimonadia epibiont interacts with the polyphosphate-accumulating bacterium Candidatus Phosphoribacter in wastewater treatment plants
- Novel "Candidatus Endobugula" hosts and distinct microbiomes in the bryozoans from the White Sea
- Beyond contact toxicity: Volatile and systemic nematode suppression by ‘Candidatus Pseudomonas auctus’ JDE115 in soybean
- A step toward synthetic endosymbiosis: introducing Escherichia coli and the trypanosomatid endosymbiont Candidatus Kinetoplastibacterium crithidii into mammalian cells using a polyethylene glycol-based fusion protocol
BibTeX
@article{warghane2026analysis,
title = {{Analysis of variable number of tandem repeats of ‘Candidatus Liberibacter asiaticus’ using CLIBASIA_01645 locus}},
author = {Ashish Warghane and Rashmi Saini and Nisarg Simariya and Yash Solanki and Gaurav Shrimali and Rajeshkumar G Chaudhary and Vaibhav Bhatt},
journal = {Frontiers in Microbiology},
year = {2026},
month = oct,
doi = {10.3389/fmicb.2026.1854860},
url = {https://www.frontiersin.org/articles/10.3389/fmicb.2026.1854860/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Analysis of variable number of tandem repeats of ‘Candidatus Liberibacter asiaticus’ using CLIBASIA_01645 locus
AU - Ashish Warghane
AU - Rashmi Saini
AU - Nisarg Simariya
AU - Yash Solanki
AU - Gaurav Shrimali
AU - Rajeshkumar G Chaudhary
AU - Vaibhav Bhatt
PY - 2026
DA - 2026/10/06
JO - Frontiers in Microbiology
DO - 10.3389/fmicb.2026.1854860
UR - https://www.frontiersin.org/articles/10.3389/fmicb.2026.1854860/full
AB - ‘ Candidatus Liberibacter asiaticus’ ( C Las) is a phloem-limited bacterium that causes Huanglongbing (HLB), the devastating citrus greening disease that has led to billions of dollars in losses throughout global citrus production. There is very little epidemiological data available regarding fine-scale molecular variability of C Las populations in different regions of the world or their distribution across various geographical landscapes. Here, we present an assessment of C Las genetic diversity using a hypervariable variable number tandem repeat (VNTR) marker (AGACACA) at the CLIBASIA_01645 locus of 344 genomic sequence data obtained from GenBank from five regions of the world (India-177, China-113, Saudi Arabia-37, Bhutan-10, and Nepal-7). The findings revealed high evolutionary plasticity and non-random distribution of TRN within four distinct classes, significantly deviating from a uniform distribution ( p < 0.05). The analyzed populations were stratified into four distinct classes: Class I (TRN ≤ 5), Class II (TRN > 5 ≤ 10), Class III (TRN > 10 ≤ 15), and Class IV (TRN > 15). The predominant type of subpopulation for all field samples was intermediate variants, with the highest frequencies observed for TRN6 (25%) and TRN7 (17.15%), possibly indicating genomic stability and/or adaptive advantages of specific tandem repeats. On the other hand, lower frequency rare variants (e.g., TRN17, TRN18, and TRN20 at 0.29%) represent some form of continued low frequency micro evolutional replication slippage and corresponding absence of some individual TRs indicates evidence of local purging forces. Crucially, the Indian C Las populations exhibited significantly greater densities of molecular diversity than populations from China, Saudi, Bhutan, and Nepal examined in this study. The distinct TRN signature profiles of these populations’ subpopulations exhibit strong geographic correlation with ecological regions, reinforcing the CLIBASIA_01645 locus as a strong marker for epidemiological surveillance for tracking global strain movement to develop target-specific HLB management programs.
SN - 1664-302X
ER -