Identification of a chromosomal deletion mutation and the dynamics of two major populations of Candidatus Liberibacter asiaticus in its hosts

Authors: Armstrong, Cheryl; ZHOU, LIJUAN - University Of Florida; LUO, WEIQI - North Carolina State University; BATUMAN, OZGUR - University Of Florida; ALABI, OLUFEMI - Texas A&M University; Duan, Ping

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/11/2021
Publication Date: 1/14/2022
Citation: Armstrong, C.M., Zhou, L., Luo, W., Batuman, O., Alabi, O., Duan, Y. 2022. Identification of a chromosomal deletion mutation and the dynamics of two major populations of Candidatus Liberibacter asiaticus in its hosts. Phytopathology. 112:81-88. https://doi.org/10.1094/PHYTO-08-21-0325-FI.
DOI: https://doi.org/10.1094/PHYTO-08-21-0325-FI

Interpretive Summary: Candidatus Liberibacter asiaticus (Las) is the most widely distributed species among the three species of Liberibacter associated with citrus huanglongbing (HLB), and the only one that has devastated the citrus industry in the United Sates. Las attacks all cultivars of citrus, and its population dynamics has played crucial roles in the long-lasting epidemics of HLB in Florida and Texas. Efforts that provide information regarding the pathogen’s ability to interact with its host may accelerate our ability to develop novel control strategies effective against HLB, thus reemphasizing the importance of the genomic analysis of Las in the fight against HLB. In this study, we re-investigated the Las genome, and identified a region deemed as a mosaic island associated with genome plasticity (instability). We further conducted a survey on more than 2,300 samples using quantitative real-time PCR, and revealed the coexistence of two major populations of Las within its hosts based upon the presence and/or absence of the mosaic island. Studies of the population dynamics exposed factors such as cultivar and geographical location that correlated with the susceptibility of the host to the disease and the overall fitness of Las in planta. These findings provide new insights into Las population dynamics and their potential contribution to HLB epidemics.

Technical Abstract: Candidatus Liberibacter asiaticus (Las) is the prominent species of Liberibacter associated with huanglongbing, a devastating disease of citrus worldwide. In this study, we report the identification of a ~8.3 kb DNA region of the Las genome containing eight putative open reading frames (ORFs) flanked by two inverted repeats, which was not present in the Las str. psy62 genome. Comparisons with other genome sequences established this region as a unique genetic element associated with genome plasticity/instability. Primers specific for both the presence (Las wild-type) and absence (Las mutant) of this region were designed to study the population dynamics and host adaptation of the two strains. Las populations with and/or without the wild-type strain were detected and differentiated in >2,300 samples that included psyllids, periwinkle, and several species of citrus. In psyllids, although a mixed population of the wild-type and mutant was observed in most samples (88%), the wild-type Las was detected alone at a rate of 11%. In contrast, none of the infected citrus plants were positive for the wild-type alone, which harbored either the mutant strain alone (8%) or a mixed population of the mutant and wild-type (92%). Furthermore, the dynamics of these two major Las populations varied with different citrus hosts while an in-depth study on grapefruit that did not rapidly succumb to disease revealed that the population of mutant alone increased with time, indicating that the absence of this genetic element is associated with the fitness of Las in planta under the selection pressure of its host.