Diversity of “Candidatus Liberibacter asiaticus” strains in Texas revealed by phage sequence analyses

Authors: DE LEON, VICTORIA - Texas A&M University; Chen, Jianchi; PARK, JONG-WON - Texas A&M University; GREG, MCCOLLUM - Retired ARS Employee; SETAMOU, MAMOUDOU - Texas A&M University; KUNTA, MADHURABABU - Texas A&M University

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/6/2024
Publication Date: 1/22/2024
Citation: De Leon, V.S., Chen, J., Park, J., Greg, M., Setamou, M., Kunta, M. 2024. Diversity of “Candidatus Liberibacter asiaticus” strains in Texas revealed by phage sequence analyses. Plant Disease. https://doi.org/10.1094/PDIS-09-23-1994-SR.
DOI: https://doi.org/10.1094/PDIS-09-23-1994-SR

Interpretive Summary: Citrus is an important economic crop in South Texas, particularly in the Rio Grande Valley. Citrus Huanglongbing (HLB) is a devastating disease, associated with an unculturable bacterium, "Candidatus Liberibacter asiaticus" that is transmitted by an insect, Asian citrus psyllid. Knowledge of HLB pathogen diversity in Texas along with strain relationships to those in Florida and California is important for effective HLB management. In this study, HLB pathogen diversity was studied using sequences of phages or viruses that infect the HLB pathogen. Research results showed that the HLB pathogen population in Texas is similar to that in Florida but different from that in California. Two distinct pathogen types were discovered, suggesting the possibility of two different introductions. Results from this study provide baseline information for further HLB research and management in Texas and other locatins in the United States.

Technical Abstract: Phages/prophages are important components of the genome of "Candidatus Liberibacter asiaticus" (CLas), an unculturable alphaproteobacterium associated with citrus Huanglongbing (HLB). Phage variations have significant contributions to CLas strain diversity research, which provide critical information for HLB management. In this study, phage variations among selected CLas strains from southern Texas were studied. The CLas strains were collected from three different CLas inhabitant environments: citrus leaf, citrus root, and Asian citrus psyllid (ACP), the vector of CLas, over a period of 24 months. Regardless the different habitats and time span, more than 90% of CLas strains consistantly had both Type 1 and Type 2 phages. The same phage type profile was observed in CLas strains from Florida, but different to those reported in California. Further studies were performed on within phage type diversity. Analyses on Type 1 specific PCR amplicon sequences (encoding an endolysin protein) revealed the presence of two groups: Type 1-A clustered around phage SC1 originated from Florida and Type 1-B clustered with phage P-SGCA5-1 detected in California. Type 1-B strains were mostly from ACP of nearby citrus orchards. On the other hand, analyses on Type 2 specific PCR amplicon sequences (encoding a putative hypothetical protein) showed a single group clustering around phage SC2 originated from Florida. The presence of two distinct Type 1 phage groups suggested the possibility of two different introductions CLas in southern Texas. Results from this study provides an initial baseline information on genomic and population diversity of CLas in Texas and demonstrate that genome sequences including phage sequences are critical resources for CLas characterization and HLB research and management.