Prophage diversity of “Candidatus Liberibacter asiaticus” strains in California

Authors: DAI, Z - South China Agricultural University; WU, F - South China Agricultural University; ZHENG, Z - South China Agricultural University; Yokomi, Raymond - Ray; KUMAGAI, L - California Department Of Food And Agriculture; CAI, W - Animal And Plant Health Inspection Service (APHIS); RASCO, J - Animal And Plant Health Inspection Service (APHIS); Polek, Marylou; DENG, Z - South China Agricultural University; Chen, Jianchi

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/7/2018
Publication Date: 3/4/2019
Citation: Dai, Z., Wu, F., Zheng, Z., Yokomi, R.K., Kumagai, L., Cai, W., Rasco, J., Polek, M., Deng, Z., Chen, J. 2019. Prophage diversity of “Candidatus Liberibacter asiaticus” strains in California. Phytopathology. 109(4):551-559. https://doi.org/10.1094/PHYTO-06-18-0185-R.
DOI: https://doi.org/10.1094/PHYTO-06-18-0185-R

Interpretive Summary: Huanglongbing (HLB) is a deadly citrus disease and is associated with a non-culturable bacterium “Candidatus Liberibacter asiaticus” (CLas). HLB has now reduced Florida citrus production by two-thirds and more than doubled production costs. The first CLas detection in California occurred in 2012 in an urban garden in Hacienda Heights (Los Angeles Co.) and has now been detected in multiple urban locations in Southern California. Knowledge of genetic diversity of California CLas strains is important to ascertain pathways of entry as well as HLB management. In this study, ten Southern California CLas strains from six urban locations were analyzed for genomic diversity using next generation sequencing, and genome sequences of the California CLas strains were acquired. Prophage sequences, the most variable part of the genome, were analyzed. Four prophage typing groups (PTGs) were identified and profiled. Results suggest multiple exotic introductions, possibly from Asia, have occurred in California. Altogether, this study provides baseline information for further HLB epidemiology research and management in California.

Technical Abstract: Huanglongbing (HLB) is a highly destructive citrus disease and is associated with a non-culturable bacterium, “Candidatus Liberibacter asiaticus” (CLas). CLas in the U.S. was first found in Florida in 2005 and is now endemic there. In California, CLas was first detected in Hacienda Heights in Los Angeles County in 2012 and, in subsequent years, has been detected in multiple urban locations in Southern California. Knowledge of the diversity of California CLas strains is important for HLB management. In this study, ten Southern California CLas strains from six urban locations were analyzed for genomic diversity using next generation sequencing (Illumina MiSeq and HiSeq). One CLas strain from Florida and three from China were used for comparative purposes. Draft genome sequences of the California CLas strains were assembled or reassembled and 16S rRNA and nrdB gene sequences confirmed CLas identity. Prophages were present in all the CLas strains and used to differentiate strains from the different collection sites. Prophage typing revealed four CLas groups: 1) PTG1 (Type 1) found in Anaheim, San Gabriel, and Riverside; 2) PTG2 (Type 2) found in Hacienda Heights; 3) PTG1-3 (both Type 1 and Type 3 ) found in Cerritos; and PTG1-2 (both Type 1 and Type 2) found in La Habra. Analyses of terL sequences showed that all California CLas strains were more related to Asiatic than Florida strains. All prophages harbored miniature inverted-repeat transposable elements (MITEs). Variations of MITEs were detected in the Cerritos strain. In addition, MITE characteristics in the San Gabriel strain separated it from the other strains within PTG1 group. Altogether, this study provides baseline information for further HLB epidemiology research in California.