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ARS Home » Pacific West Area » Riverside, California » National Clonal Germplasm Repository for Citrus » Research » Publications at this Location » Publication #334649
Title: Two “Candidatus Liberibacter asiaticus” strains recently found in California harbor different prophages

Author
item ZHENG, Z - South China Agricultural University
item WU, F - South China Agricultural University
item KUMAGAI, L - California Department Of Food And Agriculture
item Polek, Marylou
item DENG, X - South China Agricultural University
item Chen, Jianchi

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/11/2017
Publication Date: 2/20/2017
Citation: Zheng, Z., Wu, F., Kumagai, L.B., Polek, M., Deng, X., Chen, J. 2017. Two “Candidatus Liberibacter asiaticus” strains recently found in California harbor different prophages. Phytopathology. 107(6):662-668. http://dx.doi.org/10.1094/PHYTO-10-16-0385-R.

Interpretive Summary: Citrus Huanglongbing (HLB) is currently threatening citrus production worldwide. The putative pathogen of HLB is a bacterium called “Candidatus Liberibacter asiaticus”. Officially, California now has HLB, but the pathogen has only been detected in two neighborhoods in Los Angeles County; first in Hacienda Heights in 2012 and then in San Gabriel in 2015. A total of 28 trees have been eradicated after confirmation of the pathogen by regulatory officials. Stakeholder and public concerns about HLB in California are high. Little is known about the HLB pathogen, hindering effective HLB management efforts. In this study, a next generation sequencing (NGS) technology was employed to study the California HLB pathogen. Data sets containing >4 billion bp of sequence were generated from each location. Two mobile DNA elements, called prophages, were found. Analyses of the two DNA elements revealed that they were different from each other, but both were of Asiatic origin. Although the exact route of introduction remains unknown, it is likely the pathogen was introduced to California as two separate incidents. These results significantly expand our current knowledge about the HLB pathogen which will assist current efforts to eradicate HLB in California.

Technical Abstract: “Candidatus Liberibacter asiaticus” (CLas), an a-proteobacterium, is associated with citrus Huanglongbing (HLB; yellow shoot disease). In California, CLas was first detected in the residential neighborhoods in Los Angeles County of Hacienda Heights (HH) in 2012 and in San Gabriel (SG) in 2015. Although all known infected trees were destroyed in compliance with a state mandate, citrus industry stakeholder concerns about HLB in California are high. Little is known about the biology of CLas, particularly the California strains, hindering effective HLB management efforts. In this study, a next generation sequencing (NGS) technology (Illumina MiSeq) was employed to characterize the HH and SG strains of CLas. Data sets containing >4 billion (Giga) bp of sequence were generated from each sample. Two prophages (P-HHCA1-2 and PSGCA5-1) were identified by mapping MiSeq reads onto two known Florida CLas prophage sequences,SC1 and SC2. P-HHCA1-2 was a SC2-like (100% coverage and 97% identity), or Type 2, prophage with 38,920 bp. P-SGCA5-1 was a SC1-like (94% coverage and 96% identity), or Type 1, prophage with 37,487 bp in two contigs. Phylogenetic analysis revealed that P-HHCA1-2 was part of an Asiatic lineage within Type 2 prophage group. Similarly, P-SGCA5-1 was part of an Asiatic lineage within Type 1 prophage group. The Asiatic relatedness of both P-HHCA1-2 and P-SGCA5-1 was further supported by the analysis of single nucleotide polymorphisms (SNPs) in the terminase gene (CLIBASIA_05610) that has been established for CLas strain differentiation. The presence of different prophages suggested that the two California CLas strains could have been introduced from different sources.