Diversity and Plasticity of the Intracellular Plant Pathogen and Insect Symbiont Candidatus Liberibacter asiaticus as Revealed by Hypervariable Prophage Genes with Intragenic Tandem Repeats

Candidatus Liberibacter asiaticus is a psyllid-transmitted, phloem-limited alphaproteobacterium and the most prevalent species of Ca. Liberibacter associated with a devastating worldwide citrus disease known as huanglongbing (HLB). Two related and hypervariable genes (hyv(I) and hyv(II)) were identified in the prophage regions of the Psy62 Ca. Liberibacter asiaticus genome. Sequence analyses of the hyv(I) and hyv(II) genes in 35 Ca. Liberibacter asiaticus DNA isolates collected globally revealed that the hyv(I) gene contains up to 12 nearly identical tandem repeats (NITRs, 132 bp) and 4 partial repeats, while hyv(II) contains up to 2 NITRs and 4 partial repeats and shares homology with hyv(I). Frequent deletions or insertions of these repeats within the hyv(I) and hyv(II) genes were observed, none of which disrupted the open reading frames. Sequence conservation within the individual repeats but an extensive variation in repeat numbers, rearrangement, and the sequences flanking the repeat region indicate the diversity and plasticity of Ca. Liberibacter asiaticus bacterial populations in the world. These differences were found not only in samples of distinct geographical origins but also in samples from a single origin and even from a single Ca. Liberibacter asiaticus-infected sample. This is the first evidence of different Ca. Liberibacter asiaticus populations coexisting in a single HLB-affected sample. The Florida Ca. Liberibacter asiaticus isolates contain both hyv(I) and hyv(II), while all other global Ca. Liberibacter asiaticus isolates contain either one or the other. Interclade assignments of the putative Hyv(I) and Hyv(II) proteins from Florida isolates with other global isolates in phylogenetic trees imply multiple Ca. Liberibacter asiaticus populations in the world and a multisource introduction of the Ca. Liberibacter asiaticus bacterium into Florida.