Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in Candidatus Liberibacter asiaticus

Huanglongbing disease (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen Candidatus Liberibacter asiaticus is an alphaproteobacterium of the Rhizobiaceae family that has been identified as the causative agent of HLB. The virulence of Ca. Liberibacter asiaticus has been attributed, in part, to prophage-carried genes. Prophage and prophage-like elements have been identified in 12 of the 15 available Ca. Liberibacter asiaticus genomes and are classified into three prophage types. Here, we reexamined all 15 Ca. Liberibacter asiaticus genomes using a de novo prediction approach and expanded the number of prophage-like elements from 16 to 33. Further, we found that all of the Ca. Liberibacter asiaticus genomes contained at least one prophage-like sequence. Comparative analysis revealed a prevalent, albeit previously unknown, prophage-like sequence type that is a remnant of an integrated prophage. Notably, this remnant prophage is found in the Ishi-1 Ca. Liberibacter asiaticus strain that had previously been reported as lacking prophages. Our findings provide both a resource for data and new insights into the evolutionary relationship between phage and Ca. Liberibacter asiaticus pathogenicity. IMPORTANCE Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is Candidatus Liberibacter asiaticus. Prior work using mapping-based approaches identified prophage-like sequences in some Ca. Liberibacter asiaticus genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in Ca. Liberibacter asiaticus from 16 to 33 and identified at least one prophage-like sequence in all Ca. Liberibacter asiaticus strains. Furthermore, we identified a prophage-like sequence type that is a remnant of an integrated prophage-expanding the number of prophage types in Ca. Liberibacter asiaticus from 3 to 4. Overall, the findings will help researchers investigate the role of prophage in the ecology, evolution, and pathogenicity of Ca. Liberibacter asiaticus.