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

Abstract

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.” 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.”