Background: Huanglongbing (HLB) is a worldwide citrus disease caused by several Candidatus Liberibacter species. In this study, we utilize the available genome information from several HLB-associated pathogens and their relatives to systematically identify the unique genomic features and changes which accompany the evolution of these species in terms of their transition from free-living to intracellular habitats and their transition from being non-pathogenic to pathogenic.
Methods: All genomes of six Candidatus Liberibacter species were collected and analyzed using several dedicated computational strategies, including phylogenetic classification, comparative genomics, operonic analysis, ortholog analysis, and domain-centric sequence and structural analysis.
Results: By whole genomic comparisons guided by phylogenetic relationships, we detected major genomic changes of the Candidatus Liberibacter species during evolution, especially those shaped by large-region genomic inversion and recombination. We recovered and annotated all potential prophage regions, and classified them into four types. We showed that each prophage type originated from an independent gene transfer during evolution and that they are among the most constantly evolving genes on the genome. By ortholog analysis, we identified two major gene groups which were either lost or gained during evolution. We analyzed and predicted the function of many of these genes; we found that the genes lost in the descendants provide a molecular foundation of the intracellular habitats, whereas the genes gained during evolution point to mechanisms of pathogenicity.
Conclusion: The genomic features and changes that we identified through comparative genomics provide functional insight into the biology and evolution of HLB-associated bacteria. The newly identified virulence factors will help the current understanding of the pathogenesis mechanisms of the HLB disease.
Coauthors: Yongjun Tan – Saint Louis University; Cindy Wang – Saint Louis University