Functional and comparative genomic analysis of integrated prophage-like sequences inCandidatus Liberibacter asiaticus

Abstract

Huanglongbing (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen Candidatus Liberibacter asiaticus (CLas) is an alphaproteobacterium of the Rhizobiaceae family that has been identified as the cause. The virulence of CLas has been attributed, in part, to prophage encoded genes. Prophage and prophage like elements have been identified in 12 of the 15 CLas available genomes, and are classified into three prophage types. Here, we re-examined all 15 CLas genomes using a de novo prediction approach and expanded the number of prophage like elements from 16 to 33. Further, we find that all CLas contain at least one prophage-like sequence. Comparative analysis reveals 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 CLas strain that had previously been reported as lacking prophages. Our findings provide both a resource and new insights into the evolutionary relationship between phage and CLas pathogenicity.

Comparative phylogenomic analysis reveals evolutionary genomic changes and novel toxin families in endophyticLiberibacterpathogens

“…asiaticus Ishi-1, which also induced severe symptoms in citrus, suggests that the prophage might be dispensable for pathogenicity. Further, many different prophage loci are identified in both Liberibacter pathogens and the free-living ancestor 30,37 , making it more difficult to understand their functional contribution. To resolve these puzzles, we conducted a unique, comprehensive operonic association analysis to recover all the prophage loci in the Liberibacter genomes and systematically annotate the conserved phage components.…”

“…This result has clarified several confusions about the presence of the prophage loci in the Liberibacter species. For example, our phylogenetic analysis has linked the recently classified type 4 prophages from the Liberibacter pathogens 37 to the earlier LC2 prophage from the ancestral L. crescens 30 . We also uncovered a previously un-detected prophage type, the UT phage, that is present in all the C.L.…”

“…Genomic organization dissection and classification of Liberibacter prophage loci. Several prophage loci have been previously identified in Liberibacter bacteria 30,36,37 . However, their evolutionary relationships, origins, genomic organizations, and functional compositions remain unclear.…”

“…Finally, to validate and confirm the above results, we conducted extensive phylogenetic analyses on all identified orthogroups. From these analyses, we identified 323 orthogroups (about 335 genes in L. crescens BT-1) that were lost in all pathogenic descendants and 35 orthogroups (about [35][36][37] genes in each pathogen) that were gained in the ancestor of all pathogens (Fig. 5a and Supplementary Table 3 and Table 4).…”

Prophage region and short tandem repeats of “Candidatus Liberibacter asiaticus” reveal significant population structure in China

“…Moreover, the high ratio of strains with a single prophage in the Chinese Las populations (938 of 1,215 strains) is consistent with the findings of Zheng et al (2016). It is possible that another new prophage could be present in the nine strains without any of the three types of known prophages (Dominguez‐Mirazo et al, 2019).…”