Genomic Dissection of Metabolism, Prophage Elements, and Ecological Adaptations in Candidatus Liberibacter asiaticus

Candidatus Liberibacter asiaticus (CLas) is a host-dependent obligate parasite that causes citrus greening disease in citrus spp . The effective measures to control the bacteria are hindered due to the lack of an established culturing method for the characterization of CLas. Liberibacter crescens (Lcr) is the only culturable model organism to study possible strategies to culture Candidatus Liberibacter species. The in-silico characterization of CLas was conducted through functional and comparative annotation of sequence data using sequence similarity search, metabolic pathway analysis, and prophage detection tools. The comparative genome analysis of CLas strain gxpsy and Lcr strain BT-1 showed a significant genome size reduction in the CLas genome and compensating for the lost essential genes with the help of transport proteins. The study focuses on the missing genes and the unique genes in CLas, decoding the genomic and metabolic complexities. The study revealed the alternative pentose phosphate pathway utilized by the bacteria with the help of pyrophosphate fructose 6-phosphate 1-phosphotransferase (PPi-PFK) to bypass the loss of the transaldolase gene and to complete the glycolytic pathway. Also, the prophage genes are detected in the genome of CLas strains, possibly contributing to the genetic drift. This is the first report on the in-silico characterization of CLas exploring the survival strategies adopted by CLas in the metabolism to adapt to the host ecological conditions.