The Complete Genome Sequence of ‘Candidatus Liberibacter solanacearum’, the Bacterium Associated with Potato Zebra Chip Disease

Abstract

Zebra Chip (ZC) is an emerging plant disease that causes aboveground decline of potato shoots and generally results in unusable tubers. This disease has led to multi-million dollar losses for growers in the central and western United States over the past decade and impacts the livelihood of potato farmers in Mexico and New Zealand. ZC is associated with ‘Candidatus Liberibacter solanacearum’, a fastidious alpha-proteobacterium that is transmitted by a phloem-feeding psyllid vector, Bactericera cockerelli Sulc. Research on this disease has been hampered by a lack of robust culture methods and paucity of genome sequence information for ‘Ca. L. solanacearum’. Here we present the sequence of the 1.26 Mbp metagenome of ‘Ca. L. solanacearum’, based on DNA isolated from potato psyllids. The coding inventory of the ‘Ca. L. solanacearum’ genome was analyzed and compared to related Rhizobiaceae to better understand ‘Ca. L. solanacearum’ physiology and identify potential targets to develop improved treatment strategies. This analysis revealed a number of unique transporters and pathways, all potentially contributing to ZC pathogenesis. Some of these factors may have been acquired through horizontal gene transfer. Taxonomically, ‘Ca. L. solanacearum’ is related to ‘Ca. L. asiaticus’, a suspected causative agent of citrus huanglongbing, yet many genome rearrangements and several gene gains/losses are evident when comparing these two Liberibacter. species. Relative to ‘Ca. L. asiaticus’, ‘Ca. L. solanacearum’ probably has reduced capacity for nucleic acid modification, increased amino acid and vitamin biosynthesis functionalities, and gained a high-affinity iron transport system characteristic of several pathogenic microbes.

Concomitant Loss of the Glyoxalase System and Glycolysis Makes the Uncultured Pathogen “Candidatus Liberibacter asiaticus” an Energy Scavenger

“…The most economically important of the latter is "Ca. Liberibacter solanacearum," which causes economically serious diseases of solanaceous crops, for example, the "zebra chip" disease of potato (5). Attempts to culture any of the pathogenic liberibacters in axenic media have remained unsuccessful except transiently (6,7).…”

“Candidatus Liberibacter asiaticus” Prophage Late Genes May Limit Host Range and Culturability

“…Liberibacter asiaticus," "Candidatus Liberibacter americanus," and "Candidatus Liberibacter solanacearum") each contain two prophages that appear to have the full suite of genes necessary for functionality (8,23,24). Not all prophages are entirely latent during lysogeny; some prophage genes can increase the fitness and/or the virulence of the bacterial host cell but have no general role in the phage life cycle (25).…”

Bacterial Citrus Diseases: Major Threats and Recent Progress

“…Genome sequencing of several strains of CaL revealed a strong genome-size reduction, most likely reflecting their intimate biotrophic association with the host plant [54][55][56][57]. Recently, the bacterial isolate BT-1 was recovered in pure culture from the phloem sap of defoliating mountain papaya (Carica stipulata × C. pubescens) in Puerto Rico and shown to be closely related to CaLam and CaLas based on similarity of 16S rDNA and conserved protein sequences as well as on genome-wide ANI analysis [58,59].…”

“…[54][55][56][57][58][59], Lcr has become an important model to investigate biological aspects that could be relevant to grow in vitro and to control CaL species. Fagen et al [57] used RAST [60], KEGG [61] and manual annotation to compare the genome sequence of Lcr BT-1 with those of CaLas psy62 and 'Ca.…”