CRYPTIC HAPLOTYPES OF “CANDIDATUS LIBERIBACTER AFRICANUS”
W.R. Nelson, S. Eveillard, M.P. Dubrana, J.M. Bové
“Candidatus Liberibacter africanus” (Laf) has long been recognised as a causal agent of the devastating citrus disease huanglongbing (HLB) or citrus greening. This species is currently restricted to Africa, the Arabian Peninsula and some Indian Ocean islands and is vectored by the African citrus psyllid, Trioza erytreae. Blotchy mottle on citrus leaves is characteristic of the disease. Somewhat similar symptoms in the rutaceous tree Calodendrum capensis (Cape chestnut) resulted in the discovery of Laf outside commercial citrus crops in South Africa. This was classed as a subspecies of Laf (capensis, hence LafC). In subsequent surveys of commercial citrus crops and Calodendrum, both natural and ornamental specimens, LafC was not found in citrus, nor has Laf been found in C. capensis. HLB was reported from Madagascar in 1968 but no sequences from this source have so far been published. Until fairly recently, only the reference 16S rRNA gene sequences of Laf (L22533) and LafC (AF137368) had been deposited in GenBank. Both of these reference sequences contain a number of unresolved nucleotides. When these nucleotide positions are invstigated by aligning against more recently available sequences, it becomes evident that these unresolved positions represent one percentage point difference in similarity between Laf and LafC. The originally reported 97.4% similarity is therefore incorrect based on this new information. Recalculating the similarity on the full length 16S rDNA sequence results in 99.54% similarity, a value too high to justify a subspecies status. LafC should therefore be downgraded as a haplotype of Laf. Further, the six 16S rRNA gene sequences currently available in GenBank identified as Laf as a species separate into two haplotype groups. The three haplotypes of Laf are therefore: (i) LafA, designated as the first accession sequenced (L22533); (ii) LafC, i.e the former subspecies “capensis”, to recognise the priority in the use of this term; (iii) LafB, the third previously unrecognised haplotype. Thus the cryptic presence of three haplotypes is revealed by this review of the Laf 16S rDNA sequences.