To sustain epidemiological studies on coconut lethal yellowing disease (CLYD), a devastating disease in Africa caused by a phytoplasma, we developed a multilocus sequence typing (MLST) scheme for “CandidatusPhytoplasma palmicola” based on eight housekeeping genes. At the continental level, eight different sequence types were identified among 132 “CandidatusPhytoplasma palmicola”-infected coconuts collected in Ghana, Nigeria, and Mozambique, where CLYD epidemics are still very active. “CandidatusPhytoplasma palmicola” appeared to be a bacterium that is subject to strong bottlenecks, reducing the fixation of positively selected beneficial mutations into the bacterial population. This phenomenon, as well as a limited plant host range, might explain the observed country-specific distribution of the eight haplotypes. As an alternative means to increase fitness, bacteria can also undergo genetic exchange; however, no evidence for such recombination events was found for “CandidatusPhytoplasma palmicola.” The implications for CLYD epidemiology and prophylactic control are discussed. The usefulness of seven housekeeping genes to investigate the genetic diversity in the genus “CandidatusPhytoplasma” is underlined.IMPORTANCECoconut is an important crop for both industry and small stakeholders in many intertropical countries. Phytoplasma-associated lethal yellowing-like diseases have become one of the major pests that limit coconut cultivation as they have emerged in different parts of the world. We developed a multilocus sequence typing scheme (MLST) for tracking epidemics of “Ca. Phytoplasma palmicola,” which is responsible for coconut lethal yellowing disease (CLYD) on the African continent. MLST analysis applied to diseased coconut samples collected in western and eastern African countries also showed the existence of three distinct populations of “Ca. Phytoplasma palmicola” with low intrapopulation diversity. The reasons for the observed strong geographic patterns remain to be established but could result from the lethality of CLYD and the dominance of short-distance insect-mediated transmission.

This study was conducted to characterize phytoplasmas from coconut palms showing symptoms of Awka wilt disease in south and south-east Nigeria and determine if there is geographic differentiation among the phytoplasma strains. Stem samples were collected from symptomatic coconut palms in three region of Nigeria. For each sample, DNA was extracted and the 16S rDNA was amplified by PCR by using the P1/P7 primers. Amplicons were sequenced for five Nigerian strains. The sequences were compared with each other, with LDN (lethal decline Nigeria) sequence published 20 years ago, and with sequences from Ghana. A homology of 100% was observed among the 16S rDNA sequence published and the sequences of the five strains under investigation. Based on the known conservation of 16S rDNA sequences, this result suggests a relative stability of the lethal yellowing disease phytoplasma strains in the southern regions of Nigeria, and no introduction of the “Ghanaian strain”. (Résumé d'auteur

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