Multilocus Sequence Analysis Reveals Three Distinct Populations of “ Candidatus Phytoplasma palmicola” with a Specific Geographical Distribution on the African Continent

• Published in: Applied and environmental microbiology Vol. 85; no. 8; pp. e02716 - 18
• Main Authors: Pilet, Fabian, Quaicoe, Robert Nketsia, Osagie, Isaac Jesuorobo, Freire, Marcos, Foissac, Xavier
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 15.04.2019
• Subjects: Africa; Animals; Bacteria; Bacterial Typing Techniques; Candidatus Phytoplasma palmicola; Cultivation; Disease; DNA, Bacterial - genetics; Epidemics; Epidemiology; Fitness; Genes; Genes, Essential; Genetic diversity; Genetic Variation; Geographical distribution; Haplotypes; Host plants; Host range; Host Specificity; Insecta - microbiology; Insects; Lethality; Life Sciences; Microbiology and Parasitology; Multilocus sequence typing; Multilocus Sequence Typing - methods; Mutation; Pests; Phylogeny; Phytopathology and phytopharmacy; Phytoplasma; Phytoplasma - classification; Phytoplasma - genetics; Phytoplasma - isolation & purification; Plant Diseases - microbiology; Plant Microbiology; Populations; Recombination; Reproductive fitness; RNA, Ribosomal, 16S - genetics; Vegetal Biology; Yellowing; Africa; multilocus sequence typing; phytoplasma; coconut lethal yellowing disease; Candidatus Phytoplasma palmicola; maladie du jaunissement mortel de la noix de coco; CLYD
• ISSN: 0099-2240; 1098-5336; 1098-5336
• DOI: 10.1128/AEM.02716-18

Coconut 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. 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 “ Candidatus Phytoplasma palmicola” based on eight housekeeping genes. At the continental level, eight different sequence types were identified among 132 “ Candidatus Phytoplasma palmicola”-infected coconuts collected in Ghana, Nigeria, and Mozambique, where CLYD epidemics are still very active. “ Candidatus Phytoplasma 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 “ Candidatus Phytoplasma 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 “ Candidatus Phytoplasma” is underlined. IMPORTANCE Coconut 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.