New phytoplasma subgroup identified from Arecaceae palm species in Grand-Lahou, Côte d’Ivoire

Abstract

Coconut palms in the south coastal littoral of Grand-Lahou have long been affected by the Côte d’Ivoire lethal yellowing (CILY), associated with subgroup 16SrXXII-B ‘Candidatus Phytoplasma palmicola’-related strains. Recently, foliar discolouration and yellowing symptoms were observed in oil palms (Elaeis guineensis), Rônier palms (Borasus aethiopium), and raffia palms (Raphia vinifera) located in the vicinity of coconut palms (Cocos nucifera) showing CILY-like symptoms in coconut-growing villages of Grand-Lahou. Immature leaf samples were randomly collected from symptom-bearing palms, including coconut palms. Total DNA was extracted and used as a template for a nested PCR assay with universal primers that target the phytoplasma 16S rRNA gene, and the translocation protein (secA) genes. The R16F2n/R2 and SecA amplicons from representative samples of each palm species were purified, cloned, and sequenced. R16F2n/R2 sequences were over 99% identical to phytoplasmas enclosed in group 16SrXXII. Based on iPhyclassifier analyses with 17 restriction enzymes, the phytoplasmas found in C. nucifera, E. guineensis, B. aethiopium and R. vinifera were identical to each other. However, a unique Sau3AI RFLP pattern was observed, and similarity coefficients were lower than 0.97, and so a new 16SrXXII subgroup, 16SrXXII-C, was assigned. Phylogeny based on both R16F2n/R2 and SecA sequences supported this RFLP classification. The presence of the subgroup 16SrXXII-C in the same area where coconut palms are severely infected by the subgroup 16rSXXII-B could lead to different epidemiological constraints that may affect the severity of the coconut disease. Thus, the 16SrXXII-C phytoplasma poses a new threat for other Arecaceae species, which may impact CILY management and control in Grand-Lahou.