Findings from this study showed that LYD is present in all the six villages of the department of Grand-Lahou that were surveyed in the southern Côte d’Ivoire

Findings from this study showed that LYD is present in all the six villages of the department of Grand-Lahou that were surveyed in the southern Côte d’Ivoire. These strains are the most commun strain circulating in the department of Grand-Lahou and were previously confirmed over 80 % of the CILY-affected coconut palms in that region (Arocha-Rosete et al. 2014). Their sequences shared more than 97.5% (99 – 100%) identity with reference strains of all previously described species of ‘Candidatus Phytoplasma’ in West Africa (IRPCM 2004); namely with that of Awka wilt phytoplasma strain LDN from Nigeria (GenBank accession no. Y14175), CSPW strain from Ghana. Indeed, Harrison et al. (2014) assigned LDG, CSPWB, CILY and additional Côte d’Ivoire strains to subgroup 16SrXXII-B as ‘Candidatus Phytoplasma palmicola’-related strains. Our study provided evidence that the Mozambique phytoplasma is closely related to the West African LYD as previously reported (Bila et al. 2015). Our data is supported by the criteria Guidelines for the recognition of a novel candidate species of ‘Candidatus Phytoplasma’ (IRPCM 2004). This guideline stated that a strain can be described as a novel candidate species of ‘Candidatus Phytoplasma’ if its 16S rRNA gene sequence has 97.5% similarity to that of any previously described candidate species of ‘Candidatus Phytoplasma’ (IRPCM 2004).
Analysis of genetic diversity within populations of CILY isolated in different villages of the department of Grand-Lahou showed that these populations have low levels of genetic diversity (0.0041-0.0062). The low levels of diversity observed among these strains could be related to their common source and is a support for a similar geographical source for infestations in coastal Côte d’Ivoire. It is possible that a single cultivar was introduced and cultivated in Côte d’Ivoire in the past. Since the country hosts one of the five multi-site International Coconut Genebanks for Africa and the Indian Ocean, LYD disease spreading from neighboring Ghana was reported as a current threat (ProMED 2013). The neighboring west African countries origin of the phytoplasma collected in the department of Grand-Lahou is supported by the Maximum likelihood analysis which clustered them with the strains of Awka wilt phytoplasma strain LDN from Nigeria (GenBank accession no. Y14175), Awka wilt phytoplasma strain from Ghana. This is an additional support of the hypothesis that LYD in the Department of Grand-Lahou has been introduced from countries in West Africa.
Genetically depauperate populations that we isolated in the department of Grand-Lahou could have a particularly low adaptive potential and could then be vulnerable to the effects of environmental pressure. This suggests that these strains are unlikely to rapidly evolve resistance against effective control mechanisms, including biological control. Although the overall intrapopulation nucleotide diversity is low, we found a relatively higher diversity in Likpilassé (0.0064) compared to the other sites. This is particularly reflected in the field by a faster evolution of the plague in Likpilassé compared to the other sites. This indicates that exceptional disease control mechanisms have to be initiated in that locality to avoid the rapid spread of the disease in the department of Grand-Lahou and in Côte d’Ivoire. The three haplotypes found in Likpilassé are shared with the other localities. Hence, the particular virulence of the disease in that site could not be attributed to the effect of haplotype and supports the hypothesis that other factors such as farming practices could have an impact on CLYD incidence in Likpilassé. A particular approach that needs to be initiated in Likpilassé and the other localities in the study area are habitat management that could remove the incidence of pests. Indeed, Plant species found within surrounding crop fields have been shown to play a role in spreading phytoplasma diseases, as they may act as alternative reservoirs for the phytoplasmas (Weintraub and Beanland 2006) or their insect vectors (Mori et al. 2015).
Our data indicate that the strains found in that region comprise a single demographic unit. The network and AMOVA analyses showed no geographic structure between or within the six sites. Low levels of pairwise FST values found among these sites indicate a genetic homogeneity over the surveyed sites. A lack of genetic structure can result from many factors including high levels of gene flow, large effective population size and/or the presence of shared ancestral polymorphisms due to recent population divergence (Cano et al. 2008). Throughout the Department of Grand-Lahou, Phytoplasma populations appear to be highly inbred and genetically similar and depauperated.
Our data indicated that distinct haplotypes are found in different plant tissues of coconut, suggesting a multiple sources of infection. Indeed, multiple infections can occur and the ratio of the infection can determine the severity of the symptoms (Seemuller et al. 2011). Insects belonging to the order Hemiptera share several characteristics that make its members efficient vectors of phytoplasmas (Weintraub and Beanland 2006). Different insect vectors might be involved in the dispersal of phytoplasmas in the department of Grand-Lahou. There is weak probability of the dispersal by exchanging plant material since these exchanges are mainly of coconut seed and there is no evidence of the transmission of the disease from the coconut seed to the seedling (Myrie et al. 2011; Nan et al. 2014).