Population genetic analysis reveals a low level of genetic diversity of ‘Candidatus Phytoplasma aurantifolia’ causing witches’ broom disease in lime

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Abstract

Witches’ broom disease of lime (WBDL) is a serious phytoplasma disease of acid lime in Oman, the UAE and Iran. Despite efforts to study it, no systemic study attempted to characterize the relationship among the associated phytoplasma, ‘Candidatus Phytoplasma aurantifolia’, from the three countries. This study utilized sequences of the 16S rRNA, imp and secA genes to characterize 57 strains collected from Oman (38), the UAE (9) and Iran (10). Phylogenetic analysis based on the 16S rRNA gene showed that the 57 strains shared 98.5–100 % nucleotide similarity to each other and to strains of ‘Ca. P. aurantifolia’ available in GenBank. The level of genetic diversity was low based on the 16S rRNA (0-0.011), imp (0–0.002) and secA genes (0–0.015). The presence of low level of diversity among phytoplasma strains from Oman, the UAE and Iran can be explained by the movement of infected lime seedlings from one country to another through trading and exchange of infected plants. The study discusses implication of the findings on WBDL spread and management.

Figures

  • Fig. 1 Symptomatic and asymptomatic branches on an acid lime infected by ‘Ca. P. aurantifolia’
  • Table 1 Primers used for amplifying Phytoplasma genes
  • Table 2 Characteristics of samples collected from Oman, UAE and Iran
  • Table 2 continued
  • Table 3 Estimation of evolutionary divergence among phytoplasma sequences
  • Fig. 6 A map showing regions in Oman, the UAE and Iran from which samples were collected (indicated by bold circles)
  • Fig. 5 UPGMA tree showing the analysis of 57 phytoplasma strains from Oman, the UAE and Iran based on the concatenated sequences of 16S rRNA, secA and imp genes. The total length of the concat‑ enated sequences is 2239. GenBank accession numbers for the three genes of the 57 strains are listed in Table 1. The tree was prepared based on the matrix of pairwise distances using the Kimura 2 param‑ eter evolutionary model. Bootstrap values above 50 % are shown (1000 replications). All positions containing gaps and missing data were eliminated. The units indicate the number of base substitutions per site

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APA

Al-Abadi, S. Y., Al-Sadi, A. M., Dickinson, M., Al-Hammadi, M. S., Al-Shariqi, R., Al-Yahyai, R. A., … Bertaccini, A. (2016). Population genetic analysis reveals a low level of genetic diversity of ‘Candidatus Phytoplasma aurantifolia’ causing witches’ broom disease in lime. SpringerPlus, 5(1). https://doi.org/10.1186/s40064-016-3401-0

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