A Comprehensive Study on the 16S rRNA Gene of Major Phytoplasma Diseases in Sri Lanka with their Close Relatives

Phytoplasmas are plant pathogenic mollicutes that have a significant impact on the sugarcane and coconut plantations in Sri Lanka. Sugarcane and coconut have been reported as hosts for many phytoplasmas in Asia and Africa that show almost similar symptoms. A comprehensive study on the phytoplasma disease reported in Sri Lanka will be useful for prospective disease management practices. Therefore, this study aimed to analyze the 16S rRNA gene identity of phytoplasmas associated with major diseases in Sri Lanka and compare them with their close relatives worldwide to assess their genetic relationships. Seventeen phytoplasma isolates 16S rRNA gene sequences ranging from 773 bp to 1768 bp including eight SCWL and SCGS, three WCLW and four other different coconut phytoplasma, and two different grass phytoplasma sequences were retrieved from NCBI-GenBank. The ‘Candidadtus’ phytoplasma species assignment and phytoplasma groups and subgroups were determined by the iPhyClassifier tool. The sequence identity was studied by the Clustal Omega tool and phylogenetic analysis was done with the Maximum Likelihood method. All the SCWL, SCGS, CKW, and CYD belonged to ‘Ca. P. cynodontis' species. The WCLW isolates and SCWL Sri Lankan isolates showed a very close sequence identity, ranging from 98.84% to 99.89%, and clustered within the same monophyletic group in the phylogenetic tree. The two grass phytoplasma isolates found in Sri Lanka showed sequence identities ranging from 96.06% to 98.32% with WCLW phytoplasmas, which is lower than their identity with SCWL phytoplasmas. The WCLW phytoplasma also showed a close genetic and phylogenetic relationship with CKW and CYD diseases reported in neighboring countries. The two coconut phytoplasma diseases reported in African countries were more distantly related to all other phytoplasmas isolates and many INDELS were observed in the 16S rRNA gene.