Isolation and characterization of partial secA gene from coconut root wilt and arecanut yellow leaf disease phytoplasma and assessment of its possible use for sero diagnostics

A 425 bp fragment of phytoplasma sec A gene encoding SecA, a component of the Sec protein translocation system, was isolated and characterized from coconut root wilt disease and arecanut yellow leaf disease phytoplasma, both belonging to the 16SrXI-B sub group phytoplasma. The gene showed 99% nucleotide identity with sugarcane grassy shoot phytoplasma sec A gene. In the phylogenetic analysis of the translated SecA protein sequence, all the 16SrXI group phytoplasmas clustered together.  The three dimensional structure of the protein was predicted using Moddler 9.13. The validation of the predicted structure indicated that 83.6% of the amino acids lie in the favored region indicating that the predicted structure was ideal. The possible antigenic domains in the protein were also predicted using the tool SVM Trip. The antigenicity prediction of the SecA protein fragment showed the presence of 4 possible antigenic domains. The sec A gene was expressed in pET vector and the protein was used for the development of polyclonal antiserum in rabbit. Because the titre of the phytoplasma was very less, the color formation in ELISA was less intense. A technique for isolation of higher number of phytoplasma cells has to be standardized.