Comparison of 16S rDNA sequence among the phytoplasmas associated with wilt disease of coconut from different locations

Abstract

In India, the wilt disease is a major threat to coconut plantations. The diagnost ic symptoms of disease are wilting of leaflets, yellowing and marginal necrosis of the older leaves. The phytoplasma associated with the disease was identified through molecular techniques that revealed that it belongs to 16SrXI -B group. In the present study phytoplasma DNA was extracted from coconut in three locations of South India to verify the presence of molecular variability in the 16S rDNA region. Diseased samples were collected, the DNA was amplified using custom designed semi-nested primers and the PCR products were cloned and sequenced. All sequences were trimmed and aligned and the sequence variation was analyzed by calculating the nucleotide diversity (Pi) using DnaSP V5 software. Based on Pi values, the nucleotide diversity was higher between the phytoplasmas from Kasaragod and Kayamkulam (0.0102) than between the phytoplasmas from Kayamkulam and Theni (0.0083). The average number of nucleotide difference was five out of 491 nucleot ides. Based on nucleotide identity, Kayamkulam phytoplasma shared 99% identity with Theni phytoplasma. The Kasaragod and Theni phytoplasmas shared 98% nucleot ideidentity. Moreover a Weligama leaf wilt phytoplasma from SriLanka resulted to be undistinguishable from the strain detected in Theni region (100% nucleotide identity). The 16S rDNA nucleotide variability of phytoplasmas between palms was 1.21% and within palms was 1.36%.