First report of a ‘Candidatus Phytoplasma australasia’ strain in witches’ broom diseased Crotalaria retusa in India

Abstract

Crotalaria retusa, commonly known as rattle weed in India, it is commonly used as a source of various organic residues for soil nutrition enrichment and nitrogen fixation under various agro ecosystems. During May 2020, C. retusa plants exhibiting symptoms related to phytoplasma presence was observed at the College of Horticulture in Bengaluru, Karnataka, India. The plants showed shoot proliferation, reduced leaf size and stunted growth leading witches’ broom symptoms with incidence of 2 to 5%. Phytoplasma presence in symptomatic C. retusa plants was confirmed by polymerase chain reaction assays on 16Sr RNA and secY genes with specific primers. Amplified products were eluted, cloned and sequenced. The 16S rRNA sequence analysis showed that the detected phytoplasma shared 99.61% to 100% nucleotide identity on 16S rDNA with a number of ‘Candidatus Phytoplasma australasia’ strains reported from different countries across the world, and from 99.41 to 99.77% identity on the secY gene to phytoplasma strains infecting mainly horticultural crops. This result is well supported by the clustering of C. retusa phytoplasma with ‘Ca. P. australasia’ in the phylogenetic analysis on both genes. Further, the virtual RFLP pattern showed a similarity coefficient of 1.0 with ‘Ca. P. australasia’, enclosed in the 16SrII-D subgroup. This is first report of 16SrII-D phytoplasmas in C. retusa showing witches’ broom symptoms in India.