Phylogenetic analysis identifies a ‘Candidatus Phytoplasma oryzae ’-related strain associated with yellow leaf disease of areca palm (Areca catechu L.) in India

Abstract

Yellow leaf disease (YLD) with phytoplasmal aetiology is a serious disease of arecanut palm in India. The present study was undertaken to characterize the 16S rRNA and secA gene sequences of the Indian arecanut YLD phytoplasma for 'Candidatus Phytoplasma' species assignment and 16Sr group/subgroup classification. Phytoplasma 16S rRNA genes were amplified using three sets of semi-nested/nested primers, 1F7/7R3-1F7/7R2, 4Fwd/3Rev-4Fwd/5Rev and P1/P7-R16F2n/R16R2, producing amplicons of 491, 1150 and 1250 bp, respectively, from diseased samples. The amplicons were cloned and sequenced. A BLAST search showed that the sequences had 99 % similarity with sugar cane white leaf phytoplasma (16SrXI) and Napier grass stunt phytoplasma (16SrXI). Phylogenetic analysis based on the 16S rRNA gene revealed the clustering of YLD phytoplasma with the rice yellow dwarf and Bermuda grass white leaf groups. The YLD phytoplasma F2nR2 sequence shared 97.5 % identity with that of 'Candidatus Phytoplasma oryzae' and 97.8 % identity with that of 'Candidatus Phytoplasma cynodontis'. Hence, for finer differentiation, we examined the secA gene-based phylogeny, where the YLD phytoplasma clustered with Napier grass stunt and sugar cane grassy shoot phytoplasmas, both belonging to the rice yellow dwarf group. Hence, we are assigning the Indian arecanut YLD phytoplasma as a 'Candidatus Phytoplasma oryzae'-related strain. Virtual RFLP analysis of a 1.2 kb fragment of the 16S rRNA gene (F2nR2 region) identified the Indian arecanut YLD phytoplasma as a member of 16SrXI-B subgroup. We name the phytoplasma Indian yellow leaf disease phytoplasma, to differentiate it from the Hainan YLD phytoplasma, which belongs to group 16SrI.

Coconut Lethal Yellowing Diseases: A Phytoplasma Threat to Palms of Global Economic and Social Significance

“…For example, the phytoplasma associated with BCS has a high similarity with phytoplasma isolated from banana (Banana wilt associated phytoplasma, BWAP) and betel nut Areca catechu (L.) (Davis et al, 2012, 2015) and both of these crops are commonly grown with coconut palms. Betel nut is affected by another phytoplasma in India (16SrXI) that also causes LYD in coconuts (Manimekalai et al, 2010; Ramaswamy et al, 2013). …”

Association of ‘CandidatusPhytoplasma cynodontis’ with Bermuda grass white leaf disease and its new hosts in Qassim province, Saudi Arabia

“…BGWL phytoplasma was previously identified as 16SrXIV-A subgroup based on virtual RFLP in India (Khanna et al 2015). Additionally, the virtual RFLP analysis was used successfully to (i) reveal the genetic diversity among other phytoplasmas such as cactus witches' broom phytoplasma strains infecting Opuntia species in China (Cai et al 2008), (ii) grouped potato purple top phytoplasma strains to four different phytoplasma groups (16SrI, 16SrII, 16SrIII and 16SrXIII) in Mexico (Santos-Cervantes et al 2010), (iii) identified the Indian arecanut palm yellow leaf disease phytoplasma as a member of 16SrXI-B subgroup (Ramaswamy et al 2013) and (iv) classified Iranian cucumber phyllody (CuP) and squash phyllody (SqP) phytoplasmas to different phytoplasma subgroups 16SrII-M and 16SrII-D, respectively (Salehi et al 2015).…”

Detection and Molecular Identification of Aster Yellows Phytoplasma in Date Palm in Egypt

“…AY is associated with over 100 economically devastating diseases worldwide and represents the most diverse and widespread phytoplasma group (Lee et al 2004;Ramaswamy et al 2013).…”