Sequence Analysis of 16S rRNA and secA Genes Confirms the Association of 16SrI‐B Subgroup Phytoplasma with Oil Palm (Elaeis guineensis Jacq.) Stunting Disease in India

Abstract

During January 2010, severe stunting symptoms were observed in clonally propagated oil palm (Elaeis guineensis Jacq.) in West Godavari district, Andhra Pradesh, India. Leaf samples of symptomatic oil palms were collected, and the presence of phytoplasma was confirmed by nested polymerase chain reaction (PCR) using universal phytoplasma-specific primer pairs P1 ⁄ P7 followed by R16F2n ⁄ R16R2 for amplification of the 16S rRNA gene and semi-nested PCR using universal phytoplasma-specific primer pairs SecAfor1 ⁄ SecArev3 followed by SecAfor2 ⁄ SecArev3 for amplification of a part of the secA gene. Sequencing and BLAST analysis of the 1.25 kb and 480 bp of 16S rDNA and secA gene fragments indicated that the phytoplasma associated with oil palm stunting (OPS) disease was identical to 16SrI aster yellows group phytoplasma. Further characterization of the phytoplasma by in silico restriction enzyme digestion of 16S rDNA and virtual gel plotting of sequenced 16S rDNA of 1.25 kb using iPhyClassifier online tool indicated that OPS phytoplasma is a member of 16SrI-B subgroup and is a ÔCandidatus Phytoplasma asterisÕ-related strain. Phylogenetic analysis of 16S rDNA and secA of OPS phytoplasma also grouped it with 16SrI-B. This is the first report of association of phytoplasma of the 16SrI-B subgroup phytoplasma with oil palm in the world.

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

“… Similar tables can be found in earlier references including Bertaccini et al (2014) and Mehdi et al (2012). The classifications frequently change as new groups and subgroups are found and classified (Harrison et al, 2014) .…”

“…The classifications frequently change as new groups and subgroups are found and classified (Harrison et al, 2014) .a Excludes 16Sr Group I and XI phytoplasmas which are associated with diseases affecting date palms (P. dactylifera) (Mehdi et al, 2012; Gurr et al, 2015) .b Until the end of the 1990s, phytoplasmas associated with “maladie de Kaincopé” in Togo, “Awka wilt” in Nigeria and CSPWD in Ghana were thought to fall within the 16SrIV group (Tymon et al, 1998). Recently, they were included in a new group, 16SrXXII (Wei et al, 2007), incidentally cited as “Ca.…”

“…a Excludes 16Sr Group I and XI phytoplasmas which are associated with diseases affecting date palms (P. dactylifera) (Mehdi et al, 2012; Gurr et al, 2015) .…”

Effect of farming practices and farm history on incidence of coconut lethal yellowing in Mozambique

“…LY disease of palms, are also referred to as "lethal decline", "root wilt" and white tip die-back (Mehdi et al, 2012). Oropeza et al (2011) investigated the phytoplasmas distribution in different coconut parts and found a very high level of LY phytoplasmas DNA in stem, young leaves, inflorescences, stem apex and root apex.…”

African fan palm (Borassus aethiopum) and oil palm (Elaeis guineensis) are alternate hosts of coconut lethal yellowing phytoplasma in Mozambique

“…E. guineensis has previously been reported as susceptible to oil palm stunting disease in India, caused by "Ca. P. asteris"-related strain (Mehdi et al, 2012) and to Malaysian coconut yellow decline in Malaysia (Nejat et al, 2009 (Myrie et al, 2014;Harrison and Oropeza, 2008). Based on PCR, RFLP and sequence analysis, a low detection rate was also reported by Brown et al (2008) when searching for potential alternate hosts of coconut LY phytoplasma among weeds in Jamaica.…”