Detection, Identification, and Molecular Characterization of the 16SrII-D Phytoplasmas Infecting Vegetable and Field Crops in Oman

Abstract

Typical symptoms of phytoplasma infection were observed on 11 important crops in Oman that included alfalfa, sesame, chickpea, eggplant, tomato, spinach, rocket, carrot, squash, field pea, and faba bean. To identify the phytoplasmas in these crops, samples from infected and asymptomatic plants were collected, followed by amplifying and sequencing of the 16S ribosomal RNA, secA, tuf, imp, and SAP11 genes. We found that these sequences share >99% similarity with the peanut witches’ broom subgroup (16SrII-D). Whereas some sequence variation was found in the five genes among 11 phytoplasma isolates of different crops, all sequences grouped into one clade along with those of other phytoplasmas belonging to the 16SrII-D group. Thus, 16SrII-D phytoplasmas infect a diverse range of crops in Oman. Phytoplasmas in this group have not been reported to occur in carrot, spinach, rocket, and field pea previously. Within Oman, this is the first report of the presence of 16SrII-D phytoplasmas in tomato, spinach, rocket, carrot, squash, field pea, and faba bean. Sequences of the five genes enabled for better distinction of the 16SrII-D phytoplasmas that occur in Oman.

Global Status of Phytoplasma Diseases in Vegetable Crops

“…The brinjal little leaf disease was first described by Thomas and Krishnaswami (1939) in India with 100% yield loss in epidemics (Rao and Kumar, 2017). Also for this disease, five ribosomal groups were reported: 16SrI (Japan, Bangladesh, and India), 16SrII (Oman and India), 16SrVI (Turkey and India), 16SrIX (Iran) and 16SrXII (Russia and Turkey) (Okuda et al, 1997; Sertkaya et al, 2007; Kelly et al, 2009; Al-Subhi et al, 2011, 2018; Ember et al, 2011; Tohidi et al, 2015; Usta et al, 2015). Similarly phytoplasma infections in chili associated with little leaf, witches’ broom and “brote grande” were reported associated with 16SrVI (India and America) and 16SrII (Egypt) (El-Banna et al, 2007; Randall et al, 2010; Rao et al, 2017a).…”

Multilocus gene analysis reveals the presence of two phytoplasma groups in Impatiens balsamina showing flat stem and phyllody

“…Because the DNA-based classifications using 16S rRNA gene alone may be insufficient for finer differentiation of phytoplasma strains. Detection on primes amplifying nonribosomal regions, i.e., rp , secY , and tuf genes were also used to confirm and validate phytoplasma presence (Schneider et al 1997 ; Lee et al 2004 , 2006 , 2010 ; Martini et al 2004 ; Al-Subhi et al 2018 ). Moreover, universal phytoplasma specific primers for secA gene were also used (Hodgetts et al 2008 ; Bekele et al 2011 ).…”

Molecular detection and characterization of a 16SrII-D phytoplasma associated with streak yellows of date palm in Oman

“…amplify the 16S rRNA region (Deng and Hiruki 1991;Gundersen and Lee 1996). In addition, distilled water (DW) and DNA from symptomless trees were used as negative control, while alfalfa and lime witches' broom phytoplasmas were used as positive control (Al-Subhi et al 2018).…”

“…The TUF-II-F1 and TUF-II-R1 were utilized to prime the elongation factor TU targeting 1490 bp, followed by using the seminested PCR primers TUF-II-F2 and TUF-II-R1, which target 1094 bp of the tuf gene. The imp gene was amplified by using IMP-II-F1 and IMP-II-R1 primer pairs (targeting (786 bp) in the direct PCR followed by IMP-II-F1/IMP-II-R1 (targeting 717 bp) in the semi-nested PCR assay (Al-Subhi et al 2018). A partial of translocase protein A gene was amplified in semidirect PCR assays by using SecA-II-F1/SecA-II-R1 in the first reaction followed SecA-II-F1/SecAII-R4 in the second reaction.…”

“…A partial of translocase protein A gene was amplified in semidirect PCR assays by using SecA-II-F1/SecA-II-R1 in the first reaction followed SecA-II-F1/SecAII-R4 in the second reaction. The PCR reaction mix and conditions of the 16S rRNA, tuf, imp and secA were as described by Al-Subhi et al (2018).…”