Classification of a new phytoplasmas subgroup 16SrII-W associated with Crotalaria witches’ broom diseases in Oman based on multigene sequence analysis

Abstract

Background Crotalaria aegyptiaca, a low shrub is commonly observed in the sandy soils of wadis desert and is found throughout all regions in Oman. A survey for phytoplasma diseases was conducted. During a survey in a wild area in the northern regions of Oman in 2015, typical symptoms of phytoplasma infection were observed on C. aegyptiaca plants. The infected plants showed an excessive proliferation of their shoots and small leaves.ResultsThe presence of phytoplasma in the phloem tissue of symptomatic C. aegyptiaca leaf samples was confirmed by using Transmission Electron Microscopy (TEM). In addition the extracted DNA from symptomatic C. aegyptiaca leaf samples and Orosius sp. leafhoppers were tested by PCR using phytoplasma specific primers for the 16S rDNA, secA, tuf and imp, and SAP11 genes. The PCR amplifications from all samples yielded the expected products, but not from asymptomatic plant samples. Sequence similarity and phylogenetic tree analyses of four genes (16S rDNA, secA, tuf and imp) showed that Crotalaria witches’ broom phytoplasmas from Oman is placed with the clade of Peanut WB (16SrII) close to Fava bean phyllody (16SrII-C), Cotton phyllody and phytoplasmas (16SrII-F), and Candidatus Phytoplasma aurantifolia’ (16SrII-B). However, the Crotalaria’s phytoplasma was in a separate sub-clade from all the other phytoplasmas belonging to Peanut WB group. The combination of specific primers for the SAP11 gene of 16SrII-A, −B, and -D subgroup pytoplasmas were tested against Crotalaria witches’ broom phytoplasmas and no PCR product was amplified, which suggests that the SAP11 of Crotalaria phytoplasma is different from the SAP11 of the other phytoplasmas.ConclusionWe propose to assign the Crotalaria witches’ broom from Oman in a new lineage 16SrII-W subgroup depending on the sequences analysis of 16S rRNA, secA, imp, tuf, and SAP11 genes. To our knowledge, this is the first report of phytoplasmas of the 16SrII group infecting C. aegyptiaca worldwide.Electronic supplementary materialThe online version of this article (10.1186/s12866-017-1130-3) contains supplementary material, which is available to authorized users.

Multilocus sequence analysis of phytoplasma strains of 16SrII group in Iran and their comparison with related strains

“…Among 23 subgroups described within the phytoplasma group 16SrII, the natural occurrence of 21 subgroups (except for subgroups 16SrII‐C and II‐D), is reported from narrow geographical and host ranges (Al‐Subhi et al, ; Yang et al, , ). For example, phytoplasma strains of seven 16SrII subgroups (16SrII‐F to II‐L) have only been recognised in cactus plants in China.…”

“…In this study, we applied MLSA to assess the genetic divergence among the representative phytoplasmas within the group 16SrII reported from Iran and other countries. As the phytoplasma strains of subgroups 16SrII‐F to II‐W were phylogenetically close to phytoplasmas of 16SrII‐A, II‐B, II‐C and II‐D (Al‐Subhi et al, ; Cai et al, ; Yang et al, , ), it is likely that the subgroups 16SrII‐A to 16SrII‐E are the main and core subgroups within the group 16SrII.…”

“…In Iran, for example, phytoplasmas of 16SrII have been characterised in association with diseases in numerous plant species, but despite their importance, they have been poorly characterised at the molecular, biological and ecological levels. By RFLP analysis of 16S rRNA gene sequences, the phytoplasma strains of group 16SrII have been classified into 23 subgroups (Al‐Subhi, Hogenhout, Al‐Yahyai, & Al‐Sadi, ; Yang et al, , ). Until sufficient molecular and ecological evidence is obtained, all phytoplasmas belonging to this group are considered as relatives of “ Ca .…”

Stolbur and Clover Proliferation Phytoplasma Infections in Tomato from Bingöl province, Turkey

“…To date, especially the 16s rRNA gene highly conserved in prokaryotes was used to distinguish the phytoplasma group/subgroup as a conventionally marker gene in numerous research. Besides, immunodominant membrane proteins (imp), elongation factor (tuf), ribosomal protein (rp), chaperonin (cpn60), protein translocase subunit (secY), RNA polymerase βsubunit (rpoB), and secreted aster yellows phytoplasma strain witches' broom (AY-WB) protein 11 (SAP11) genes have been preferred by various researchers as supportive tools for more detailed classification of phytoplasma strains (Davis et al, 2013;Alvarez et al, 2014;Pérez-López et al, 2014;Al-Subhi et al, 2017).…”

Genetic analysis of ‘CandidatusPhytoplasma aurantifolia’ associated with witches’ broom on acid lime trees

“…The 21 strains have already been characterized in our previous study based on the 16S rRNA ( Table 1 ) and were found to belong to the 16S rRNA subgroup II-B ( Al-Ghaithi et al, 2017 ). Therefore, polymerase chain reaction (PCR) were conducted for the imp and SAP11 genes as described by Al-Subhi et al (2017) . Imp-R1, Imp-F1, and Imp-F2 primers were used for the amplification of the imp gene using a two-stage PCR.…”