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

Abstract

Phytoplasmas of the group 16SrII (peanut witches'-broom group) are among the most important phytoplasmas identified in Iran. These phytoplasmas are so diverse that they have been classified within 23 subgroups, among which phytoplasmas of subgroups 16SrII-B, -C and -D have been recognised in Iran. In this study, we used multilocus sequence analysis as a tool to find the extent of genetic diversity and phylogeny of representative phytoplasmas of 16SrII in Iran in comparison to reference phytoplasma strains characterised elsewhere. The genes used were 16S rRNA, secY, rplV-rpsC, imp and a hypothetical protein (inmp). Analysis of this study showed that phytoplasmas of 16SrII could be resolved into at least three main phylogenetic lineages. One lineage comprised phytoplasmas of the subgroups 16SrII-A and II-D, another included strains of subgroups 16SrII-B and II-C and the third lineage comprised phytoplasmas belonging to 16SrII-E. The significance of host adaptation and geographical distribution in relation to the genetic diversity of these phytoplasmas is discussed. Among five different genetic loci used in this study, imp gene displayed the highest genetic diversity, hence considered as the most powerful genetic tool for differentiation of closely related phytoplasmas. K E Y W O R D S16SrII, classification, multilocus analysis, phylogenetic analysis, Phytoplasma

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

“…The results further confirmed the validity and utility of these four genes as additional molecular markers for characterization of phytoplasma strains belonging to 16SrI-B and 16SrII-D subgroups. Multilocus genes have been successfully used earlier for finer differentiation of closely related subgroup phytoplasmas strains (Martini et al 2007 ; Bohunická et al 2018 ; Siampour et al 2019 ). However, in the present study, all the four genes used provided similar results of grouping and subgrouping classification of rose balsam phytoplasma strains indicating that the rose balsam phytoplasma strains identified from two states of India do not have significant genetic diversity among themselves.…”

Multilocus sequence typing and phylogenetic analysis revealed two distinct almond witches'‐broom phytoplasma subpopulations in Iran

“…Findings of this study confirmed the suitability of imp gene in fine differentiation of closely related phytoplasmas within the group 16SrIX. Similarly, imp gene has been used in several studies as a genetic marker for differentiation of closely related phytoplasmas (Bohunická et al, 2018; Siampour, Izadpanah, Martini, & Salehi, 2019). The topology of the imp ‐based phylogenetic tree was comparable to that depicted based on conserved rp gene.…”

“…Total DNA extracted from two periwinkle plants infected by cucumber phyllody phytoplasma (CuPh, 16SrII‐D; GenBank accession no. KY412986) were also utilised as positive controls in PCR assays (Siampour, Izadpanah, Martini, & Salehi, 2019).…”

“…However, the resolving power of 16S rRNA gene is insufficient for differentiation of biologically or ecologically distinct phytoplasma strains. This was implemented with the use of less conserved markers such as ribosomal protein (rp) or secY genes for differentiation of closely related phytoplasmas (Lee et al, 2010; Martini et al, 2007; Siampour, Izadpanah, Martini, & Salehi, 2019).…”

Pest categorisation of the non‐EU phytoplasmas of tuber‐forming Solanum spp.

“…P. aurantifolia' or 'Ca. P. australasiae' (Siampour et al, 2019), although the latter species has not been further supported (IRPCM, 2004). Phytoplasma infecting S. tuberosum are categorised here, and they include 'GD32 (Cheng et al, 2019), St_JO_10, 14, 17 (Salem et al, 2019), PPT-SA (Omar et al, 2018), Rus-343F (Girsova et al, 2016), PPT-GTO29, PPT-GTO30, PPT-SINTV (Santos-Cervantes et al, 2010), Potato Huayao Survey 2 (Hodgetts et al, 2009), Potato hair sprouts, PHS (Leyva-Lopez et al, 2002).…”