Molecular characterization and phylogeny of phytoplasma associated with bunchy top disease in its new host Okra (<Emphasis Type="Italic">Abelmoschus esculentus</Emphasis>) in India reveal a novel lineage within the 16SrI group

Okra plants with bunchy top disease were found to be prevalent during the period of August–October 2009 in New Delhi, India. The common symptoms observed were shortening of internodes, aggregation of leaves at the apical region, reduced leaf lamina, stem reddening, fruit bending, phyllody and stunting of plants. The disease incidence ranged from 2–60% accompanied by significant reductions in production of both flowers and seeds. Nested polymerase chain reaction targeting phytoplasma specific 16S rDNA and rp genes revealed all symptomatic plants to be positive for phytoplasma. Homology searches depicted its closest identity to phytoplasmas of 16SrI ‘Candidatus Phytoplasma asteris’, like the Sugarcane yellows and Periwinkle phyllody phytoplasmas. Profiles for 16S rDNA obtained with 10 restriction endonucleases, differed in TaqI sites for two phytoplasma isolates (BHND5 & 10) from the standard pattern of 16SrI-B subgroup, the latter was seen in the case of isolate BHND1. Restriction fragment analysis of rp genes with AluI, Tsp509I matched with patterns of the rpI-B phytoplasmas. Phylogenetic reconstruction of rp genes revealed okra bunchy top phytoplasma (BHND1) as a divergent isolate, the subsequent sequence analysis of which showed the presence of a novel BslI site. These significant differences suggest that multiple phytoplasma strains are affecting okra, one of which is a diverging lineage within the 16SrI-B group while others represent a new 16SrI subgroup not reported so far. Additionally, this is the first report of a phytoplasma associated disease in okra plants worldwide.     

Latent infection of asymptomatic Hawaiian sugarcane cultivars with 16SrI and 16SrXI phytoplasmas

Leaves from sugarcane were collected at the Hawaiian sugarcane breeding station and from recent and previous Hawaiian plantation fields and tested for phytoplasma by nested PCR, quantitative PCR and partly by the 16S/23S internal spacer sequence. Phytoplasmas were found in samples of 10 of the 11 tested cultivars from the station and identified as strains 16SrI phytoplasma (aster yellows phytoplasma) and 16SrXI phytoplasma (rice yellow dwarf phytoplasma). Hot water treatment could partially eliminate the phytoplasmas, but sugarcane plants in the Hawaiian plantations, which routinely use hot-water-treated seed cane cuttings, were nevertheless infected by 16SrXI phytoplasma. Samples from abandoned sugarcane plantations contained 16SrI phytoplasma or 16SrXI phytoplasma. The titre of phytoplasma was very low in all cases, i.e., at or below the detection threshold of quantitative PCR, and no difference in phytoplasma infection was observed between healthy-looking, green plants and plants that had YLS symptoms. Apparently the Hawaiian sugarcane cultivars have some kind of phytoplasma resistance under the growth conditions in Hawaii. The latent presence of phytoplasma strains calls for awareness and rigorous treatment of sugarcane setts even in cases, where YLS was so far exclusively related to the presence of Sugarcane yellow leaf virus.     

Note: Molecular identification of ‘Candidatus phytoplasma asteris’ inducing histological anomalies inSilene nicaeensis

Numerous plants ofSilene nicaeensis having symptoms resembling those associated with the presence of phytoplasmas were observed in an extensive coastal area in the south of Italy. Microscopic observation showed histological abnormalities in the organization of tissues in symptomatic plants, and molecular tests, including PCR/RFLP analyses and nucleic acid sequencing, revealed the presence of phytoplasmas belonging to the aster yellows group (‘Candidatus phytoplasma asteris’). This is the first report of phytoplasma infection inS. nicaeensis, a wild species that colonizes the Calabrian coast. http://www.phytoparasitica.org posting June 12, 2008     

Detection of ‘<Emphasis Type="Italic">Candidatus</Emphasis> Phytoplasma brasiliense’ in a new geographic region and existence of two genetically distinct populations’

‘Candidatus Phytoplasma brasiliense’, a phytoplasma taxon associated with hibiscus witches’ broom disease was first described in 2001 in Brazil. In September 2007, a peach tree (Prunus persica) displaying yellowing symptoms reminiscent of phytoplasma infection was sampled in Guba region of Azerbaijan. A phytoplasma was detected in the diseased peach tree by nested PCR amplification of its 16S rDNA with universal primers for phytoplasmas. Phylogenetical analyses of the amplified 16S rDNA showed that the phytoplasma infecting the peach tree corresponded to ‘Ca. P. brasiliense’, a species never reported in Euro-Mediterranean area. To set up a detection assay, cloning of a ‘Ca. P. brasiliense’ DNA fragment was undertaken by comparative RAPD. The amplified dnaK-dnaJ genetic locus was used to design a nested PCR assay able to amplify all ‘Ca. P. brasiliense’ isolates of the subgroup 16SrXV-A without amplifying the related members of the group 16SrII. This assay also allowed confirming the first detection of ‘Ca. P. brasiliense’ in diseased basil collected in south Lebanon.     

First report of <Emphasis Type="Italic">Candidatus</Emphasis> Phytoplasma prunorum infecting almonds in Tunisia

Candidatus Phytoplasma prunorum was detected for the first time in almond (Prunus dulcis Mill.) cv. ‘Abiod’ in Tunisia. Infected trees showed emergence of new growth during dormancy and leafed out before flowers opened in addition to early defoliation in summer. Phytoplasma was detected by nested polymerase chain reaction (PCR) using universal phytoplasma primer pairs P1/P7 and F2n/R2. A band with expected size was observed in samples collected from five symptomatic, but not symptomless almond trees. PCR products (1.2 kbp) were used for restriction fragment length polymorphism (RFLP) analysis after digestion with endonucleases RsaI and SspI. RFLP patterns obtained were similar to those reported previously for the European stone fruit yellows (ESFY, 16SrX-B). Identification has been further confirmed by PCR using ESFY specific primer pairs (ECA1/ECA2). This is the first report of Ca. Phytoplasma prunorum infecting almonds in Tunisia.     

Molecular characterization of the phytoplasmas associated with toon trees and periwinkle in India

In November 2008 in Himachal Pradesh and Chandigarh regions in India, toon trees and periwinkles were observed to have formed short internodes, small leaves and witches’-broom symptoms, typical of phytoplasma infection. The symptomatic toon and periwinkle samples were tested with universal PCR tests, and the 16S rRNA, rplB-rpsC, secA and secY genes were sequenced. The causal agents belonged to subgroup 16SrI-B of ‘Candidatus Phytoplasma asteris’, based on 16S rDNA, ribosomal protein gene, secA and secY phylogenetic analysis.     

Molecular identification of a phytoplasma associated with Russian olive witches’ broom in Iran

Russian olive trees (Elaeagnus angustifolia) showing witches’ broom symptoms typical of phytoplasma infection were observed in the Urmia region of Iran. A phytoplasma named Russian olive witches’ broom phytoplasma (ROWBp-U) was detected from all symptomatic samples by amplification of the 16S rRNA gene and 16S/23S rDNA spacer region using the polymerase chain reaction (PCR) which gave a product of expected length. DNA from symptomless plants used as a negative control yielded no product. The sequence of the 16S rRNA gene and 16S/23S rDNA spacer region of ROWBp-U showed 99% similarity with the homologous genes of members of the aster yellows group. We also detected a phytoplasma in neighboring alfalfa plants (AlWBp-U) showing severe witches’ broom symptoms. An 1107 bp PCR product from the 16S rRNA gene showed 99% homology with the corresponding product in ROWBp-U, suggesting the presence of the same phytoplasma actively vectored in the area. Further observations showed that Russian olive trees with typical ROWB symptoms were present in an orchard near Tehran which is located over 530 km south-east of the original Urmia site. The corresponding sequence of this phytoplasma (ROWBp-T) showed 99% homology to that of the ROWBp-U. A sequence homology study based on the 16S rRNA gene and 16S/23S rDNA spacer region of ROWBp-U and other phytoplasmas showed that ROWBp-U is most closely related to the 16SrI group. To our knowledge, this is the first report of a phytoplasma infection in a member of the Elaeagnaceae.     

A Leafhopper (Hishimonus sellatus) Transmits Phylogenetically Distant Phytoplasmas: Rhus Yellows and Hovenia Witches' Broom Phytoplasma

Phytoplasmas causing a severe decline of three tree species, i.e., Rhus javanica, Hovenia tomentella and Zizyphus jujuba, in Japan were examined for their transmissibility by a leafhopper species Hishimonus sellatus, and for their phylogenetic relatedness. By H. sellatus, Rhus yellows (RhY) phytoplasma was transmissible to white clover and periwinkle seedlings, causing typical symptoms in these plants. Jujube witches' broom (JWB) phytoplasma was also transferred to the host plant, Z. jujuba, by the leafhopper. Because JWB phytoplasma was transmitted to Hovenia tomentella and caused the same symptoms as Hovenia witches' broom (HWB), JWB phytoplasma may be very closely related to HWB phytoplasma. RFLP analysis of the PCR products of 16S rDNA revealed that RhY phytoplasma belongs to the Aster yellows (AY) group, and JWB and HWB phytoplasmas belong to a different group (possibly Elm yellows group). Thus, we found that one species of leafhopper can carry phylogenetically distant phytoplasmas. Received 23 April 2001/ Accepted in revised form 29 October 2001     

Occurrence of rocket larkspur witches’ broom caused by “<Emphasis Type="Italic">Candidatus</Emphasis> Phytoplasma asteris” in Japan

In October 2001, a disease of rocket larkspur (Cosolida ambigua (L.) P. W. Ball et Heyw), characterized by witches’ broom, yellows and virescence of flowers, was found in Yakage Town in Okayama Prefecture. Electron microscopy revealed the presence of phytoplasma-like bodies in the phloem of diseased plants. The causal phytoplasma was identified as “Candidatus Phytoplasma asteris” based on 16S rDNA sequence analysis, and demonstrated to be acquired by the leafhopper Macrosteles striifrons. The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession number AB258330.     

Leafhoppers Exitianus atratus and Amplicephalus funzaensis transmit phytoplasmas of groups 16SrI and 16SrVII in Colombia

The phytoplasmas of groups 16SrI (‘Candidatus Phytoplasma asteris’) and 16SrVII (‘Ca. Phytoplasma fraxini’) have been associated with phytoplasma diseases in several urban tree species in Bogotá, Colombia and surrounding areas. The insect vectors responsible for this phytoplasma transmission are unknown. The objectives of this study were to test for the presence of phytoplasmas in leafhopper species (Cicadellidae) collected in areas with diseased trees and to determine the phytoplasma transmission ability of two of these species. Leafhoppers of nine species were collected at two sampling sites and tested by nested or double nested PCR using primers for the 16S rRNA gene. The amplicons were subjected to RFLP and/or sequencing analysis. Phytoplasmas of group 16SrI were detected in morphospecies MF05 (Haldorus sp.), group 16SrVII in MF07 (Xestocephalus desertorum), MF08 (Empoasca sp.) and MF09 (Typhlocybinae), and both groups 16SrI and 16SrVII in MF01 (Empoasca sp.), MF02 (Typhlocybinae), MF03 (Scaphytopius sp.), MF04 (Amplicephalus funzaensis) and MF06 (Exitianus atratus). Transmission tests to uninfected bean plants (Phaseolus vulgaris) were performed using field collected A. funzaensis and E. atratus individuals in separate assays. After 5 weeks, the test plants exposed to individuals of both species of leafhoppers showed symptoms, suggesting phytoplasma infection. Phytoplasma groups 16SrI and 16SrVII were detected in the two groups of exposed plants, indicating that A. funzaensis and E. atratus were able to transmit both groups of phytoplasmas. This is the first report of insect vectors for phytoplasmas of group 16SrVII in the world and of 16SrI in South America.     

New natural host plants of ‘Candidatus Phytoplasma pini’ in Poland and the Czech Republic

The presence of phytoplasmas in seven coniferous plant species (Abies procera, Pinus banksiana, P. mugo, P. nigra, P. sylvestris, P. tabuliformis and Tsuga canadensis) was demonstrated using nested PCR with the primer pairs P1/P7 followed by R16F2n/R16R2. The phytoplasmas were detected in pine trees with witches’ broom symptoms growing in natural forest ecosystems and also in plants propagated from witches’ brooms. Identification of phytoplasmas was done using restriction fragment length polymorphism analysis (RFLP) of the 16S rDNA gene fragment with AluI, MseI and RsaI endonucleases. All samples showed RFLP patterns similar to the theoretical pattern of ‘Candidatus Phytoplasma pini’, based on the sequence of the reference isolate Pin127S. Nested PCR‐amplified products, obtained with primers R16F2n/R16R2, were sequenced. Comparison of the 16S rDNAs obtained revealed high (99·8–100%) nucleotide sequence identity between the phytoplasma isolates. The isolates were also closely related to four other phytoplasma isolates found in pine trees previously. Based on the results of RFLP and sequence analyses, the phytoplasma isolates tested were classified as members of the ‘Candidatus Phytoplasma pini’, group 16SrXXI.     

竹丛枝植原体16SrDNA片段克隆与序列分析

利用植原体16SrRNA基因序列设计合成的引物,对表现丛枝的竹子植株总DNA进行直接PCR及巢式PCR扩增,得到长1.2kb的目的片段。将此片段与pGEMTEasy载体连接并转化到大肠杆菌DH5α感受态细胞中。通过酶切、PCR鉴定,对筛选得到的重组阳性克隆进行核酸序列测定及同源性比较分析,结果表明其与植原体16SrⅠ组中的西方翠菊黄化植原体(SAY)同源率为99%。依据16SrDNA序列建立了竹子丛枝病植原体株系的系统进化树。对云南竹子丛枝病植原体株系分类鉴定与已报道的结果相似。     

A disease associated with phytoplasma in <Emphasis Type="Italic">Parthenium hysterophorus</Emphasis>

A disease on parthenium weed (Parthenium hysterophorus L.) was observed in June 2008 in Danzhou of Hainan Province. Infected weeds showed phytoplasma-like associated symptoms such as severe stunting, excessive proliferation of shoots, inflorescence-clustering, green petal, small leaves and witches’-broom. The original cause of phytoplasma was further confirmed by polymerase chain reaction (PCR). PCR products of 1.8 kb were obtained using the universal primers pair (P1/P7) designed to amplify the entire 16S rDNA and the 16/23S intergenic spacer region in a direct PCR assay. The primers pair R16F2n/R2 was used to amplify a PCR product of 1.2 kb. Restriction fragment length polymorphism (RFLP) was used to analyze the partial 16S rDNA sequences (1.2 kb) of all phytoplasma DNA digested with five endonucleases (Kpn I, Hpa II, Taq I, Rsa I, EcoR I). The RFLP patterns of the strain were found to be identical with that of the reference peanut witches’-broom phytoplasma. Based on the RFLP data, it is suggested that the phytoplasma strain belongs to subgroup 16SrII-A. This is the first demonstration of a 16SrII-A group phytoplasma associated with parthenium weed.     

The first detection of ‘<Emphasis Type="Italic">Candidatus</Emphasis> Phytoplasma trifolii’ in <Emphasis Type="Italic">Rhododendron</Emphasis> hybridum

Four Rhododendron hybridum plants (from cvs Moravanka and Don Juan), all exhibited symptoms of shortened axillary shoots, reduced leaves with vein clearing and yellowing, undeveloped flowers, and general stunting in a rhododendron nursery garden in southern Bohemia in 2007. Electron microscopy examination of ultra-thin sections revealed the presence of numerous polymorphic phytoplasma-like bodies in the phloem tissue of leaf midribs and petioles. The phytoplasma etiology of this disease was further confirmed by polymerase chain reaction (PCR) using universal phytoplasma primers. Restriction fragment length polymorphism (RFLP) analysis of amplification products obtained with a R16F2/R16R2 primer pair from all symptomatic plants indicated the presence of phytoplasma from the 16SrVI-A subgroup. A detailed comparison of the amplified sequences and phylogenetic analysis confirmed that the phytoplasma belonged to the subgroup 16SrVI-A (clover proliferation phytoplasma group). This is the first report of the natural occurrence of ‘Candidatus Phytoplasma trifolii’ in plants of Rhododendron hybridum.     

安徽桑黄花型萎缩病植原体16S rDNA序列分析及分子检测

 Mulberry yellow dwarf(MYD)disease is an quarantine disease and the causal agent is a phytoplasma.Two pairs of published universal primer, P1/P7 and Rm16F2/Rm16R1, based on the 16S-23S rDNA sequence of phytoplasma and total DNA extracted from infected mulberry tissues were employed for PCR and nested-PCR detection.The results revealed that a phytoplasma-specific 1 830 bp fragment with a G+C content of 46.01% was sequenced(GenBank accession No.GQ249410).The sequence shared 99.7% and 99.8% identity with aster yellows, the representatiive phytoplasma in 16SrI group, and mulberry dwarf phytoplasma classified into subgroup B in 16SrI group and named as the MYD phytoplasma strain Anhui(MYD-Anh).A phylogenetic tree based on 16S rDNA sequences was constructed and showed that MYD-Anh was clustered into 16SrI group.Identity of 16S rDNA sequence between MYD-Anh and mulberry yellow dwarf phytoplasma strain Zhenjiang(MD-zj) was nearly 100%, and they might belong to the same strain.Nested-PCR was used to detect the pathogenic phytoplasma from the differential tissues of mulberry infected with MYD-Anh.The results showed that a phytoplasma-specific 1.4 kb fragment was amplified with total DNA extracted from bark and vein.Nested-PCR was more sensitive than PCR for detecting MYD phytoplasma.     

Development and evaluation of a one‐hour DNA extraction and loop‐mediated isothermal amplification assay for rapid detection of phytoplasmas

A rapid DNA extraction and loop‐mediated isothermal amplification (LAMP) procedure was developed and evaluated for the detection of two specific groups of phytoplasmas from infected plant material. Primers based upon the 16–23S intergenic spacer (IGS) region were evaluated in LAMP assays for amplification of group 16SrI (aster yellows group) and group 16SrXXII (Cape St Paul wilt group) phytoplasma strains. DNA could be extracted from leaf material (16SrI phytoplasmas) or coconut trunk borings (16SrXXII phytoplasmas) onto the membranes of lateral flow devices, and small sections of these membranes were then added directly into the LAMP reaction mixture and incubated for 45 min at 65°C. Positive reactions were detected through the hydroxyl napthol blue colorimetric assay within 1 h of the start of DNA extraction, and were confirmed by subsequent agarose gel electrophoresis of the LAMP products. The level of detection was comparable to that obtained by nested PCR using conventional 16S rDNA phytoplasma‐specific primers. Furthermore, the assays were specific for the phytoplasmas they were designed to detect – the 16SrI assay only detected 16SrI phytoplasmas and not those from any other phylogenetic groups, whilst the 16SrXXII assay only detected 16SrXXII phytoplasmas. The DNA extractions and LAMP assay are easy to perform, requiring minimal equipment, and may therefore form the basis of a rapid and reliable field‐detection system for phytoplasmas.     

Electron microscopy and molecular identification of phytoplasmas associated with strawberry green petals in the Czech Republic

The presence of phytoplasma inFragaria ananassa x Duch cv Senga Sengana showing strawberry green petals symptoms was observed by electron microscopy of phloem tissue. No phytoplasmas were found in asymptomatic strawberry plants used as controls. Nucleic acids extracted from these plants were used in nested-PCR assays with primers amplifying 16S rRNA sequences specifie for phytoplasmas. Bands of 1.2 kb were obtained and the subsequent nested-PCR with specific primers and RFLP analyses allowed to classify the detected phytoplasmas in the aster yellows group (16SrI). They belonged to the subgroup I-C of which type strain is clover phyllody phytoplasma.     

Occurrence and distribution of ‘Candidatus Phytoplasma trifolii’ associated with diseases of solanaceous crops in Lebanon

A survey for phytoplasma diseases in tomato and pepper fields in Lebanon was conducted during 2003 and 2004. Tomato plants with stunting, yellowing or purplish leaves, proliferation of laterals buds, hypertrophic calyxes and virescent flowers were found in 25% of the tomato fields surveyed, where they represented 2–8% of the plants. Pepper plants displaying stunting and yellowing of leaves, were found in 27% of the fields and 1–4% of the plants were affected. Phytoplasmas infecting tomato and pepper had identical 16S-rDNA RFLP profiles and sequences. A phytoplasma isolate named PTL was transmitted by dodder from a diseased tomato plant to a periwinkle (Catharanthus roseus) plant in which it induced leaf yellowing, virescence and phyllody. 16S-rDNA phylogenetic analysis classified PTL as a strain of ‘Candidatus Phytoplasma trifolii’.     

云南泡桐丛枝病植原体核糖体蛋白基因片段序列分析

 应用植原体核糖体蛋白基因通用引物对rpF1/rpR1,对采自云南省曲靖市的泡桐丛枝病植原体DNA (PaWB-QJ)进行PCR扩增,得到1.3 kb的特异片段,证明此病株中存在植原体。将此片段与pGEM-T Easy载体连接并转化大肠杆菌JM109感受态细胞,进行PCR鉴定、核糖体蛋白基因部分核苷酸序列测定及分析。结果表明,该株系(PaWB-QJ)核糖体蛋白基因片段长1 244 bp,包含rps19、rpl22和rps3基因。对PaWB-QJ株系的核糖体蛋白基因序列的同源性比较结果显示与16S rI-B亚组的翠菊黄化(Aster yellows,AY)、长春花黄化(Periwinkle yellows,PY)和泡桐丛枝德国株系(Paulownia witches'-broom,PaWB-German)的亲缘关系最近,达到99.0%以上,而与其它组中的株系明显低于97.0%,所以认为该植原体株系属于翠菊黄化组B亚组(16SrI-B)。     

Transmission and detection of toria [<Emphasis Type="Italic">Brassica rapa</Emphasis> L. subsp. <Emphasis Type="Italic">dichotoma</Emphasis> (Roxb.)] phyllody phytoplasma and identification of a potential vector

Phyllody disease associated with 16SrIX phytoplasma was observed in the range of 4.1–11% in 10 different lines of toria [Brassica rapa L. subsp. dichotoma (Roxb.)] in experimental fields of the Indian Agricultural Research Institute, New Delhi, India during 2008 and 2009. The toria phyllody (TP) phytoplasma was detected in all the symptomatic and 13.3% of asymptomatic toria plants by nested PCR. The phytoplasma was detected in midrib, flower part, siliquae, stem, and root of infected plants as well as seeds. TP was transmitted by grafting and by dodder to toria and nine other rapeseed/mustard species as confirmed by nested PCR. However, symptoms of phytoplasma infection were induced only in toria, yellow sarson [Brassica rapa L. subsp. trilocularis (Roxb.)], brown sarson [Brassica rapa L. subsp. sarson (Prain)], rapeseed (B. napus subsp. oleifera), and rocket or taramira (Eruca sativa) but not in mustard (B. juncea), black mustard (B. nigra), Ethiopian mustard (B. carinata), B. tournefortii and white mustard (Sinapis alba). Transmission of TP phytoplasma to periwinkle (Catharanthus roseus) was successful only through dodder, but no transmission to tomato (Lycopersicon esculentum) or brinjal (Solanum melongena) was found. TP phytoplasma was detected in Laodelpax striatellus, an abundant planthopper in toria fields, which indicates that this planthopper may be a potential vector for TP phytoplasma.