Clover Phyllody Phytoplasma Research Articles

Clover phyllody phytoplasma (phyllody of clover)

clover phyllody phytoplasma (phyllody of clover)

First Report of a 16SrI‐C Phytoplasma Infecting Celery (Apium graveolens) with Stunting, Bushy Top and Phyllody in the Czech Republic

AbstractApium graveolens L. plants showing stunting, purplish/whitening of new leaves, flower abnormalities and bushy tops were observed in South Bohemia (Czech Republic) during 2011 and 2012. Transmission electron microscopy observations showed phytoplasmas in phloem sieve tube elements of symptomatic but not healthy plants. Polymerase chain reactions with universal and group‐specific phytoplasma primers followed by restriction fragment length polymorphism analyses and sequencing of 16S rDNA enabled classification of the detected phytoplasmas into the aster yellows group, ribosomal subgroup 16SrI‐C. Identical analyses of the ribosomal protein genes rpl22 and rps3 were used for further classification and revealed affiliation of the phytoplasmas with the rpIC subgroups. This is the first report of naturally occurring clover phyllody phytoplasma in A. graveolens in both the Czech Republic and worldwide.

First Report of 16SrIII-B Phytoplasma Subgroup Associated with Virescence of Arnica montana in Serbia.

Arnica montana L. is a high altitude perennial plant, indigenous to Europe, but it is not native in the flora of Serbia. Plantain introduction of A. montana began a few years ago in the Tara mountain region, Western Serbia (43°53'44.17″N 19°33'11.62″E, 1,008 m ASL). The mountainous climate in this region is characterized by 850 mm of precipitation per year and an average decade temperature range from 11 to 25°C in the vegetation period of May through September. The main soil type is dystric cambisol, exhibiting a slightly acidic reaction (pH 6.4). Seeds of A. montana cv. ARBO were obtained from the Agricultural Research Centre of Finland. Seedlings were produced in a greenhouse during the period March through April and planted in May 2008. Virescence symptoms were observed starting from May 2010. A. montana exhibited symptoms mainly on flowers, like green leaflike structures instead of flowers and proliferation of acillary buds. Later in the season, flowers were malformed and consequently failed to produce seeds. Plant material for analyses was collected during 2010 and 2011 from an experimental field located at Tara mountain. Total DNA was extracted from the leaf midveins of 14 symptomatic and six symptomless plants (3). Nested PCR was carried out with primers P1/P7 followed by P1/16S-Sr and R16F2n/R16R2 primers, resulting with the DNA fragments amplification of expected size: 1.8, 1.5, and 1.2 kb, respectively, in all symptomatic samples tested. No phytoplasmas were detected in symptomless samples. PCR products of 1.2 kb, obtained by R16F2n/R16R2 primers from symptomatic samples, were digested independently with four restriction enzymes (Alu I, Tru I, Hpa II and Hha I) and the RFLP patterns were compared with those of Stolbur (Stol), Aster Yellows (AY), Flavescence Doree-C (FD-C), Poinsettia Branch-Inducing (PoiBI) and Clover Yellow Edge (CYE) phytoplasmas (2). RFLP patterns from all symptomatic A. montana samples were identical to CYE pattern. Comparison of the 16S rDNA sequence of representative symptomatic sample Am4, deposited under accession number JX297491 in NCBI GenBank, with other phytoplasmas from the database revealed 99% identity with members of 16SrIII-B phytoplasma group: Clover yellow edge phytoplasma strain CYE (JQ944798.1), 'Euscelidius variegatus' phytoplasma strain AP-I (HQ589197.1), Clover phyllody phytoplasma strain CP (HQ589196.1), etc. In Serbia, phytoplasma belonging 16SrIII-B subgroup has been identified in Cirsium arvense (4) and pear plants (1). To our knowledge, this is the first report of a natural infection of A. montana by phytoplasma. Cultivation of A. montana provides the necessary raw material for medicament production. The flower heads are widely used for the topical treatment of bruises and sprains in phytopharmaceutical preparations.Taking into consideration that monoculture plantation growing of perennials favorites rapid spreading of infections, the present study tended to examine the potential threat of virescence, which could be the limiting factor of ex-situ conservation of this endangered plant by its cultivation.

Genome drafts of four phytoplasma strains of the ribosomal group 16SrIII

By applying a coverage-based read selection and filtration through a healthy plant dataset, and a post-assembly contig selection based on homology and linkage, genome sequence drafts were obtained for four phytoplasma strains belonging to the 16SrIII group (X disease clade), namely Vaccinium Witches' Broom phytoplasma (647 754 nt in 272 contigs), Italian Clover Phyllody phytoplasma strain MA (597 245 nt in 197 contigs), Poinsettia branch-inducing phytoplasma strain JR1 (631 440 nt in 185 contigs) and Milkweed Yellows phytoplasma (583 806 nt in 158 contigs). Despite assignment to different 16SrIII subgroups, the genomes of the four strains were similar, comprising a highly conserved core (92-98 % similar in their nucleotide sequence among each other over alignments about 500 kb in length) and a minor strain-specific component. As far as their protein complement was concerned, they did not differ significantly in their basic metabolism potential from the genomes of other wide-host-range phytoplasmas sequenced previously, but were distinct from strains of other species, as well as among each other, in genes encoding functions conceivably related to interactions with the host, such as membrane trafficking components, proteases, DNA methylases, effectors and several hypothetical proteins of unknown function, some of which are likely secreted through the Sec-dependent secretion system. The four genomes displayed a group of genes encoding hypothetical proteins with high similarity to a central domain of IcmE/DotG, a core component of the type IVB secretion system of Gram-negative Legionella spp. Conversely, genes encoding functional GroES/GroEL chaperones were not detected in any of the four drafts. The results also indicated the significant role of horizontal gene transfer among different 'Candidatus Phytoplasma' species in shaping phytoplasma genomes and promoting their diversity.

Phytoplasmas infecting sour cherry and lilac represent two distinct lineages having close evolutionary affinities with clover phyllody phytoplasma

Phytoplasmas infecting sour cherry and lilac in Lithuania were found to represent two lineages related to clover phyllody phytoplasma (CPh), a subgroup 16SrI-(R/S)C (formerly 16SrI-C) strain exhibiting rRNA interoperon sequence heterogeneity. 16S rDNAs amplified from the cherry bunchy leaf (ChBL) and lilac little leaf (LcLL) phytoplasmas were identical or nearly identical to those of operon rrnA and operon rrnB, respectively, of CPh. There was no evidence of 16S rRNA interoperon sequence heterogeneity in either LcLL or ChBL phytoplasma. Based on collective RFLP patterns of 16S rDNA, ChBL was classified in subgroup 16SrI-R, and LcLL was classified in new subgroup 16SrI-S. The ribosomal protein (rp) gene sequences from LcLL phytoplasma were identical to those of CPh, and strain LcLL was classified in rp subgroup rpI-C. By contrast, rp gene sequences from ChBL phytoplasma differed from those of subgroup rpI-C; based on RFLP patterns of rp gene sequences, ChBL was classified in new rp subgroup rpI-O. Single nucleotide polymorphisms (SNPs), designated here by a new SNP convention, marked members of rp subgroup rpI-C, and distinguished LcLL and CPh from ChBL and other non-rpI-C phytoplasmas in group 16SrI. The results raise questions concerning phytoplasma biodiversity assessment based on rRNA genes alone and encourage the supplemental use of a single copy gene in phytoplasma identification and classification, while drawing attention to a possible role of horizontal gene transfer in the evolutionary history of these lineages.

Clover phyllody phytoplasma. [Distribution map

Abstract A new distribution map is provided for Clover phyllody phytoplasma. Phytoplasma. Hosts: Polyphagous including poppy anemone ( Anemone coronaria ), strawberry ( Fragaria spp.), buttercup ( Ranunculus spp.), white clover ( Trifolium repens ) and zinnia ( Zinnia elegans ). Information is given on the geographical distribution in Europe (Belarus, Belgium, Bulgaria, Czech Republic, France, Germany, Hungary, Ireland, Italy (Mainland Italy), Lithuania, Portugal, Romania, Russia, Switzerland, UK), Asia (India (Himachal Pradesh), Japan), North America (Canada (New Brunswick, Nova Scotia, Prince Edward Island, Quebec), USA (Florida)), Oceania (Australia (Victoria)).

Identification of a phytoplasma from the aster yellows group infecting purple coneflower (Echinacea purpurea) in Slovenia

Purple coneflower (Echinacea purpurea) (Asteraceae family), is a perennial flowering plant native to eastern North America which is widely grown as an ornamental and medicinal plant. Since 2002, phytoplasma-like symptoms have been observed in several gardens in the Savinja valley in Slovenia. Disease incidence (5–30%) has varied between years and increases with plant age. The symptoms seen include plant weakness, leaf yellowing, and floral malformations particularly virescence and phyllody. For molecular identification of the pathogen, the total DNA was isolated from samples of several parts of an infected plant and from a plant without symptoms using a CTAB protocol (Kump & Javornik, 1996). PCR was carried out using three universal 16S rDNA-specific primers P1/P7, Fu5/Ru3 and R16F2n/R16R2. All three primer pairs gave a single PCR products from tissue with symptoms, with the expected lengths of ~1·8, 0·9, and 1·2 kbp, but no products from samples from plants without symptoms. All PCR products were TA cloned (Promega T-easy), sequenced and assembled into a single sequence of a total length of 1840 bp, which was deposited in GenBank (Accession No. EU416172). A blast search revealed 100% sequence identity for the entire contig with poa stunt phytoplasma (DQ640502) and clover phyllody phytoplasma strain CPh (AF222066) sequences, both belonging to the 16SrI-C subgroup of the aster yellows group (AY). Other matches with high sequence similarities (98–99%) also belonged to aster yellows phytoplasma members, e.g. onion yellows phytoplasma (AP006628.2), epilobium phyllody phytoplasma (AY101386), silene virescence phytoplasma (AY744070) and to the Czech strain of purple coneflower phyllody phytoplasma (EF546778). Phytoplasmas belonging to the AY group have been previously identified in purple coneflower in the USA, Canada (Stanosz & Heimann, 1997; Lee et al., 2008) and in the Czech Republic. This is the first report of detection of an isolate of ‘Candidatus Phytoplasma asteris’ (subgroup 16SrI-C) infecting purple coneflower in Slovenia.

First Report of Elm Yellows Phytoplasma Infecting Clover in China.

In the summer of 2008, phyllody and enlarged petioles resembling symptoms of phytoplasma infection were observed on clover (Trifolium repens) plants in lawns on the campus of Northwest A&F University. Typical phytoplasma-like bacteria were observed in the phloem cells when ultra-thin sections from leaf midrib tissues were examined with transmission electron microscopy. Nested PCR assays were used to verify the association of phytoplasma with the disease. Total DNA was extracted from the phloem of leaf midribs from 20 symptomatic plants and six symptomless plants using the modified CTAB method (1). Using the phytoplasma universal primer pair R16mF2/R16mR1 followed by specific primers R16F2n/R16R2 (4), PCR products of 1.4 and 1.2 kb were amplified, respectively, from symptomatic plants only. Jujube witches'-broom (JWB) and paulownia witches'-broom (PaWB) phytoplasma DNA samples served as controls and were used to study group relationships. After sequencing of the 16S rDNA fragment (GenBank Accession No. FJ436792), a BLAST search determined that the clover phytoplasma shared closest homology (99.6%) with JWB (GenBank Accession No. FJ154846) phytoplasmas compared with lesser identity (90.4%) with PaWB (GenBank Accession No. EF199937). Subsequent restriction fragment length polymorphism analysis of the PCR-amplified 1.2-kb 16S rDNA R16(1)F1/R1 fragment indicated that the phytoplasma associated with the disease belongs to subgroup 16SrV-B of the elm yellows phytoplasma group. Clover phyllody phytoplasma were previously reported to infect clover in Canada (GenBank Accession No. L33762) (3) and Italy (GenBank Accession No. X77482) (2). The phytoplasma reported here shared 86.7 and 90.0% identity with the clover phyllody phytoplasma above, respectively, much lower than that with Elm yellows phytoplasma group. To our knowledge, this is the first report of Elm yellows phytoplasma infecting clover in China.

Purple coneflower with reddening and phyllody: a new host of clover phyllody phytoplasma

Echinacea purpurea plants showing yellowing/reddening and phyllody symptoms were observed in southern Bohemia. Transmission electron microscopy observations showed phytoplasmas in sieve cells of symptomatic plants, but not in healthy ones. Direct and nested polymerase chain reaction with phytoplasma specific primers and subsequent restriction fragment length polymorphism analyses of 16S rDNA as well as sequence analyses of the 16S–23S ribosomal operon (1789 bp) enabled the classification of the detected phytoplasmas in the aster yellows group, ribosomal subgroup 16SrI-C. Identical analyses of the transcription factor tuf gene and the ribosomal protein rpl22, rps3 genes were used for further classification, and revealed the affiliations of the phytoplasmas to the tufIC and rpIC subgroups, respectively. The presence of clover phyllody phytoplasmas in purple coneflowers is a new record for this species.

Molecular characterization of phytoplasmas in lilies with fasciation in the Czech Republic

Lilium spp. with symptoms of severe fasciation were observed in Southern and central Bohemia during the period 1999–2003. Nucleic acids extracted from symptomatic and asymptomatic plants were used in nested-PCR assays with primers amplifying 16S-23S rRNA sequences specific for phytoplasmas. The subsequent nested-PCR with phytoplasma group-specific primers followed by RFLP analyses and the 16S ribosomal gene sequencing, allowed classification of the detected phytoplasmas in the aster yellows group, subgroups 16SrI-B and 16SrI-C alone, and in mixed infection. Samples infected by 16SrI-C phytoplasmas showed different overlapping RFLP profiles after TruI digestion of R16F2/R2 amplicons. Two of these amplicons were sequenced, one of them directly and the other after cloning; sequence analyses and blast alignment confirmed the presence of two different overlapping patterns in samples studied. The sequences obtained were closely related, respectively, to operon A and operon B ribosomal sequences of the clover phyllody phytoplasma. Direct PCR followed by RFLP analyses of the tuf gene with two restriction enzymes showed no differences from reference strain of subgroup 16SrI-C. Infection with aster yellows phytoplasmas of 16SrI-B subgroup in asymptomatic lilies cv. Sunray was also detected.

A comparison of different phytoplasma DNA extraction methods using competitive PCR

The primer pair 16endF-Tmod, specific for the16S/23S rDNA spacer region, amplifies different length fragments when the target DNA belongs to phytoplasmas of the X-clade and AP-clade in compared with phytoplasmas of the AY-clade. The cloned 16S/23S spacer of the tagete witches’-broom phytoplasma (TWB, AY-clade) was used in a competitive PCR assay to quantify the DNA of the apple proliferation phytoplasma (AP, AP-clade) and the clover phyllody phytoplasma (CP, X-clade) present in the nucleic acids extracted from infected periwinkle plants. Thus, four methods, normally used for the extraction of phytoplasma DNA from infected plant tissue, were compared to determine which was the most efficient in recovering phytoplasma nucleic acids. The different methods detected relatively minor differences in the yields obtained. It was concluded that the sampling and detection protocols are more critical than the DNA extraction method as far as sensitivity is concerned.

Natural infection of subterranean clover in Italy by a phytoplasma

Subterranean clover, growing in experimental plots in northern Italy, showed dwarfing, phyllody and leaf reddening. These symptoms were associated with Italian clover phyllody phytoplasma.

Geminivirus-related extrachromosomal DNAs of the X-clade phytoplasmas share high sequence similarity.

Southern blot hybridization analysis revealed that the extrachromosomal DNAs (EC-DNAs) associated with Vaccinium witches' broom (VAC) and walnut witches' broom phytoplasmas and various strains of the Italian clover phyllody phytoplasma (ICPh) were highly homologous among themselves but distinct from EC-DNAs of aster yellows related phytoplasmas occurring in the same insect and plant hosts and collected at the same site as the ICPh strains. The EC-DNAs of various strains of the ICPh differed significantly in number and size, more markedly among samples from different host plant species than among samples from the same host plant species. However, experiments on insect-mediated transmission suggested that the size variation is not associated with plant host specificity. Sequence analysis of cloned fragments revealed the presence of highly conserved ORFs (with substantially invariant putative translation products) but also the presence of regions rich in short direct and inverted repeats, which may be the cause of the size variations. The partial sequence of an EC-DNA associated with VAC encoding a putative replication-associated protein indicated their close phylogenetic relationship with geminiviruses.

Characterization and classification of phytoplasmas from wild and cultivated plants by RFLP and sequence analysis of ribosomal DNA

Restriction fragment length polymorphism and sequence analysis of PCR-amplified ribosomal DNA were used to identify and classify phytoplasmas associated with diseases of various wild and cultivated plants. The diseases examined were either not known before or the presumable causal agents were not yet identified and characterized or were only known from other geographic areas. New diseases examined were those causing virescence and phyllody of Bunias orientalis and Cardaria draba. Both were associated with strains of the aster yellows phytoplasma. The same type of aster yellows phytoplasma was also found to be associated with yellows and phyllody diseases of Portulaca oleracea, Stellaria media, Daucus carota ssp. sativus, and Cyclamen persicum. In German and French DNA samples from diseased Trifolium repens, the clover phyllody phytoplasma was identified, which could clearly be distinguished from other phytoplasmas of the aster yellows group. Strains of the stolbur phytoplasma were detected in big bud-affected tomatoes and almost exclusively in Convolvulus arvensis. In Cirsium arvense and Picris echioides two distinct phytoplasmas were identified which showed relationship to the sugarcane white leaf phytoplasma group but may represent a new group or subgroup. In Conyza (syn.: Erigeron) canadensis a phytoplasma of the X-disease group was detected. A strain from Gossypium hirsutum showed the same restriction profiles as the faba bean phyllody phytoplasma.

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.

Molecular characterization of a phytoplasma causing Phyllody in Clover and other herbaceous hosts in Northern Italy

Red clover (Trifolium pratense) and Ladino clover (Trifolium repens) plants showing phytoplasma-associated symptoms (yellowing/reddening, virescence and phyllody) have been recovered in Friuli-Venezia Giulia, Italy. Using AluI RFLP analysis of PCR amplified 16S rDNA we showed that the disease can be caused independently by two phylogenetically distinct phytoplasmas. One of them showed the very typical 16S rDNA RFLP pattern of the agent of Clover Phyllody in Canada (CCPh). The 16S rDNA of the other phytoplasma (Italian Clover Phyllody phytoplasma, ICPhp) has been PCR amplified, cloned and sequenced. The sequence revealed high similarity (>98%) with phytoplasmas belonging to the X disease cluster, which includes organisms not reported to cause phyllody on their hosts. The analysis by AluI RFLP of the PCR amplified pathogen 16S rDNA from other herbaceous plants (Crepis biennis, Taraxacum officinale, Leucanthemum vulgare) collected nearby with phytoplasma-associated symptoms showed similar patterns. Southern blot hybridization of their EcoRI digested total DNA revealed identical RFLP patterns, suggesting that the causative agent may be the same organism.