Genome wide sequence analysis grants unbiased definition of species boundaries in “Candidatus Phytoplasma”

The phytoplasmas are currently named using the Candidatus category, as the inability to grow them in vitro prevented (i) the performance of tests, such as DNA-DNA hybridization, that are regarded as necessary to establish species boundaries, and (ii) the deposition of type strains in culture collections. The recent accession to complete or nearly complete genome sequence information disclosed the opportunity to apply to the uncultivable phytoplasmas the same taxonomic approaches used for other bacteria. In this work, the genomes of 14 strains, belonging to the 16SrI, 16SrIII, 16SrV and 16SrX groups, including the species “Ca. P. asteris”, “Ca. P. mali”, “Ca. P. pyri”, “Ca. P. pruni”, and “Ca. P. australiense” were analyzed along with Acholeplasma laidlawi, to determine their taxonomic relatedness. Average nucleotide index (ANIm), tetranucleotide signature frequency correlation index (Tetra), and multilocus sequence analysis of 107 shared genes using both phylogenetic inference of concatenated (DNA and amino acid) sequences and consensus networks, were carried out. The results were in large agreement with the previously established 16S rDNA based classification schemes. Moreover, the taxonomic relationships within the 16SrI, 16SrIII and 16SrX groups, that represent clusters of strains whose relatedness could not be determined by 16SrDNA analysis, could be comparatively evaluated with non-subjective criteria. “Ca. P. mali” and “Ca. P. pyri” were found to meet the genome characteristics for the retention into two different, yet strictly related species; representatives of subgroups 16SrI-A and 16SrI-B were also found to meet the standards used in other bacteria to distinguish separate species; the genomes of the strains belonging to 16SrIII were found more closely related, suggesting that their subdivision into Candidatus species should be approached with caution.     

Differentiation and Classification of Phytoplasmas Associated with Almond and GF‐677 Witches'‐Broom Diseases using rRNA and rp Genes

Stone fruits are affected by several diseases associated with plant pathogenic phytoplasmas. Previous studies have been shown that phytoplasma agents of almond and GF‐677 witches'‐broom (AlmWB and GWB, respectively) diseases belong to pigeon pea witches'‐broom (16SrIX) phytoplasma group. In this study, partial biological and molecular characterization was used to compare and classify phytoplasma agents of Khafr AlmWB (KAlmWB) and Estahban GWB (EGWB) diseases. Production of different symptoms in periwinkle indicated that agents of KAlmWB and EGWB are differentiable. Expected fragments were amplified from diseased almond and GF‐677 trees in direct PCR using phytoplasma universal primer pairs P1/P7 and rpF1/rpR1 and nested PCR using P1/P7 followed by R16F2n/ R16R2 primer pair. 16S‐rDNA Restriction fragment length polymorphism (RFLP) as well as phylogenetic analysis of rplV‐rpsC and 16S–23S rRNA spacer region sequences classified KAlmWB and EGWB phytoplasmas within 16SrIX‐C (rpIX‐C) and 16SrIX‐B (rpIX‐B) subgroups, respectively.     

Molecular study of two distinct phytoplasma species associated with streak yellows of date palm in Iran

A disease with symptoms similar to palm lethal yellowing was noticed in the early 2013 in Khuzestan Province (Iran) in date palm (Phoenix dactylifera). Infected trees displaying symptoms of streak yellows and varied in the incidence and severity of yellowing. A study was initiated to determine whether phytoplasma was the causal agent. Polymerase chain reaction–restriction fragment length polymorphism (PCR‐RFLP) methods using universal phytoplasma primers pairs R16mF1/mR1 and M1/M2 were employed to detect putative phytoplasma(s) associated with date palm trees. Nested PCR using universal primers revealed that 40 out of 53 trees were positive for phytoplasma while asymptomatic date palms from another location (controls) tested negative. RFLP analyses and DNA sequencing of 16S rDNA indicated that the presence of two different phytoplasmas most closely related to clover proliferation (CP) phytoplasma (group 16SrVI) and ash yellows (AY) phytoplasma (group 16SrVII). Sequence analysis confirmed that palm streak yellows phytoplasmas in each group were uniform and to be phylogenetically closest to “CandidatusP. fraxini” (MF374755) and “Ca. P. trifolii” isolate Rus‐CP361Fc1 (KX773529). Result of RFLP analysis of secA gene of positive samples using TruI and TaqI endonuclease is in agreement with rDNA analysis. On this basis, both strains were classified as members of subgroups 16SrVI‐A and 16SrVII‐A. This is the first report of a phytoplasma related to CP and AY phytoplasma causing date palm yellows disease symptoms.     

植原体黄化病的检疫及其防控技术研究进展

植物黄化病是一种常见的而且危害严重的病害.近年来,外来有害生物的入侵给我国造成了巨额经济损失,并且对我国农林业生产安全和生态环境造成了严重的威胁,对植物检疫工作提出了新挑战.对几种由植原体引起的植物黄化病的症状、病原分类及其检疫技术和综合防控措施进行综述.     

植原体免疫主导膜蛋白Imp基因原核表达载体构建及表达

旨在构建植原体免疫主导膜蛋白Imp基因原核表达载体,并进行初步表达。以重组克隆质粒pMD18-T-Imp为模板,PCR扩增Imp基因片段。构建表达载体pET-28a(+)-Imp,转化宿主菌E.coliBL21(DE3)。筛选阳性克隆,提取重组质粒作PCR鉴定、酶切鉴定及IPTG诱导表达鉴定。PCR及双酶切结果显示,重组质粒pET-28a(+)-Imp构建成功。经IPTG诱导BL21(pET-28a(+)-Imp)表达约20 kD的蛋白,与预期的携带6×His-Tag的目的蛋白(19.5 kD)大小相符,主要以包涵体形式存在。结果显示,构建的表达载体pET-28a(+)-Imp在E.coliBL21(DE3)中能够达一定量表达,为进一步纯化Imp蛋白奠定基础。     

植原体DNA提取方法的改良

在总结多种植原体DNA提取方法的基础上 ,发展了一种提取植原体DNA新方法。用此方法提取的DNA经琼脂糖凝胶电泳检测到大于 15kb的DNA主带 ,基本无DNA碎带 ,不用RNase处理 ,也无RNA干扰 ,OD2 60 / 2 80 值显示产物纯度较高 ,无需任何处理 ,即可以作为模板扩增     

小麦蓝矮病植原体胸苷酸激酶基因(tmk)的分离、原核表达及酶活性分析

[目的]克隆、表达小麦蓝矮病(WBD)植原体胸苷酸激酶基因(tmk),并分析酶活性,进一步研究胸苷酸激酶在植原体感染宿主及繁殖过程中的功能和作用机理,更好地防治植原体病害.[方法]PCR方法扩增tmk基因并进行序列分析,连接pET30a( )表达载体后原核表达,经Ni-NTA柱层析纯化后进行酶催化活性分析.[结果]首次从小麦蓝矮病(WBD)植原体基因组中分离出胸苷酸激酶基因(tmk),该基因包含tmk-1和tmk-2两种,大小分别为630 bp和624 bp,其编码的氨基酸序列均包含3个与结合NTP/NMP相关的保守功能区.表达的融合蛋白TMK-1活性极低,酶活仅16.4 U/mg,而 TMK-2酶活高达112.41 U/mg,且其最适催化条件为32℃、pH 7.3、1.5 mmol/L Mg2 和 1 mmol/L ATP.[结论]分析了胸苷酸激酶活性中心的一级结构序列及其催化活性随条件变化而改变的性质,为深入研究小麦蓝矮病植原体胸苷酸激酶在侵染寄主及其在宿主体内增殖的转录性质奠定基础.     

植原体的最新分类研究动态

简要介绍了植原体分类研究历史与现状, 综述了最新的植原体分类方法和植原体候选种的描述规则, 指出了我国在植原体分类鉴定方面与当今世界先进水平的差距及今后发展方向。     

Use of Heteroduplex Mobility Analysis (HMA) for Differentiating Phytoplasma Isolates Causing Witches' Broom Disease on Populus nigra cv Italica and Stolbur or Big Bud Symptoms on Tomato

Heteroduplex mobility analysis (HMA) was performed to distinguish French and German isolates of phytoplasmas from Populus nigra cv Italica witches broom. The French isolate was similar to the phytoplasma responsible for the European aster yellows while the German isolate was different but closely related to it. When phytoplasmas inducing similar "stolbur" symptoms in tomato were compared to HMA, a high degree of genetic differences was observed among the reference stolbur C (StC) isolate, the European aster yellows and the other phytoplasmas inducing stolbur or big bud symptoms in tomato. Pseudo-stolbur B and D from Brazil were differentiated from the reference St C using this method.     

Rapid detection of “Candidatus Phytoplasma mali” by recombinase polymerase amplification assays

Isothermal recombinase polymerase amplification (RPA) assays for the specific detection of “Candidatus Phytoplasma mali (Ca. P. mali),” the causal agent of apple proliferation, were developed. The assays amplify a fragment of the imp gene and amplimers were detected either by fluorescence in real‐time mode (TwistAmp^®exo assay) using a fluorophore‐labelled probe or by direct visualization employing a lateral flow device (TwistAmp^®nfo assay/Milenia^®HybriDetect). The RPA assays specifically amplified DNA from “Ca. P. mali” strains, and cross‐reactivity with other phytoplasmas or plant DNA was not observed. The limit of detection was determined with a cloned imp standard, and positive results were obtained down to 10 copies with both RPA assay formats. In comparison with a TaqMan real‐time PCR assay based on the same target gene, the RPA assays were equally sensitive, but results were obtained faster. Simplified nucleic acid extraction procedures from plant tissue with Tris‐ and CTAB‐based buffers revealed that crude Tris–DNA extracts were a suitable source for RPA tests while larger concentrations of CTAB were inhibitory. This is the first report of RPA‐based assays for the detection of “Ca. P. mali”. The assays are suitable for high‐throughput screening of plant material and point‐of‐care diagnostic and can be potentially combined with a simplified DNA extraction procedure.