České Budějovice, Czech Republic
České Budějovice, Czech Republic

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Franova J.,Institute of Plant Molecular Biology | de Sousa E.,National Institute of Agrarian and Veterinary Research INIAV | Koloniuk I.,Institute of Plant Molecular Biology | Mimoso C.,National Institute of Agrarian and Veterinary Research INIAV | And 5 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2016

A new phytoplasma was identified in naturally infected blackberry plants exhibiting witches’ broom symptoms in Portugal. The 16S rRNA gene sequence revealed that it is related to ‘Candidatus Phytoplasma rubi’ (16SrV-E ribosomal subgroup) and RFLP analysis revealed a unique profile following Mse I endonuclease digestion of R16F2n/R2 amplicons that distinguished it from the strains belonging to previously established 16SrV phytoplasma subgroups. The in silico restriction analyses confirmed that the phytoplasma strain from blackberry is different from all the other strains reported in group 16SrV. Phylogeny of the 16S rRNA gene sequences, sequence analyses of 16S–23S, tuf, rplV-rpsC, rplF-rplR, rplO-SecY-map and uvrB-degV genetic loci, as well as the variability of unique oligonucleotide sequences defined for ‘Candidatus Phytoplasma rubi’ confirmed the uniqueness of this phytoplasma strain from Portugal for which a novel ribosomal subgroup, 16SrV-I, is proposed. The representative of this new subgroup was named blackPort phytoplasma (Portuguese blackberry phytoplasma). © 2016, Microbiology Society. All rights reserved.


Koloniuk I.,Institute of Plant Molecular Biology | Hrabakova L.,Institute of Plant Molecular Biology | Hrabakova L.,University of South Bohemia | Petrzik K.,Institute of Plant Molecular Biology
Mitochondrial DNA | Year: 2014

The complete mitochondrial genome of the ascomycete fungus Phomopsis longicolla was sequenced using Illumina HiSeq platform. It consists of 53,439 bp with high (65.6%) A + T content and includes 14 conserved protein subunits of the mitochondrial oxidative phosphorylation system, two ribosomal RNAs and 25 tRNA genes. To our knowledge, this is the first complete mitochondrial genome of the Diaporthales member. © 2014 Informa UK Ltd. All rights reserved: reproduction in whole or part not permitted


Franova J.,Institute of Plant Molecular Biology | Pribylova J.,Institute of Plant Molecular Biology | Koloniuk I.,Institute of Plant Molecular Biology | Podrabska K.,Institute of Plant Molecular Biology | Spak J.,Institute of Plant Molecular Biology
Journal of Phytopathology | Year: 2016

Primula acaulis (L.) Hill. plants showing stunting, leaf-yellowing and virescence were first discovered in the Czech Republic. Polymerase chain reactions with subsequent restriction fragment length polymorphism analyses and sequencing enabled classification of the detected phytoplasmas into the aster yellows group, ribosomal subgroup 16SrI-B, tufI-B, rpI-B, groELIB-III and SecY-IB subgroups. Phylogeny of the 16S rRNA gene sequences as well as sequence analysis of several chromosomal regions, such as the 16S-23S ribosomal operon, ribosomal proteins, spc ribosomal protein operon, genes for elongation factor EF-Tu, molecular chaperonin large subunit GroEL, immunodominant membrane protein, ribosome recycling factor, urydilate kinase, ATP- and Zn2+-dependent proteases not only confirmed its affiliation with the 'Candidatus Phytoplasma asteris' species but also enabled its detailed molecular characterization. The less researched regions of phytoplasma genome (amp, adk, hflB, pyrH-frr genes) could be valuable as additional markers for phytoplasma through differentiation especially within the 16SrI-B ribosomal subgroup. © 2016 Blackwell Verlag GmbH.


Rossner Jr. P.,Academy of Sciences of the Czech Republic | Rossnerova A.,Academy of Sciences of the Czech Republic | Spatova M.,Academy of Sciences of the Czech Republic | Beskid O.,Academy of Sciences of the Czech Republic | And 6 more authors.
Mutagenesis | Year: 2013

Populations living in industrialised regions are at higher risk of a number of diseases and shortened life span. These negative effects are primarily brought about by damage to cells and macromolecules caused by environmental pollutants. In this study, we analysed the effect of exposure to benzo[a]pyrene, a particulate matter of aerodynamic diameter < 2.5 μm (PM2.5), and benzene on oxidative stress markers [including 8-oxo-7,8-dihydro-2′- deoxyguanosine (8-oxodG), 15-F2t-isoprostane (15-F2t-IsoP) and protein carbonyls] and cytogenetic parameters (stable and unstable chromosomal aberrations). The samples were collected from subjects living in the Ostrava region characterised by very high levels of air pollution and in Prague with comparatively lower concentrations of pollutants in three seasons (winter 2009, summer 2009 and winter 2010). Despite several-fold higher concentrations of air pollutants in the Ostrava region, the levels of stable aberrations (genomic frequency of translocations per 100 cells, percentage of aberrant cells and frequency of acentric fragments) were mostly comparable in both locations. The frequency of unstable aberrations measured as the number of micronuclei was unexpectedly significantly lower in the Ostrava region subjects in both seasons of 2009. Urinary excretion of 8-oxodG did not differ between locations in either season. Lipid peroxidation measured as levels of 15-F2t-IsoP in blood plasma was elevated in the Ostrava subjects sampled in 2009. Protein oxidation was higher in Prague samples collected in summer 2009. Multivariate analyses conducted separately in subjects from Prague and Ostrava showed a negative association between the frequency of micronuclei and concentrations of benzo[a]pyrene and PM2.5 in both regions. A positive relationship was observed between lipid peroxidation and air pollution; protein oxidation seems to be positively affected by PM2.5 in both regions. © The Author 2012. Published by Oxford University Press on behalf of the UK Environmental Mutagen Society. All rights reserved.


PubMed | University of South Bohemia, 1Hirosaki University, Institute of Plant Molecular Biology, Hirosaki University and 2 more.
Type: | Journal: The Journal of general virology | Year: 2016

Apple fruit crinkle viroid (AFCVd) is a tentative member of the genus Apscaviroid, family Pospiviroidae. AFCVd has a narrow host range and is known to infect apple, hop, and persimmon as natural hosts. In this study, tomato, cucumber, and wild hop have been identified as new experimental herbaceous hosts Foliar symptoms were very mild or virtually undetectable, but fruits of infected tomato were small, cracked, and distorted. These symptoms resemble those observed on some AFCVd-sensitive apple cultivars. After transfer to tomato, cucumber, and wild hop, sequence changes were detected in a natural AFCVd isolate from hop, and major variants in tomato, cucumber, and wild hop differed in 10, 8, or 2 nucleotides respectively from the predominant one in the inoculum. The major variants in tomato and cucumber were almost identical, and the one in wild hop was very similar to the one in cultivated hop. Detailed analyses of the host-dependent sequence changes that appear in a naturally-occuring AFCVd isolate from hop after transfer to tomato using small RNA deep sequence data and infectivity studies with dimeric RNA transcripts followed by progeny analysis indicate that the major AFCVd variant in tomato emerged by selection of a minor variant present in the inoculum (i.e., hop) followed by 1-2 host-dependent de novo mutations. Comparison of the secondary structures of major variants in hop, tomato, and persimmon after transfer to tomato suggested that maintenance of stem-loop structures in the left-hand half of the molecule is critical for infection.


PubMed | Institute of Plant Molecular Biology, Heinrich Heine University Düsseldorf and U.S. Department of Agriculture
Type: | Journal: RNA biology | Year: 2016

Viroids are non-coding single-stranded circular RNA molecules that replicate autonomously in infected host plants causing mild to lethal symptoms. Their genomes contain about 250-400 nucleotides, depending on viroid species. Members of the family Pospiviriodeae, like the Potato spindle tuber viroid (PSTVd), replicate via an asymmetric rolling-circle mechanism using the host DNA-dependent RNA-PolymeraseII in the nucleus, while members of Avsunviroidae are replicated in a symmetric rolling-circle mechanism probably by the nuclear-encoded polymerase in chloroplasts. Viroids induce the production of viroid-specific small RNAs (vsRNA) that can direct (post-)transcriptional gene silencing against host transcripts or genomic sequences. Here, we used deep-sequencing to analyze vsRNAs from plants infected with different PSTVd variants to elucidate the PSTVd quasipecies evolved during infection. We recovered several novel as well as previously known PSTVd variants that were obviously competent in replication and identified common strand-specific mutations. The calculated mean error rate per nucleotide position was less than 5 10


PubMed | Institute of Plant Molecular Biology
Type: Journal Article | Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis | Year: 2014

The complete mitochondrial genome of the ascomycete fungus Phomopsis longicolla was sequenced using Illumina HiSeq platform. It consists of 53,439bp with high (65.6%) A+T content and includes 14 conserved protein subunits of the mitochondrial oxidative phosphorylation system, two ribosomal RNAs and 25 tRNA genes. To our knowledge, this is the first complete mitochondrial genome of the Diaporthales member.

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