Universal primers for plasmid detection and method for their relative quantification in phytoplasma-infected plants

Abstract Rep gene occurring in the majority of plasmids associated with phytoplasmas was selected as a target for real-time PCR together with single-copy Tuf gene from the phytoplasma genome. Rep-specific primers amplified products from host plants infected with phytoplasmas of groups 16SrI, -II, -III, -V, -X, and -XII. Relative concentrations of plasmids ranged depending on strain from 1-2 copies to several hundred copies per each phytoplasma studied. Primers targeting the rep gene are proposed for direct PCR detection of phytoplasma plasmids from experimental periwinkle host as well as from natural plant hosts

Discriminating 16Sr groups of phytoplasmas by an oligonucleotide microarray targeting 16S-23S spacer region

Abstract A microarray detecting phytoplasma 16Sr groups -I, -II, -III, -V, -VI, -X and -XII was developed based on probes targeting 16S-23S spacer region. Despite that it is considered as more suitable than 16S rDNA for the fine differentiation of phytoplasmas, the microarray did not demonstrate discriminatory potential higher than the only phytoplasma microarray published so far based on 16S rDNA. Nevertheless the method used was cheaper and faster bringing the microarray towards routine analysis

Mixed Infection of Blackcurrant with a Novel Cytorhabdovirus and Black Currant-Associated Nucleorhabdovirus

A virome screen was performed on a new breeding line, KB1, of blackcurrant. Rhabdovirus-like particles were observed by electron microscopy in ultrathin sections of flower stalks, and the complete genome sequence of a novel virus, provisionally named blackcurrant rhabdovirus 2 (BCRV2), was determined and verified using high-throughput sequencing. The genomic organization of BCRV2 was characteristic of cytorhabdoviruses (family Rhabdoviridae) and included seven genes: 3′-N-P′-P-P3-M-G-L-5′. BLASTP analysis revealed that the putative L protein had the highest amino acid sequence identity (75%) with strawberry virus 2. BCRV2 was detected in Cryptomyzus galeopsidis, but efficient transmission by this aphid was not confirmed. Of note, we observed coinfection of the KB1 line with blackcurrant-associated rhabdovirus (BCaRV) by RT-PCR. This is likely the first evidence of the presence of a cyto- and a nucleorhabdovirus in a single host

The alkalophilic fungus <i>Sodiomyces alkalinus</i> hosts beta- and gammapartitiviruses together with a new fusarivirus - Fig 3

<p>Phylogeny of the <i>Sodiomyces</i> sp. based on the ITS rDNA sequences (A), with the origin location of dsRNA-containing strains and phylogeny of the SaFV1 isolates based on the whole genome sequence (B).</p

Amino acid sequence identities (in %) of ORF1 (under the diagonal) and ORF2 (above the diagonal) between the SaFV1-containing isolates of <i>S</i>. <i>alkalinus</i>.

<p>Amino acid sequence identities (in %) of ORF1 (under the diagonal) and ORF2 (above the diagonal) between the SaFV1-containing isolates of <i>S</i>. <i>alkalinus</i>.</p

Phylogeny of SaPV1 and CtParV1-SAL in relation to other partitiviruses.

<p>ML phylogenetic tree generated from the CP amino acid sequence with 1000 bootstrap replicates.</p

Potential secondary structures of 3´end, and ORF1-ORF2 intergenic region of Sodiomyces alkalinus fusarivirus 1 (SaFV1).

<p>a) Potential secondary structures of 3´end (from 6183–6239 nucleotides) and b) ORF1-ORF2 intergenic region (from 4590 to 4659 nucleotides). The ΔG values (kcal/mol) were calculated using RNAfold program. UAA stop codons and AUG codon are marked.</p

Comparative codon-usage analysis of viruses from <i>S</i>. <i>alkalinus</i>.

<p>Frequency of [XYG + XYC] of <i>S</i>. <i>alkalinus</i> was computed from codon frequencies of RPB2 and TEF1-alpha protein coding genes sequenced previously [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0187799#pone.0187799.ref001" target="_blank">1</a>], data for <i>Colletotrichum</i> sp. were from <a href="http://www.kazusa.or.jp/" target="_blank">http://www.kazusa.or.jp</a>.</p