Phylogenetic tree constructed by parsimony analyses of deduced malate dehydrogenase peptide sequences of available phytoplasmas, <i>Clostridium botulinum</i> strains ATCC3502 and ATCC19397, <i>Bacillus subtilis</i> subsp. <i>subtilis</i>, and <i>Bacillus cereus</i> employing <i>Escherichia coli</i> strain K12 as outgroup.

<p>Accession numbers are given in parentheses. Numbers on the branches are bootstrap values obtained for 1,000 replicates (only values above 60% are shown). The tree is drawn to scale, with branch lengths calculated using the average pathway method, and are in the units of the number of changes over the whole sequence. The scale bar represents 20 amino acid substitutions.</p

COG categories assigned to expressed gene products identified by RNA-Seq and/or proteome analysis (orange) versus the deduced protein content of '<i>Ca</i>. P. mali' strain AT (green).

<p>Values indicate total number reached in each category.</p

Experimental hosts and genes used in qRT-PCR experiments with their correlating average (Ø) C_T and ΔC_T values after normalization (short amplicons).

<p>Experimental hosts and genes used in qRT-PCR experiments with their correlating average (Ø) C_T and ΔC_T values after normalization (short amplicons).</p

Phylogenetic tree constructed by parsimony analyses of the deduced peptide sequences of acetate kinase of available <i>Mollicutes</i> in HAMAP database, <i>Spiroplasma citri</i>, <i>Clostridium botulinum</i>, <i>Erysipelothrix rhusiopathiae</i>, <i>Bacillus subtilis</i> subsp.

<p><i>subtilis</i>, <i>Lactobacillus plantarum</i><b>, </b><i>Enterococcus faecalis</i><b>, </b><i>Streptococcus pneumonia</i><b>, </b><b>and </b><i>Lactococcus lactis</i><b> subsp. </b><i>lactis</i><b> employing </b><i>Escherichia coli</i><b> and </b><i>Salmonella typhimurium</i><b> as outgroup.</b> One of the two most parsimonious trees is shown. Accession numbers are given in parentheses. Numbers on the branches are bootstrap values obtained for 1,000 replicates (only values above 60% are shown). The tree is drawn to scale, with branch lengths calculated using the average pathway method, and are in the units of the number of changes over the whole sequence. The scale bar represents 50 amino acid substitutions.</p

Genome circle of ‘<i>Ca</i>. P. mali’ strain AT highlights gene expression.

<p>Circular patterns (from outside to inside): 1 (outer circle), scale in base pairs of the chromosome; 2 (black), predicted protein coding sequences; 3, tRNAs (grey) & rRNAs (green); 4 (dark blue), identified proteins of ‘<i>Ca</i>. P. mali’; 5 (red), expressed genes of ‘<i>Ca</i>. P. mali’ identified by RNA-Seq; 6 (dark green), expressed genes (proteome and transcriptome) without similarity to NRPROT entries excluding the <i>Acholeplasmataceae</i> entries; 7 (magenta), assigned proteins of the mulberry dwarf phytoplasma; and 8 (olive and pink), G + C skew. Expressed genes located in the terminal ends (identical in sequence) were marked twice.</p

Experimental hosts and genes used in qRT-PCR experiments with their correlating average (Ø) C_T and ΔC_T values after normalization (long amplicons).

<p>Experimental hosts and genes used in qRT-PCR experiments with their correlating average (Ø) C_T and ΔC_T values after normalization (long amplicons).</p

RT-PCR confirming the expression of <i>pgi</i>, <i>pfkA</i>, <i>fba</i>, <i>tpiA</i>, <i>pduL</i>, <i>ackA</i>, <i>degV</i> and SAP11-like gene.

<p>RNA was obtained from <i>Nicotiana occidentalis</i>, <i>Malus domestica</i>, <i>Catharanthus roseus</i> infected by ‘<i>Ca</i>. P. mali’ strain AT. The RT-PCR products were separated on a 1.4% TAE agarose gel. Lane number nine was used for negative control applying water as template (example SAP11-like gene). The product size of around 200 bp was estimated by the 50 bp DNA ladder (Lifetechnologies) loaded on first and last lane of each gel.</p

Primer pairs used in (q)RT-PCR reactions.

<p>Primer pairs used in (q)RT-PCR reactions.</p