Differential abundance of predicted CDS found in the 501 selected sequences and the total predicted <i>P. infestans</i> CDS, based on KOG functional categories.

<p>The differential abundance (<i>y</i> axis) of predicted CDS to assignable categories (<i>x</i> axis) is shown. KOG categories are as follows (from: <a href="http://www.ncbi.nlm.nih.gov/COG/" target="_blank">http://www.ncbi.nlm.nih.gov/COG/</a>): J, Translation; A, RNA processing and modification; K, Transcription; L, Replication, recombination and repair; B, Chromatin structure and dynamics; D, Cell cycle control, cell division, chromosome partitioning; Y, Nuclear structure; V, Defense mechanisms; T, Signal transduction mechanisms; M, Cell wall/membrane/envelope biogenesis; N, Cell motility; Z, Cytoskeleton; W, Extracellular structures; U, Intracellular trafficking, secretion, and vesicular transport; O, Posttranslational modification, protein turnover, chaperones; C, Energy production and conversion; G, Carbohydrate transport and metabolism; E, Amino acid transport and metabolism; F Nucleotide transport and metabolism; H, Coenzyme transport and metabolism; I, Lipid transport and metabolism; P, Inorganic ion transport and metabolism; Q, Secondary metabolites biosynthesis, transport and catabolism; R, General function prediction only; S Function unknown.</p

Distribution of ESTs within contigs after clustering (using CAP3) the 22,795 sequences downloaded from GenBank.

<p>Distribution of ESTs within contigs after clustering (using CAP3) the 22,795 sequences downloaded from GenBank.</p

Different criteria used to separate the <i>P. infestans</i> sequences from host sequences produces results that differ notably among them.

<p>12,900 unitigs containing host and pathogen sequences were used to test different approaches to separate both types of sequences. The scheme represents the number of sequences obtained using GC content and a BLAST cut-off e-value combined with different ratio cut-offs: ((Alignment length * %ID)/Unitig length). (a) GC >52%; (b) e-value cut-off of 10⁻¹⁵ (c) e-value cut-off of 10^-15and ratio >50%; (d) e-value cut-off of 10⁻¹⁵ and ratio >60%; (e) e-value cut-off of 10⁻¹⁵ and ratio >70%; (f) e-value cut-off of 10⁻¹⁵ and ratio >80%; (g) e-value cut-off of 10⁻¹⁵ and ratio >90%.</p

Summary of resulting candidate <i>Phytophthora infestans</i> sequences after separating 12,900 unitigs containing pathogen and host sequences using different selection criteria.

<p>The sequences identified as belonging to <i>P. infestans</i> but also having a hit against potato and tomato ESTs or any Solanaceae are shown to the right.</p>a<p>((Alignment length * %ID)/Unitig length).</p

Number of ESTs falling into different GC content ranges among a total of 403 ESTs that had a hit against the <i>P. infestans</i> genes.

<p>Number of ESTs falling into different GC content ranges among a total of 403 ESTs that had a hit against the <i>P. infestans</i> genes.</p

GenBank accession numbers and descriptions of the sequences used for this study.

<p>GenBank accession numbers and descriptions of the sequences used for this study.</p

Main workflow of analysis followed in this study.

<p>Main workflow of analysis followed in this study.</p

Comparison of the genomic structure of <i>Xam</i> CIO151 with that of closely related members from the genus <i>Xanthomonas</i>.

<p>Scaffolds of <i>Xam</i> CIO151 were ordered based on the alignment with the complete genome sequence of <i>X. euvesicatoria</i>, <b><i>Xeu</i></b>, and then genome comparisons were performed using MUMmer (<b>A</b>). Alignment of ordered scaffolds of <i>Xam</i> CIO151 with the complete genome sequences of <i>X. axonopodis</i> pv. citri str. 306, <b><i>Xac</i></b> (<b>B</b>); <i>X. campestris</i> pv. campestris str. 8004, <b><i>Xcc</i></b> (<b>C</b>); <i>X. albilineans</i>, <b><i>Xal</i></b> (<b>D</b>); and <i>Xanthomonas oryzae</i> pv. <i>oryzae</i> PXO99^A, <b><i>Xoo</i></b> (<b>E</b>) chromosomes. Scaffolds classified as parts of the chromosome of <i>Xam</i> CIO151 are shown in the y-axis. Red dots represent conserved segments while blue dots represent inverted regions.</p

Characteristics of VNTR loci for 65 <i>Xam</i> draft genome sequences.

1<p>: Repeat unit sizes are given in bp.</p>2 and 3<p>: Minimal and maximal numbers of repeats (only those in integer numbers) are given.</p>4<p>Number of samples with a complete VNTR locus in the draft genome sequence is given.</p>5<p>Number of different VNTR patterns (haplotypes) is given.</p>6<p>Hunter-Gaston discriminatory index (HGDI) scores are given.</p

Putative pathogenicity elements identified in the genome of <i>Xam</i> CIO151.

1<p>Number indicates CDS identified by key word searches in iANT.</p