Journal: The botulinum journal

Article Title: Exploring genomic diversity in Clostridium botulinum using DNA microarrays

doi: 10.1504/tbj.2012.050195

Figure Lengend Snippet: Scheme used to select probes for the Group I subtyping microarray Notes: A total of 225 probes were selected. 146 probes corresponding to strain variable regions of the ATCC 3502 genome sequence were selected based on CGH analysis using Group I types A, B, and F test strains. In silico analysis was used to select the remaining probes representing genes not present in ATCC 3502, specific for either OkraB or LanglelandF strains, or other specific genes of interest.

Article Snippet: High density CGH microarrays Our laboratory developed a comparative genomic hybridisation (CGH) microarray featuring a total of 384,771 overlapping probes (~50–70 bp) representing the ATCC 3502 type A genome sequence in order to evaluate the level of genomic diversity among C. botulinum strains ( Raphael et al., 2008 ).

Techniques: Microarray, Sequencing, In Silico

Journal: The botulinum journal

Article Title: Exploring genomic diversity in Clostridium botulinum using DNA microarrays

doi: 10.1504/tbj.2012.050195

Figure Lengend Snippet: Matrix of correlation coefficients of the hybridisation results for bont/F5 encoding strains using the Group I subtyping microarray (see online version for colours)

Article Snippet: High density CGH microarrays Our laboratory developed a comparative genomic hybridisation (CGH) microarray featuring a total of 384,771 overlapping probes (~50–70 bp) representing the ATCC 3502 type A genome sequence in order to evaluate the level of genomic diversity among C. botulinum strains ( Raphael et al., 2008 ).

Techniques: Hybridization, Microarray

Journal: The botulinum journal

Article Title: Exploring genomic diversity in Clostridium botulinum using DNA microarrays

doi: 10.1504/tbj.2012.050195

Figure Lengend Snippet: Hybridisation of the Group II subtyping microarray by type E (n = 15), type B (n = 4) and type F (n = 3) C. botulinum strains Notes: Shown is the average % of probes hybridised (i.e., where log10 of the ratio of probe fluorescent compared to background ≥ 1.0) for each toxin serotype indicated. Error bars depict standard deviations.

Article Snippet: High density CGH microarrays Our laboratory developed a comparative genomic hybridisation (CGH) microarray featuring a total of 384,771 overlapping probes (~50–70 bp) representing the ATCC 3502 type A genome sequence in order to evaluate the level of genomic diversity among C. botulinum strains ( Raphael et al., 2008 ).

Techniques: Hybridization, Microarray

Journal: PLoS ONE

Article Title: Comparative Genomics Reveals Insight into Virulence Strategies of Plant Pathogenic Oomycetes

doi: 10.1371/journal.pone.0075072

Figure Lengend Snippet: Species name, accession numbers, host/substrate and geographical origin of the Pythium strains sequenced in this study.

Article Snippet: The sequences of six Pythium genomes ( Py. aphanidermatum (DAOM BR444 = CBS 132490), Py. arrhenomanes (ATCC 12531 = CBS 324.62), Py. irregulare (DAOM BR486 = CBS 250.28), Py. iwayamai (DAOM 242034 = CBS 132417), Py. ultimum var. sporangiiferum (DAOM BR650 = CBS 219.65), and Py. vexans (DAOM BR484 = CBS 119.80); ) that provide a broad representation of the genus Pythium ( ) were generated using pyrosequencing with the Roche 454 or the Illumina Genome Analyzer (GA) II sequencing-by-synthesis platform.

Techniques:

Journal: PLoS ONE

Article Title: Comparative Genomics Reveals Insight into Virulence Strategies of Plant Pathogenic Oomycetes

doi: 10.1371/journal.pone.0075072

Figure Lengend Snippet: The predicted proteomes of the seven Pythium species were clustered using OrthoMCL to identify orthologs and close paralogs. The number of gene families shared between the species and total number of clustered genes (numbers in parentheses) are indicated. The numbers outside the Venn diagram show the total number of orthologous clusters and number of genes (in parentheses) within those clusters for each species. Pap, Pythium aphanidermatum; Par, Pythium arrhenomanes ; Pir, Pythium irregulare ; Piw, Pythium iwayamai ; Puls, Pythium ultimum var. sporangiiferum ; Pult, Pythium ultimum var. ultimum ; Pve, Pythium vexans.

Article Snippet: The sequences of six Pythium genomes ( Py. aphanidermatum (DAOM BR444 = CBS 132490), Py. arrhenomanes (ATCC 12531 = CBS 324.62), Py. irregulare (DAOM BR486 = CBS 250.28), Py. iwayamai (DAOM 242034 = CBS 132417), Py. ultimum var. sporangiiferum (DAOM BR650 = CBS 219.65), and Py. vexans (DAOM BR484 = CBS 119.80); ) that provide a broad representation of the genus Pythium ( ) were generated using pyrosequencing with the Roche 454 or the Illumina Genome Analyzer (GA) II sequencing-by-synthesis platform.

Techniques:

Journal: PLoS ONE

Article Title: Comparative Genomics Reveals Insight into Virulence Strategies of Plant Pathogenic Oomycetes

doi: 10.1371/journal.pone.0075072

Figure Lengend Snippet: The CAZymes coding genes were annotated using the CAZymes Analysis Toolkit- CAT according to the CAZy database in combination with protein family domain analyses. Gene families absent in at least 2 species are underlined. Comparison of total CAZymes from different classes is listed in . CE, carbohydrate esterase; GH, glycoside hydrolase; GT, glycosyl transferase; PL, polysaccharide lyase; Pap, Pythium aphanidermatum ; Par, Pythium arrhenomanes ; Pir, Pythium irregulare ; Piw, Pythium iwayamai ; Pult, Pythium ultimum var. ultimum ; Puls, Pythium ultimum var. sporangiiferum ; Pve, Pythium vexans ; Phin, Phytophthora infestans ; Phrm, Phytophthora ramorum ; Phsj, Phytophthora sojae ; Hpa, Hyaloperonospora arabidopsidis ; Thps, Thalassiosira pseudonana ; Phtr, Phaeodactylum tricornutum .

Article Snippet: The sequences of six Pythium genomes ( Py. aphanidermatum (DAOM BR444 = CBS 132490), Py. arrhenomanes (ATCC 12531 = CBS 324.62), Py. irregulare (DAOM BR486 = CBS 250.28), Py. iwayamai (DAOM 242034 = CBS 132417), Py. ultimum var. sporangiiferum (DAOM BR650 = CBS 219.65), and Py. vexans (DAOM BR484 = CBS 119.80); ) that provide a broad representation of the genus Pythium ( ) were generated using pyrosequencing with the Roche 454 or the Illumina Genome Analyzer (GA) II sequencing-by-synthesis platform.

Techniques: Comparison

Journal: PLoS ONE

Article Title: Comparative Genomics Reveals Insight into Virulence Strategies of Plant Pathogenic Oomycetes

doi: 10.1371/journal.pone.0075072

Figure Lengend Snippet: (A) The typical architecture of a YxSL[RK] effector candidate inferred from 141 sequences from seven Pythium species, Phytophthora infestans , and Phytophthora sojae . The consensus sequence pattern of the YxSL[RK] motif was calculated using WebLogo . The bigger the letter, the more conserved the amino acid site. Please note that the numbers in the sequence logo refer to the corresponding positions in the alignment and thus differ from the average position of the motifs. (B) The YxSL[RK] motif distribution in the proteomes of Pythium species, Phytophthora infestans and Phytophthora sojae is shown. The YxSL[RK] sequence is over-represented in the secretome of Pythium and Phytophthora species relative to the non-secreted proteome ( P ≤0.05). The YxSL[RK] motifs were counted only if they were within the first 30 to 150 residues from the signal peptide. The frequency was calculated as percentage of either all secreted proteins or all non-secreted proteins. Pult, Pythium ultimum var. ultimum ; Puls, Pythium ultimum var. sporangiiferum ; Pir, Pythium irregulare ; Piw, Pythium iwayamai ; Par, Pythium arrhenomanes ; Pap, Pythium aphanidermatum ; Pve, Pythium vexans ; Phin, Phytophthora infestans ; Phrm, Phytophthora ramorum ; Phsj, Phytophthora sojae ; Hpa, Hyaloperonospora arabidopsidis . (C) The typical architecture of an LxLYLAR/K effector motif inferred from 129 sequences from 7 Pythium species. The consensus sequence pattern of the LxLYLAR/K motif was calculated using WebLogo . The bigger the letter, the more conserved the amino acid site. Please note that the numbers in the sequence logo are referring to the corresponding positions in the alignment and thus differ from the average position of the motifs. (D) Number of CRN effector proteins in oomycetes. The number of candidate CRN effectors estimated by Hidden Markov Model (HMM) searches in combination with two other computational methods is shown. The number of CRN effectors from Pythium ultimum var. ultimum , Phytophthora species and H. arabidopsidis were taken from published genome datasets , , , . Pult, Pythium ultimum var. ultimum ; Puls, Pythium ultimum var. sporangiiferum ; Pir, Pythium irregulare ; Piw, Pythium iwayamai ; Par, Pythium arrhenomanes ; Pap, Pythium aphanidermatum ; Pve, Pythium vexans ; Phin, Phytophthora infestans ; Phrm, Phytophthora ramorum ; Phsj, Phytophthora sojae ; Hpa, Hyaloperonospora arabidopsidis .

Article Snippet: The sequences of six Pythium genomes ( Py. aphanidermatum (DAOM BR444 = CBS 132490), Py. arrhenomanes (ATCC 12531 = CBS 324.62), Py. irregulare (DAOM BR486 = CBS 250.28), Py. iwayamai (DAOM 242034 = CBS 132417), Py. ultimum var. sporangiiferum (DAOM BR650 = CBS 219.65), and Py. vexans (DAOM BR484 = CBS 119.80); ) that provide a broad representation of the genus Pythium ( ) were generated using pyrosequencing with the Roche 454 or the Illumina Genome Analyzer (GA) II sequencing-by-synthesis platform.

Techniques: Sequencing

Journal: PLoS ONE

Article Title: Comparative Genomics Reveals Insight into Virulence Strategies of Plant Pathogenic Oomycetes

doi: 10.1371/journal.pone.0075072

Figure Lengend Snippet: The circle is a graphical representation of the selected regions from Pythium arrhenomanes (contigs 8, 17, 26, 41, 68, 131, 170, 285, 707) Pythium irregulare (contigs 28, 92, 103, 106, 119, 123, 129, 132, 140, 163, 195, 226, 372, 396), Pythium aphanidermatum (scaffolds 4, 6, 23, 80, 88, 96, 115, 150, 327), Pythium iwayamai (contigs 18, 28, 29, 61, 235), Pythium ultimum var. sporangiiferum (contigs 4, 6, 34, 106, 121, 134, 150, 173, 181, 222, 231, 257, 319, 404, 437, 458, 533, 726), Pythium vexans (contigs 9, 31,42, 94, 151, 160, 209, 220, 347), Phytophthora infestans (supercontig 1.2), Hyaloperonospora arabidopsidis (scaffolds 5, 6, 7, 8, 9) and Thalassiosira pseudonana (chromosome 3). Numbers along each ideogram are sequence lengths in kbp. Syntenic regions were identified through reciprocal best matches between gene models and block identification using MCscan . Each line radiating from Py. ultimum var. ultimum (scf1117875581354) links a syntenic gene pair. Each species is represented by a genus-species abbreviation and colored as Pythium ultimum var. ultimum (Pult) in blue, Pythium arrhenomanes (Par) in orange, Pythium irregulare (Pir) in yellow, Pythium aphanidermatum (Pap) in dark brown, Pythium iwayamai (Piw) in green, Pythium ultimum var. sporangiiferum (Puls) in dark red, Pythium vexans (Pve) in purple, Phytophthora infestans (Phin) in brick red, Hyaloperonospora arabidopsidis (Hpa) in olive green, and Thalassiosira pseudonana (Thaps) in light purple.

Article Snippet: The sequences of six Pythium genomes ( Py. aphanidermatum (DAOM BR444 = CBS 132490), Py. arrhenomanes (ATCC 12531 = CBS 324.62), Py. irregulare (DAOM BR486 = CBS 250.28), Py. iwayamai (DAOM 242034 = CBS 132417), Py. ultimum var. sporangiiferum (DAOM BR650 = CBS 219.65), and Py. vexans (DAOM BR484 = CBS 119.80); ) that provide a broad representation of the genus Pythium ( ) were generated using pyrosequencing with the Roche 454 or the Illumina Genome Analyzer (GA) II sequencing-by-synthesis platform.

Techniques: Sequencing, Blocking Assay