putative pathogenicity related proteins Search Results


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  • 99
    ATCC t denticola atcc 35405 virulence related fhbb
    Circular representation of the T. pedis T A4 genome and complete genome alignment with T. <t>denticola</t> . (A.) Circular representation of the T. pedis T A4 genome. The CDSs are shown in violet where the outer circle represents predictions on the plus strand and the second circle those on the minus strand. CDSs with a best BLASTP hit in T. denticola <t>ATCC</t> 35405 are colored red and shown in the third circle. The fourth circle represents genes with best BLASTP hits in T. brennaborense (black), F. nucleatum (green), F. alocis (blue) and T. succinifaciens (grey). G+C skew is drawn in the inner circle. (B.) Complete genome alignment between T. pedis T A4 and T. denticola ATCC 35405. Dots represent maximum unique matches (MUMs) between the genomes. MUMs oriented in the same direction are depicted as red dots and reverse complemented MUMs are depicted as blue dots.
    T Denticola Atcc 35405 Virulence Related Fhbb, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    ATCC mce family protein mce6a
    Circular representation of the T. pedis T A4 genome and complete genome alignment with T. <t>denticola</t> . (A.) Circular representation of the T. pedis T A4 genome. The CDSs are shown in violet where the outer circle represents predictions on the plus strand and the second circle those on the minus strand. CDSs with a best BLASTP hit in T. denticola <t>ATCC</t> 35405 are colored red and shown in the third circle. The fourth circle represents genes with best BLASTP hits in T. brennaborense (black), F. nucleatum (green), F. alocis (blue) and T. succinifaciens (grey). G+C skew is drawn in the inner circle. (B.) Complete genome alignment between T. pedis T A4 and T. denticola ATCC 35405. Dots represent maximum unique matches (MUMs) between the genomes. MUMs oriented in the same direction are depicted as red dots and reverse complemented MUMs are depicted as blue dots.
    Mce Family Protein Mce6a, supplied by ATCC, used in various techniques. Bioz Stars score: 95/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    SPSS Inc caenopores
    Circular representation of the T. pedis T A4 genome and complete genome alignment with T. <t>denticola</t> . (A.) Circular representation of the T. pedis T A4 genome. The CDSs are shown in violet where the outer circle represents predictions on the plus strand and the second circle those on the minus strand. CDSs with a best BLASTP hit in T. denticola <t>ATCC</t> 35405 are colored red and shown in the third circle. The fourth circle represents genes with best BLASTP hits in T. brennaborense (black), F. nucleatum (green), F. alocis (blue) and T. succinifaciens (grey). G+C skew is drawn in the inner circle. (B.) Complete genome alignment between T. pedis T A4 and T. denticola ATCC 35405. Dots represent maximum unique matches (MUMs) between the genomes. MUMs oriented in the same direction are depicted as red dots and reverse complemented MUMs are depicted as blue dots.
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    88
    Miraculins putative proteinase inhibitor miraculin
    Circular representation of the T. pedis T A4 genome and complete genome alignment with T. <t>denticola</t> . (A.) Circular representation of the T. pedis T A4 genome. The CDSs are shown in violet where the outer circle represents predictions on the plus strand and the second circle those on the minus strand. CDSs with a best BLASTP hit in T. denticola <t>ATCC</t> 35405 are colored red and shown in the third circle. The fourth circle represents genes with best BLASTP hits in T. brennaborense (black), F. nucleatum (green), F. alocis (blue) and T. succinifaciens (grey). G+C skew is drawn in the inner circle. (B.) Complete genome alignment between T. pedis T A4 and T. denticola ATCC 35405. Dots represent maximum unique matches (MUMs) between the genomes. MUMs oriented in the same direction are depicted as red dots and reverse complemented MUMs are depicted as blue dots.
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    90
    Medicago faba bean
    Circular representation of the T. pedis T A4 genome and complete genome alignment with T. <t>denticola</t> . (A.) Circular representation of the T. pedis T A4 genome. The CDSs are shown in violet where the outer circle represents predictions on the plus strand and the second circle those on the minus strand. CDSs with a best BLASTP hit in T. denticola <t>ATCC</t> 35405 are colored red and shown in the third circle. The fourth circle represents genes with best BLASTP hits in T. brennaborense (black), F. nucleatum (green), F. alocis (blue) and T. succinifaciens (grey). G+C skew is drawn in the inner circle. (B.) Complete genome alignment between T. pedis T A4 and T. denticola ATCC 35405. Dots represent maximum unique matches (MUMs) between the genomes. MUMs oriented in the same direction are depicted as red dots and reverse complemented MUMs are depicted as blue dots.
    Faba Bean, supplied by Medicago, used in various techniques. Bioz Stars score: 90/100, based on 108 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    ATCC b multivorans atcc 17616
    Circular representation of the T. pedis T A4 genome and complete genome alignment with T. <t>denticola</t> . (A.) Circular representation of the T. pedis T A4 genome. The CDSs are shown in violet where the outer circle represents predictions on the plus strand and the second circle those on the minus strand. CDSs with a best BLASTP hit in T. denticola <t>ATCC</t> 35405 are colored red and shown in the third circle. The fourth circle represents genes with best BLASTP hits in T. brennaborense (black), F. nucleatum (green), F. alocis (blue) and T. succinifaciens (grey). G+C skew is drawn in the inner circle. (B.) Complete genome alignment between T. pedis T A4 and T. denticola ATCC 35405. Dots represent maximum unique matches (MUMs) between the genomes. MUMs oriented in the same direction are depicted as red dots and reverse complemented MUMs are depicted as blue dots.
    B Multivorans Atcc 17616, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 459 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    ATCC c violaceum atcc 12472
    Circular representation of the T. pedis T A4 genome and complete genome alignment with T. <t>denticola</t> . (A.) Circular representation of the T. pedis T A4 genome. The CDSs are shown in violet where the outer circle represents predictions on the plus strand and the second circle those on the minus strand. CDSs with a best BLASTP hit in T. denticola <t>ATCC</t> 35405 are colored red and shown in the third circle. The fourth circle represents genes with best BLASTP hits in T. brennaborense (black), F. nucleatum (green), F. alocis (blue) and T. succinifaciens (grey). G+C skew is drawn in the inner circle. (B.) Complete genome alignment between T. pedis T A4 and T. denticola ATCC 35405. Dots represent maximum unique matches (MUMs) between the genomes. MUMs oriented in the same direction are depicted as red dots and reverse complemented MUMs are depicted as blue dots.
    C Violaceum Atcc 12472, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 693 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    ATCC b thetaiotaomicron vpi 5482
    Selection of B. <t>thetaiotaomicron</t> <t>VPI</t> 5482 mutants with increased biofilm capacities. (A) Schematic representation of the positive-selection strategy used to identify transposon mutants with increased biofilm production. BF, biofilm formation. (B) Biofilm biomass formation on the internal spatulas of continuous-flow biofilm microfermentors after 24 h. (Left) Wild-type B. thetaiotaomicron VPI 5482; (middle and right) microfermentors and spatulas inoculated with a culture enriched for biofilm production after 4 cycles of positive selection. (C) Comparison of the biofilm formation capacities of WT B. thetaiotaomicron and eight identified mutants with an insertion in the BT3147 gene. (Bottom) Crystal violet staining in 96-well microtiter plates; (top) corresponding biomass quantification after resuspension in an acetone-ethanol mix and absorbance measured at 575 nm. Biofilm formation capacities of the WT (VPI 5482) have been set to 100%. Error bars indicate standard deviations from 3 technical replicates. *, P
    B Thetaiotaomicron Vpi 5482, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 178 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    84
    Millipore molecules mrna translation inhibitors
    Selection of B. <t>thetaiotaomicron</t> <t>VPI</t> 5482 mutants with increased biofilm capacities. (A) Schematic representation of the positive-selection strategy used to identify transposon mutants with increased biofilm production. BF, biofilm formation. (B) Biofilm biomass formation on the internal spatulas of continuous-flow biofilm microfermentors after 24 h. (Left) Wild-type B. thetaiotaomicron VPI 5482; (middle and right) microfermentors and spatulas inoculated with a culture enriched for biofilm production after 4 cycles of positive selection. (C) Comparison of the biofilm formation capacities of WT B. thetaiotaomicron and eight identified mutants with an insertion in the BT3147 gene. (Bottom) Crystal violet staining in 96-well microtiter plates; (top) corresponding biomass quantification after resuspension in an acetone-ethanol mix and absorbance measured at 575 nm. Biofilm formation capacities of the WT (VPI 5482) have been set to 100%. Error bars indicate standard deviations from 3 technical replicates. *, P
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    93
    ATCC cms atcc 33113 genome sequence
    Selection of B. <t>thetaiotaomicron</t> <t>VPI</t> 5482 mutants with increased biofilm capacities. (A) Schematic representation of the positive-selection strategy used to identify transposon mutants with increased biofilm production. BF, biofilm formation. (B) Biofilm biomass formation on the internal spatulas of continuous-flow biofilm microfermentors after 24 h. (Left) Wild-type B. thetaiotaomicron VPI 5482; (middle and right) microfermentors and spatulas inoculated with a culture enriched for biofilm production after 4 cycles of positive selection. (C) Comparison of the biofilm formation capacities of WT B. thetaiotaomicron and eight identified mutants with an insertion in the BT3147 gene. (Bottom) Crystal violet staining in 96-well microtiter plates; (top) corresponding biomass quantification after resuspension in an acetone-ethanol mix and absorbance measured at 575 nm. Biofilm formation capacities of the WT (VPI 5482) have been set to 100%. Error bars indicate standard deviations from 3 technical replicates. *, P
    Cms Atcc 33113 Genome Sequence, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 28 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    ATCC a baumannii acicu
    (A) Comparison of the numbers of transporters in A. <t>baumannii</t> <t>ACICU,</t> A. baumannii ATCC 17978, A. baylyi ADP1, E. coli MG1655, Mycobacterium tuberculosis H37Rv, P. aeruginosa PAO1, Pseudomonas fluorescens Pf-5, and S. aureus ). Only the main transporter classes are shown, with the number of transporters per Mb of genome given for each bacterial species. The color codes for the transporter classes are given on the right. (B) Comparison of the number of predicted drug efflux systems in A. baumannii ACICU and ATCC 17978, and A. baylyi ). Only family members that clearly clustered with known multidrug efflux transporters were counted. Genetically associated membrane fusion or outer membrane proteins were not considered. The color codes for the transporter classes are given on the right.
    A Baumannii Acicu, supplied by ATCC, used in various techniques. Bioz Stars score: 90/100, based on 119 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    ATCC l garvieae strains atcc 49156
    (A) Comparison of the numbers of transporters in A. <t>baumannii</t> <t>ACICU,</t> A. baumannii ATCC 17978, A. baylyi ADP1, E. coli MG1655, Mycobacterium tuberculosis H37Rv, P. aeruginosa PAO1, Pseudomonas fluorescens Pf-5, and S. aureus ). Only the main transporter classes are shown, with the number of transporters per Mb of genome given for each bacterial species. The color codes for the transporter classes are given on the right. (B) Comparison of the number of predicted drug efflux systems in A. baumannii ACICU and ATCC 17978, and A. baylyi ). Only family members that clearly clustered with known multidrug efflux transporters were counted. Genetically associated membrane fusion or outer membrane proteins were not considered. The color codes for the transporter classes are given on the right.
    L Garvieae Strains Atcc 49156, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Biotechnology Information metal transporters
    (A) Comparison of the numbers of transporters in A. <t>baumannii</t> <t>ACICU,</t> A. baumannii ATCC 17978, A. baylyi ADP1, E. coli MG1655, Mycobacterium tuberculosis H37Rv, P. aeruginosa PAO1, Pseudomonas fluorescens Pf-5, and S. aureus ). Only the main transporter classes are shown, with the number of transporters per Mb of genome given for each bacterial species. The color codes for the transporter classes are given on the right. (B) Comparison of the number of predicted drug efflux systems in A. baumannii ACICU and ATCC 17978, and A. baylyi ). Only family members that clearly clustered with known multidrug efflux transporters were counted. Genetically associated membrane fusion or outer membrane proteins were not considered. The color codes for the transporter classes are given on the right.
    Metal Transporters, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Syntaxin syntaxin pen1
    (A) Comparison of the numbers of transporters in A. <t>baumannii</t> <t>ACICU,</t> A. baumannii ATCC 17978, A. baylyi ADP1, E. coli MG1655, Mycobacterium tuberculosis H37Rv, P. aeruginosa PAO1, Pseudomonas fluorescens Pf-5, and S. aureus ). Only the main transporter classes are shown, with the number of transporters per Mb of genome given for each bacterial species. The color codes for the transporter classes are given on the right. (B) Comparison of the number of predicted drug efflux systems in A. baumannii ACICU and ATCC 17978, and A. baylyi ). Only family members that clearly clustered with known multidrug efflux transporters were counted. Genetically associated membrane fusion or outer membrane proteins were not considered. The color codes for the transporter classes are given on the right.
    Syntaxin Pen1, supplied by Syntaxin, used in various techniques. Bioz Stars score: 89/100, based on 82 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    ATCC a hydrophila strains
    Tli1Tli2 AH are the cognate immunity proteins to Tle1 AH . A. <t>hydrophila</t> NJ-35 and the ∆ clpV strain were used as the predator strains. ClpV , which encodes a putative ATPase required for T6SS function, was deleted to construct the T6SS − strain (∆ clpV ). The prey strains included the gene deletion mutant ∆ tle1 - tli1tli2 AH and its single or double restoration strains of immunity genes, they are, C∆ tli1 AH (∆ tle1 - tli1tli2 AH / pMMB- tli1 AH ), C∆ tli2 AH (∆ tle1 - tli1tli2 AH / pMMB- tli2 AH ) and C∆ tli1tli2 AH (∆ tle1 - tli1tli2 AH / pMMB- tli1tli2 AH ). The predator and prey strains were cultured at a ratio of 5:1, and surviving prey cells were serially diluted and determined on the LB plate containing antibiotics. Data are presented as the mean ± standard deviation (error bars) of three independent experiments. ## P
    A Hydrophila Strains, supplied by ATCC, used in various techniques. Bioz Stars score: 88/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    ATCC amoebophilus asiaticus
    Abundance of proteins with eukaryotic domains in proteomes of “ Ca . <t>Amoebophilus</t> <t>asiaticus”</t> and other bacteria. Proteins with eukaryotic domains are most abundant in intracellular bacteria. The percentage of proteins with eukaryotic domains
    Amoebophilus Asiaticus, supplied by ATCC, used in various techniques. Bioz Stars score: 90/100, based on 93 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    ATCC cea g2066
    Abundance of proteins with eukaryotic domains in proteomes of “ Ca . <t>Amoebophilus</t> <t>asiaticus”</t> and other bacteria. Proteins with eukaryotic domains are most abundant in intracellular bacteria. The percentage of proteins with eukaryotic domains
    Cea G2066, supplied by ATCC, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    oipa  (ATCC)
    93
    ATCC oipa
    Abundance of proteins with eukaryotic domains in proteomes of “ Ca . <t>Amoebophilus</t> <t>asiaticus”</t> and other bacteria. Proteins with eukaryotic domains are most abundant in intracellular bacteria. The percentage of proteins with eukaryotic domains
    Oipa, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Illumina Inc verticillium dahliae strain vd991
    Homology analysis of lineage‐specific ( LS ) genes between Verticillium <t>dahliae</t> and Fusarium spp. Identity matrix of <t>Vd991</t> LS genes and Fusarium spp. genes. The matrix was constructed using protein‐coding genes from Vd991 that had higher identities with Fusarium spp. genes than with the two other V. dahliae genes. The color gradient from white to red represents identities from 0 to 100%.
    Verticillium Dahliae Strain Vd991, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    tn5398  (ATCC)
    85
    ATCC tn5398
    Homology analysis of lineage‐specific ( LS ) genes between Verticillium <t>dahliae</t> and Fusarium spp. Identity matrix of <t>Vd991</t> LS genes and Fusarium spp. genes. The matrix was constructed using protein‐coding genes from Vd991 that had higher identities with Fusarium spp. genes than with the two other V. dahliae genes. The color gradient from white to red represents identities from 0 to 100%.
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    99
    ATCC a baumannii atcc 17978
    Homology analysis of lineage‐specific ( LS ) genes between Verticillium <t>dahliae</t> and Fusarium spp. Identity matrix of <t>Vd991</t> LS genes and Fusarium spp. genes. The matrix was constructed using protein‐coding genes from Vd991 that had higher identities with Fusarium spp. genes than with the two other V. dahliae genes. The color gradient from white to red represents identities from 0 to 100%.
    A Baumannii Atcc 17978, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 3130 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa dntp mixture
    Homology analysis of lineage‐specific ( LS ) genes between Verticillium <t>dahliae</t> and Fusarium spp. Identity matrix of <t>Vd991</t> LS genes and Fusarium spp. genes. The matrix was constructed using protein‐coding genes from Vd991 that had higher identities with Fusarium spp. genes than with the two other V. dahliae genes. The color gradient from white to red represents identities from 0 to 100%.
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    Image Search Results


    Circular representation of the T. pedis T A4 genome and complete genome alignment with T. denticola . (A.) Circular representation of the T. pedis T A4 genome. The CDSs are shown in violet where the outer circle represents predictions on the plus strand and the second circle those on the minus strand. CDSs with a best BLASTP hit in T. denticola ATCC 35405 are colored red and shown in the third circle. The fourth circle represents genes with best BLASTP hits in T. brennaborense (black), F. nucleatum (green), F. alocis (blue) and T. succinifaciens (grey). G+C skew is drawn in the inner circle. (B.) Complete genome alignment between T. pedis T A4 and T. denticola ATCC 35405. Dots represent maximum unique matches (MUMs) between the genomes. MUMs oriented in the same direction are depicted as red dots and reverse complemented MUMs are depicted as blue dots.

    Journal: PLoS ONE

    Article Title: Genome-Wide Relatedness of Treponema pedis, from Gingiva and Necrotic Skin Lesions of Pigs, with the Human Oral Pathogen Treponema denticola

    doi: 10.1371/journal.pone.0071281

    Figure Lengend Snippet: Circular representation of the T. pedis T A4 genome and complete genome alignment with T. denticola . (A.) Circular representation of the T. pedis T A4 genome. The CDSs are shown in violet where the outer circle represents predictions on the plus strand and the second circle those on the minus strand. CDSs with a best BLASTP hit in T. denticola ATCC 35405 are colored red and shown in the third circle. The fourth circle represents genes with best BLASTP hits in T. brennaborense (black), F. nucleatum (green), F. alocis (blue) and T. succinifaciens (grey). G+C skew is drawn in the inner circle. (B.) Complete genome alignment between T. pedis T A4 and T. denticola ATCC 35405. Dots represent maximum unique matches (MUMs) between the genomes. MUMs oriented in the same direction are depicted as red dots and reverse complemented MUMs are depicted as blue dots.

    Article Snippet: There were no homologues in T. pedis T A4 to the T. denticola ATCC 35405 virulence related fhbB (TDE0108) and oppA (TDE1071) genes.

    Techniques:

    Selection of B. thetaiotaomicron VPI 5482 mutants with increased biofilm capacities. (A) Schematic representation of the positive-selection strategy used to identify transposon mutants with increased biofilm production. BF, biofilm formation. (B) Biofilm biomass formation on the internal spatulas of continuous-flow biofilm microfermentors after 24 h. (Left) Wild-type B. thetaiotaomicron VPI 5482; (middle and right) microfermentors and spatulas inoculated with a culture enriched for biofilm production after 4 cycles of positive selection. (C) Comparison of the biofilm formation capacities of WT B. thetaiotaomicron and eight identified mutants with an insertion in the BT3147 gene. (Bottom) Crystal violet staining in 96-well microtiter plates; (top) corresponding biomass quantification after resuspension in an acetone-ethanol mix and absorbance measured at 575 nm. Biofilm formation capacities of the WT (VPI 5482) have been set to 100%. Error bars indicate standard deviations from 3 technical replicates. *, P

    Journal: Journal of Bacteriology

    Article Title: A Putative Type V Pilus Contributes to Bacteroides thetaiotaomicron Biofilm Formation Capacity

    doi: 10.1128/JB.00650-18

    Figure Lengend Snippet: Selection of B. thetaiotaomicron VPI 5482 mutants with increased biofilm capacities. (A) Schematic representation of the positive-selection strategy used to identify transposon mutants with increased biofilm production. BF, biofilm formation. (B) Biofilm biomass formation on the internal spatulas of continuous-flow biofilm microfermentors after 24 h. (Left) Wild-type B. thetaiotaomicron VPI 5482; (middle and right) microfermentors and spatulas inoculated with a culture enriched for biofilm production after 4 cycles of positive selection. (C) Comparison of the biofilm formation capacities of WT B. thetaiotaomicron and eight identified mutants with an insertion in the BT3147 gene. (Bottom) Crystal violet staining in 96-well microtiter plates; (top) corresponding biomass quantification after resuspension in an acetone-ethanol mix and absorbance measured at 575 nm. Biofilm formation capacities of the WT (VPI 5482) have been set to 100%. Error bars indicate standard deviations from 3 technical replicates. *, P

    Article Snippet: Our approach to uncover the biofilm potential and biofilm-related functions of B. thetaiotaomicron VPI 5482 resulted in the identification of two putative Mfa1-like proteins (BT3148 and BT3147) potentially involved in biofilm formation in B. thetaiotaomicron .

    Techniques: Selection, Staining

    C-terminal truncation of the BT3147 protein promotes B. thetaiotaomicron biofilm formation. (A, top) Schematic genetic organization of the BT3147 Δ 9 ΔBT3146-BT3145 mutant; (middle) comparison of the biofilm formation capacities of WT B. thetaiotaomicron VPI 5482 and the indicated mutant or plasmid-containing strains; (bottom) crystal violet staining in 96-well microtiter plates. Shown is the corresponding quantification after resuspension in acetone-ethanol and the absorbance measured at 575 nm. Biofilm formation capacities of the WT (VPI 5482) have been set to 100%. Error bars indicate standard deviations from 3 biological replicates. **, P

    Journal: Journal of Bacteriology

    Article Title: A Putative Type V Pilus Contributes to Bacteroides thetaiotaomicron Biofilm Formation Capacity

    doi: 10.1128/JB.00650-18

    Figure Lengend Snippet: C-terminal truncation of the BT3147 protein promotes B. thetaiotaomicron biofilm formation. (A, top) Schematic genetic organization of the BT3147 Δ 9 ΔBT3146-BT3145 mutant; (middle) comparison of the biofilm formation capacities of WT B. thetaiotaomicron VPI 5482 and the indicated mutant or plasmid-containing strains; (bottom) crystal violet staining in 96-well microtiter plates. Shown is the corresponding quantification after resuspension in acetone-ethanol and the absorbance measured at 575 nm. Biofilm formation capacities of the WT (VPI 5482) have been set to 100%. Error bars indicate standard deviations from 3 biological replicates. **, P

    Article Snippet: Our approach to uncover the biofilm potential and biofilm-related functions of B. thetaiotaomicron VPI 5482 resulted in the identification of two putative Mfa1-like proteins (BT3148 and BT3147) potentially involved in biofilm formation in B. thetaiotaomicron .

    Techniques: Mutagenesis, Plasmid Preparation, Staining

    The B. thetaiotaomicron VPI 5482 strain forms poor biofilms compared to different isolates. (A and B) Biofilm formation in a 96-well-plate biofilm assay followed by crystal violet staining of B. thetaiotaomicron ( Bt ) VPI 5482 and various biofilm-forming B. thetaiotaomicron isolates (see also Fig. S1 in the supplemental material). Error bars indicate standard deviations from 3 technical replicates. *, P

    Journal: Journal of Bacteriology

    Article Title: A Putative Type V Pilus Contributes to Bacteroides thetaiotaomicron Biofilm Formation Capacity

    doi: 10.1128/JB.00650-18

    Figure Lengend Snippet: The B. thetaiotaomicron VPI 5482 strain forms poor biofilms compared to different isolates. (A and B) Biofilm formation in a 96-well-plate biofilm assay followed by crystal violet staining of B. thetaiotaomicron ( Bt ) VPI 5482 and various biofilm-forming B. thetaiotaomicron isolates (see also Fig. S1 in the supplemental material). Error bars indicate standard deviations from 3 technical replicates. *, P

    Article Snippet: Our approach to uncover the biofilm potential and biofilm-related functions of B. thetaiotaomicron VPI 5482 resulted in the identification of two putative Mfa1-like proteins (BT3148 and BT3147) potentially involved in biofilm formation in B. thetaiotaomicron .

    Techniques: Biofilm Production Assay, Staining

    (A) Comparison of the numbers of transporters in A. baumannii ACICU, A. baumannii ATCC 17978, A. baylyi ADP1, E. coli MG1655, Mycobacterium tuberculosis H37Rv, P. aeruginosa PAO1, Pseudomonas fluorescens Pf-5, and S. aureus ). Only the main transporter classes are shown, with the number of transporters per Mb of genome given for each bacterial species. The color codes for the transporter classes are given on the right. (B) Comparison of the number of predicted drug efflux systems in A. baumannii ACICU and ATCC 17978, and A. baylyi ). Only family members that clearly clustered with known multidrug efflux transporters were counted. Genetically associated membrane fusion or outer membrane proteins were not considered. The color codes for the transporter classes are given on the right.

    Journal: Antimicrobial Agents and Chemotherapy

    Article Title: Whole-Genome Pyrosequencing of an Epidemic Multidrug-Resistant Acinetobacter baumannii Strain Belonging to the European Clone II Group

    doi: 10.1128/AAC.01643-07

    Figure Lengend Snippet: (A) Comparison of the numbers of transporters in A. baumannii ACICU, A. baumannii ATCC 17978, A. baylyi ADP1, E. coli MG1655, Mycobacterium tuberculosis H37Rv, P. aeruginosa PAO1, Pseudomonas fluorescens Pf-5, and S. aureus ). Only the main transporter classes are shown, with the number of transporters per Mb of genome given for each bacterial species. The color codes for the transporter classes are given on the right. (B) Comparison of the number of predicted drug efflux systems in A. baumannii ACICU and ATCC 17978, and A. baylyi ). Only family members that clearly clustered with known multidrug efflux transporters were counted. Genetically associated membrane fusion or outer membrane proteins were not considered. The color codes for the transporter classes are given on the right.

    Article Snippet: Among the novel functions gained by A. baumannii ACICU, there are (i) improved membrane transport potential (76.2 transporters per Mb of genome compared with 57.2 transporters per Mb in ATCC 17978 and 62.5 transporters per Mb in ADP1); (ii) expanded drug resistance (which accounts for the panresistant phenotype); and (iii) alteration of the cell envelope (novel genes for the synthesis of the cell wall), adherence properties (surface adhesion proteins fused to putative cytotoxin binding domains), potential changes in the pathogenic potential (hemagglutinin/hemolysin-related proteins), and a high number of hypothetical and/or functionally uncharacterized proteins, often associated with regions of prophage origin.

    Techniques:

    Tli1Tli2 AH are the cognate immunity proteins to Tle1 AH . A. hydrophila NJ-35 and the ∆ clpV strain were used as the predator strains. ClpV , which encodes a putative ATPase required for T6SS function, was deleted to construct the T6SS − strain (∆ clpV ). The prey strains included the gene deletion mutant ∆ tle1 - tli1tli2 AH and its single or double restoration strains of immunity genes, they are, C∆ tli1 AH (∆ tle1 - tli1tli2 AH / pMMB- tli1 AH ), C∆ tli2 AH (∆ tle1 - tli1tli2 AH / pMMB- tli2 AH ) and C∆ tli1tli2 AH (∆ tle1 - tli1tli2 AH / pMMB- tli1tli2 AH ). The predator and prey strains were cultured at a ratio of 5:1, and surviving prey cells were serially diluted and determined on the LB plate containing antibiotics. Data are presented as the mean ± standard deviation (error bars) of three independent experiments. ## P

    Journal: Veterinary Research

    Article Title: Identification of a new effector-immunity pair of Aeromonas hydrophila type VI secretion system

    doi: 10.1186/s13567-020-00794-w

    Figure Lengend Snippet: Tli1Tli2 AH are the cognate immunity proteins to Tle1 AH . A. hydrophila NJ-35 and the ∆ clpV strain were used as the predator strains. ClpV , which encodes a putative ATPase required for T6SS function, was deleted to construct the T6SS − strain (∆ clpV ). The prey strains included the gene deletion mutant ∆ tle1 - tli1tli2 AH and its single or double restoration strains of immunity genes, they are, C∆ tli1 AH (∆ tle1 - tli1tli2 AH / pMMB- tli1 AH ), C∆ tli2 AH (∆ tle1 - tli1tli2 AH / pMMB- tli2 AH ) and C∆ tli1tli2 AH (∆ tle1 - tli1tli2 AH / pMMB- tli1tli2 AH ). The predator and prey strains were cultured at a ratio of 5:1, and surviving prey cells were serially diluted and determined on the LB plate containing antibiotics. Data are presented as the mean ± standard deviation (error bars) of three independent experiments. ## P

    Article Snippet: Also, we identified some putative Tle1 family effectors in A. hydrophila strains with known genome sequences, and interestingly, these strains have been determined to be virulent [ – ], implying that Tle1 may be related to A. hydrophila virulence.

    Techniques: Construct, Mutagenesis, Cell Culture, Standard Deviation

    Tle1 AH is required for the interbacterial antagonism of A. hydrophila NJ-35. Predator and prey cells at a ratio of 5:1 were cocultured to assay the recovery of surviving prey cells by determining colony forming unit (CFU). A. hydrophila NJ-35 and its mutant derivatives ∆ clpV , ∆ tle1 AH or C∆ tle1 AH were used as the predator strains. ClpV , which encodes a putative ATPase required for T6SS function, was deleted to construct the T6SS − strain (∆ clpV ). “LB” indicates incubation of E. coli with sterile LB medium alone and serves as the control. A E. coli BL21 as the prey strain. B V. parahaemolyticus RIMD 2210633 as the prey strain. C Aeromonas strains as the preys, including A. hydrophila strains ATCC 7966, J-1 and NJ-3, A. sobria CS-2, A. media NJ-8 and A. veronii XH-14. Lane 1, the wild-type A. hydrophila NJ-35; Lane 2, ∆ clpV (T6SS − ); Lane 3, ∆ tle1 AH . Data are presented as the mean ± standard deviation (error bars) of three independent experiments. *** P

    Journal: Veterinary Research

    Article Title: Identification of a new effector-immunity pair of Aeromonas hydrophila type VI secretion system

    doi: 10.1186/s13567-020-00794-w

    Figure Lengend Snippet: Tle1 AH is required for the interbacterial antagonism of A. hydrophila NJ-35. Predator and prey cells at a ratio of 5:1 were cocultured to assay the recovery of surviving prey cells by determining colony forming unit (CFU). A. hydrophila NJ-35 and its mutant derivatives ∆ clpV , ∆ tle1 AH or C∆ tle1 AH were used as the predator strains. ClpV , which encodes a putative ATPase required for T6SS function, was deleted to construct the T6SS − strain (∆ clpV ). “LB” indicates incubation of E. coli with sterile LB medium alone and serves as the control. A E. coli BL21 as the prey strain. B V. parahaemolyticus RIMD 2210633 as the prey strain. C Aeromonas strains as the preys, including A. hydrophila strains ATCC 7966, J-1 and NJ-3, A. sobria CS-2, A. media NJ-8 and A. veronii XH-14. Lane 1, the wild-type A. hydrophila NJ-35; Lane 2, ∆ clpV (T6SS − ); Lane 3, ∆ tle1 AH . Data are presented as the mean ± standard deviation (error bars) of three independent experiments. *** P

    Article Snippet: Also, we identified some putative Tle1 family effectors in A. hydrophila strains with known genome sequences, and interestingly, these strains have been determined to be virulent [ – ], implying that Tle1 may be related to A. hydrophila virulence.

    Techniques: Mutagenesis, Construct, Incubation, Standard Deviation

    Predicted DUF4123-associated T6SS effector-immunity (EI) gene modules in 14 A. hydrophila strains. All the strains used to search for putative effectors are listed in Table 2 . The gray arrows indicate DUF4123, the purple arrows indicate the putative effectors, and yellow arrows indicate immunity genes. The arrows indicate the direction of transcription.

    Journal: Veterinary Research

    Article Title: Identification of a new effector-immunity pair of Aeromonas hydrophila type VI secretion system

    doi: 10.1186/s13567-020-00794-w

    Figure Lengend Snippet: Predicted DUF4123-associated T6SS effector-immunity (EI) gene modules in 14 A. hydrophila strains. All the strains used to search for putative effectors are listed in Table 2 . The gray arrows indicate DUF4123, the purple arrows indicate the putative effectors, and yellow arrows indicate immunity genes. The arrows indicate the direction of transcription.

    Article Snippet: Also, we identified some putative Tle1 family effectors in A. hydrophila strains with known genome sequences, and interestingly, these strains have been determined to be virulent [ – ], implying that Tle1 may be related to A. hydrophila virulence.

    Techniques:

    Tle1 AH is a phospholipase effector secreted by T6SS of A. hydrophila NJ-35 . A T6SS-dependent secretion of Tle1 AH was confirmed by Western blot on whole cells and supernatants of A. hydrophila NJ-35 and the ∆ clpV strain. ClpV , which encodes a putative ATPase required for T6SS function, was deleted to construct the T6SS − strain (∆ clpV ). The anti-His antibody was used to measure the production of Tle1 AH and anti-GroEL antibody served as an internal reference. GroEL: heat shock protein Hsp60. B Growth of E. coli TOP10 producing peri-Tle1 AH and peri-Tle1 AHS303A in LB broth. pBAD/His was used for construction of the expression vectors for tle1 AH and its point mutant tle1 AHS303A (the catalysis site of Tle1 AH at position 303 mutated from serine to alanine). To achieve periplasmic localization, the PelB leader sequence was fused in front of the tle1 AH and tle1 AHS303A . Cultures were induced by l -arabinose ( l -Ara) at the indicated time by the arrow. A growth curve was drawn by measuring the OD 600 every 30 min. Data are presented as the mean ± standard deviation (error bars) of three independent experiments. The expression of peri-Tle1 AH and peri-Tle1 AHS303A was detected in E. coli TOP10 by Western blot using anti-His antibody.

    Journal: Veterinary Research

    Article Title: Identification of a new effector-immunity pair of Aeromonas hydrophila type VI secretion system

    doi: 10.1186/s13567-020-00794-w

    Figure Lengend Snippet: Tle1 AH is a phospholipase effector secreted by T6SS of A. hydrophila NJ-35 . A T6SS-dependent secretion of Tle1 AH was confirmed by Western blot on whole cells and supernatants of A. hydrophila NJ-35 and the ∆ clpV strain. ClpV , which encodes a putative ATPase required for T6SS function, was deleted to construct the T6SS − strain (∆ clpV ). The anti-His antibody was used to measure the production of Tle1 AH and anti-GroEL antibody served as an internal reference. GroEL: heat shock protein Hsp60. B Growth of E. coli TOP10 producing peri-Tle1 AH and peri-Tle1 AHS303A in LB broth. pBAD/His was used for construction of the expression vectors for tle1 AH and its point mutant tle1 AHS303A (the catalysis site of Tle1 AH at position 303 mutated from serine to alanine). To achieve periplasmic localization, the PelB leader sequence was fused in front of the tle1 AH and tle1 AHS303A . Cultures were induced by l -arabinose ( l -Ara) at the indicated time by the arrow. A growth curve was drawn by measuring the OD 600 every 30 min. Data are presented as the mean ± standard deviation (error bars) of three independent experiments. The expression of peri-Tle1 AH and peri-Tle1 AHS303A was detected in E. coli TOP10 by Western blot using anti-His antibody.

    Article Snippet: Also, we identified some putative Tle1 family effectors in A. hydrophila strains with known genome sequences, and interestingly, these strains have been determined to be virulent [ – ], implying that Tle1 may be related to A. hydrophila virulence.

    Techniques: Western Blot, Construct, Expressing, Mutagenesis, Sequencing, Acetylene Reduction Assay, Standard Deviation

    Tle1 AH is a potential T6SS effector in A. hydrophila NJ-35. A Genetic organization of T6SS-related proteins containing the DUF4123 domain in A. hydrophila NJ-35. The numbers below refer to the gene locus tag (U876-XXXXX). Sequencing data for NJ-35 can be obtained from the National Center for Biotechnology Information (accession number: CP006870). B Sequence alignment of conserved catalytic motifs (labeled in red) compared between Tle families. Sequence logos were generated from alignments of the catalytic motifs from the families Tle1-4 (Gly - X-Ser-X-Gly, X is for any amino acid). * represents the catalytic residues. C Phylogenetic analyses of Tle1 AH (AKJ35788.1) with representative members of the families Tle1-4. Figure was prepared using MEGA7.0.

    Journal: Veterinary Research

    Article Title: Identification of a new effector-immunity pair of Aeromonas hydrophila type VI secretion system

    doi: 10.1186/s13567-020-00794-w

    Figure Lengend Snippet: Tle1 AH is a potential T6SS effector in A. hydrophila NJ-35. A Genetic organization of T6SS-related proteins containing the DUF4123 domain in A. hydrophila NJ-35. The numbers below refer to the gene locus tag (U876-XXXXX). Sequencing data for NJ-35 can be obtained from the National Center for Biotechnology Information (accession number: CP006870). B Sequence alignment of conserved catalytic motifs (labeled in red) compared between Tle families. Sequence logos were generated from alignments of the catalytic motifs from the families Tle1-4 (Gly - X-Ser-X-Gly, X is for any amino acid). * represents the catalytic residues. C Phylogenetic analyses of Tle1 AH (AKJ35788.1) with representative members of the families Tle1-4. Figure was prepared using MEGA7.0.

    Article Snippet: Also, we identified some putative Tle1 family effectors in A. hydrophila strains with known genome sequences, and interestingly, these strains have been determined to be virulent [ – ], implying that Tle1 may be related to A. hydrophila virulence.

    Techniques: Sequencing, Labeling, Generated

    Tle1 AH is required for the virulence and colonization of A. hydrophila NJ-35. A Determination of the LD 50 values of the wild-type and tle1 AH mutant strains in zebrafish. Zebrafish were intraperitoneally (i.p.) injected with tenfold serially diluted bacterial suspensions. The control group was i.p. injected with sterile PBS only. B Competitive assays of NJ-35 and Δ tle1 AH in crucian carp. Strains were mixed at a ratio of 1:1 and inoculated to fish by intraperitoneal injection. After 24 h, heart, hepatopancreas, spleen and kidney were harvested for counting of the number of colony-forming units (CFU) per gram of sample. Data are presented as the mean ± standard deviation (error bars) of three independent experiments. *** P

    Journal: Veterinary Research

    Article Title: Identification of a new effector-immunity pair of Aeromonas hydrophila type VI secretion system

    doi: 10.1186/s13567-020-00794-w

    Figure Lengend Snippet: Tle1 AH is required for the virulence and colonization of A. hydrophila NJ-35. A Determination of the LD 50 values of the wild-type and tle1 AH mutant strains in zebrafish. Zebrafish were intraperitoneally (i.p.) injected with tenfold serially diluted bacterial suspensions. The control group was i.p. injected with sterile PBS only. B Competitive assays of NJ-35 and Δ tle1 AH in crucian carp. Strains were mixed at a ratio of 1:1 and inoculated to fish by intraperitoneal injection. After 24 h, heart, hepatopancreas, spleen and kidney were harvested for counting of the number of colony-forming units (CFU) per gram of sample. Data are presented as the mean ± standard deviation (error bars) of three independent experiments. *** P

    Article Snippet: Also, we identified some putative Tle1 family effectors in A. hydrophila strains with known genome sequences, and interestingly, these strains have been determined to be virulent [ – ], implying that Tle1 may be related to A. hydrophila virulence.

    Techniques: Mutagenesis, Injection, Fluorescence In Situ Hybridization, Standard Deviation

    Abundance of proteins with eukaryotic domains in proteomes of “ Ca . Amoebophilus asiaticus” and other bacteria. Proteins with eukaryotic domains are most abundant in intracellular bacteria. The percentage of proteins with eukaryotic domains

    Journal: Journal of Bacteriology

    Article Title: The Genome of the Amoeba Symbiont “Candidatus Amoebophilus asiaticus” Reveals Common Mechanisms for Host Cell Interaction among Amoeba-Associated Bacteria

    doi: 10.1128/JB.01379-09

    Figure Lengend Snippet: Abundance of proteins with eukaryotic domains in proteomes of “ Ca . Amoebophilus asiaticus” and other bacteria. Proteins with eukaryotic domains are most abundant in intracellular bacteria. The percentage of proteins with eukaryotic domains

    Article Snippet: Amoebophilus asiaticus” encodes a putative type VI secretion system which is distantly related to described type VI secretion systems (Aasi_1072 to Aasi_1806).

    Techniques:

    Ultrastructure of “ Ca . Amoebophilus asiaticus” 5a2 within its Acanthamoeba host cell. (A) Transmission electron micrograph showing the distribution of “ Ca . Amoebophilus asiaticus” in its Acanthamoeba host cell. (B and C)

    Journal: Journal of Bacteriology

    Article Title: The Genome of the Amoeba Symbiont “Candidatus Amoebophilus asiaticus” Reveals Common Mechanisms for Host Cell Interaction among Amoeba-Associated Bacteria

    doi: 10.1128/JB.01379-09

    Figure Lengend Snippet: Ultrastructure of “ Ca . Amoebophilus asiaticus” 5a2 within its Acanthamoeba host cell. (A) Transmission electron micrograph showing the distribution of “ Ca . Amoebophilus asiaticus” in its Acanthamoeba host cell. (B and C)

    Article Snippet: Amoebophilus asiaticus” encodes a putative type VI secretion system which is distantly related to described type VI secretion systems (Aasi_1072 to Aasi_1806).

    Techniques: Transmission Assay

    General features of the “ Ca . Amoebophilus asiaticus” genome.

    Journal: Journal of Bacteriology

    Article Title: The Genome of the Amoeba Symbiont “Candidatus Amoebophilus asiaticus” Reveals Common Mechanisms for Host Cell Interaction among Amoeba-Associated Bacteria

    doi: 10.1128/JB.01379-09

    Figure Lengend Snippet: General features of the “ Ca . Amoebophilus asiaticus” genome.

    Article Snippet: Amoebophilus asiaticus” encodes a putative type VI secretion system which is distantly related to described type VI secretion systems (Aasi_1072 to Aasi_1806).

    Techniques:

    Homology analysis of lineage‐specific ( LS ) genes between Verticillium dahliae and Fusarium spp. Identity matrix of Vd991 LS genes and Fusarium spp. genes. The matrix was constructed using protein‐coding genes from Vd991 that had higher identities with Fusarium spp. genes than with the two other V. dahliae genes. The color gradient from white to red represents identities from 0 to 100%.

    Journal: The New Phytologist

    Article Title: Comparative genomics reveals cotton‐specific virulence factors in flexible genomic regions in Verticillium dahliae and evidence of horizontal gene transfer from Fusarium

    doi: 10.1111/nph.14861

    Figure Lengend Snippet: Homology analysis of lineage‐specific ( LS ) genes between Verticillium dahliae and Fusarium spp. Identity matrix of Vd991 LS genes and Fusarium spp. genes. The matrix was constructed using protein‐coding genes from Vd991 that had higher identities with Fusarium spp. genes than with the two other V. dahliae genes. The color gradient from white to red represents identities from 0 to 100%.

    Article Snippet: Table S1 Primers used in the study Table S2 PacBio RS II and Illumina raw data of genome sequences Table S3 Key parameters of the genome assembly of the Verticillium dahliae strain Vd991by PacBio RS II biotechnology Table S4 Improvement in genome sequence quality of Verticillium dahliae strain Vd991 with Illumina MiSeq data Table S5 Key parameters of the genome assembly of the Verticillium dahliae Vd991 Table S6 Physical locations of Verticillium dahliae Vd991 genomic regions relative to reference genomes of V. dahliae JR2 and VdLs.17 Table S7 Location of rearrangements in the Verticillium dahliae Vd991 genome compared with JR2 and VdLs.17 genomes Table S8 Comparison of gene models among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S9 Gene synteny among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S10 Analysis and comparisons of specific gene content among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S11 Fungi nonsupervised orthologous groups (fuNOG) annotations of protein coding genes among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S12 Functional annotation of potential pathogenicity and virulence‐related factors among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S13 Classification of the subfamilies of CAZymes in the genomes of the three Verticillium dahliae isolates Vd991, JR2, and VdLs.17 Table S14 Protein kinase annotation among the three genomes of Verticillium dahliae isolates Vd991, JR2 and VdLs.17 Table S15 Annotation of transcription factors among the three genomes of Verticillium dahliae isolates Vd991, JR2, and VdLs.17 Table S16 Percentages of protein‐coding genes with functional annotations in the genomes of the three Verticillium dahliae isolates Vd991, JR2, and VdLs.17.

    Techniques: Construct

    Presentation of lineage‐specific ( LS ) genes and gene synteny relationships among the three Verticillium dahliae strains Vd991, JR 2 and VdLs.17. The genes were arranged by the ortholog clustering results with the physical location from chromosomes one to eight of the JR 2 reference genome. UN indicates an unknown chromosome location of genes in V. dahliae . LS genes are marked in red, green and blue for Vd991, JR 2 and VdLs.17, respectively. Triangular blocks indicate the LSR s.

    Journal: The New Phytologist

    Article Title: Comparative genomics reveals cotton‐specific virulence factors in flexible genomic regions in Verticillium dahliae and evidence of horizontal gene transfer from Fusarium

    doi: 10.1111/nph.14861

    Figure Lengend Snippet: Presentation of lineage‐specific ( LS ) genes and gene synteny relationships among the three Verticillium dahliae strains Vd991, JR 2 and VdLs.17. The genes were arranged by the ortholog clustering results with the physical location from chromosomes one to eight of the JR 2 reference genome. UN indicates an unknown chromosome location of genes in V. dahliae . LS genes are marked in red, green and blue for Vd991, JR 2 and VdLs.17, respectively. Triangular blocks indicate the LSR s.

    Article Snippet: Table S1 Primers used in the study Table S2 PacBio RS II and Illumina raw data of genome sequences Table S3 Key parameters of the genome assembly of the Verticillium dahliae strain Vd991by PacBio RS II biotechnology Table S4 Improvement in genome sequence quality of Verticillium dahliae strain Vd991 with Illumina MiSeq data Table S5 Key parameters of the genome assembly of the Verticillium dahliae Vd991 Table S6 Physical locations of Verticillium dahliae Vd991 genomic regions relative to reference genomes of V. dahliae JR2 and VdLs.17 Table S7 Location of rearrangements in the Verticillium dahliae Vd991 genome compared with JR2 and VdLs.17 genomes Table S8 Comparison of gene models among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S9 Gene synteny among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S10 Analysis and comparisons of specific gene content among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S11 Fungi nonsupervised orthologous groups (fuNOG) annotations of protein coding genes among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S12 Functional annotation of potential pathogenicity and virulence‐related factors among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S13 Classification of the subfamilies of CAZymes in the genomes of the three Verticillium dahliae isolates Vd991, JR2, and VdLs.17 Table S14 Protein kinase annotation among the three genomes of Verticillium dahliae isolates Vd991, JR2 and VdLs.17 Table S15 Annotation of transcription factors among the three genomes of Verticillium dahliae isolates Vd991, JR2, and VdLs.17 Table S16 Percentages of protein‐coding genes with functional annotations in the genomes of the three Verticillium dahliae isolates Vd991, JR2, and VdLs.17.

    Techniques:

    Phylogenetic relationships between lineage‐specific ( LS ) genes from Verticillium dahliae Vd991, JR 2 d VdLs.17 and genes from Fusarium species. (a) Phylogenetic analyses were performed on nucleic acid sequences of orthologs of the single‐copy genes among 20 representative fusarias. Magnaporthe oryzae was set as the outgroup. V. dahliae strains are marked in red. (b–e) Evolutionary relationships between four LS genes from the lineage‐specific region G‐ LRS 2 in Vd991 and homologous genes in Fusarium spp. were inferred using the maximum likelihood method (1000 bootstraps). Genes for phylogenetic analysis of VEDA _05193 (b), VEDA _05195 (c), VEDA _05196 (d), and VEDA _05197 (e). Alphanumeric codes are standard gene accession numbers from reference genome databases. Clades that include genes from cotton wilt pathogens V. dahliae Vd991 and Fusarium oxysporum f. sp. vasinfectum are drawn in red.

    Journal: The New Phytologist

    Article Title: Comparative genomics reveals cotton‐specific virulence factors in flexible genomic regions in Verticillium dahliae and evidence of horizontal gene transfer from Fusarium

    doi: 10.1111/nph.14861

    Figure Lengend Snippet: Phylogenetic relationships between lineage‐specific ( LS ) genes from Verticillium dahliae Vd991, JR 2 d VdLs.17 and genes from Fusarium species. (a) Phylogenetic analyses were performed on nucleic acid sequences of orthologs of the single‐copy genes among 20 representative fusarias. Magnaporthe oryzae was set as the outgroup. V. dahliae strains are marked in red. (b–e) Evolutionary relationships between four LS genes from the lineage‐specific region G‐ LRS 2 in Vd991 and homologous genes in Fusarium spp. were inferred using the maximum likelihood method (1000 bootstraps). Genes for phylogenetic analysis of VEDA _05193 (b), VEDA _05195 (c), VEDA _05196 (d), and VEDA _05197 (e). Alphanumeric codes are standard gene accession numbers from reference genome databases. Clades that include genes from cotton wilt pathogens V. dahliae Vd991 and Fusarium oxysporum f. sp. vasinfectum are drawn in red.

    Article Snippet: Table S1 Primers used in the study Table S2 PacBio RS II and Illumina raw data of genome sequences Table S3 Key parameters of the genome assembly of the Verticillium dahliae strain Vd991by PacBio RS II biotechnology Table S4 Improvement in genome sequence quality of Verticillium dahliae strain Vd991 with Illumina MiSeq data Table S5 Key parameters of the genome assembly of the Verticillium dahliae Vd991 Table S6 Physical locations of Verticillium dahliae Vd991 genomic regions relative to reference genomes of V. dahliae JR2 and VdLs.17 Table S7 Location of rearrangements in the Verticillium dahliae Vd991 genome compared with JR2 and VdLs.17 genomes Table S8 Comparison of gene models among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S9 Gene synteny among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S10 Analysis and comparisons of specific gene content among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S11 Fungi nonsupervised orthologous groups (fuNOG) annotations of protein coding genes among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S12 Functional annotation of potential pathogenicity and virulence‐related factors among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S13 Classification of the subfamilies of CAZymes in the genomes of the three Verticillium dahliae isolates Vd991, JR2, and VdLs.17 Table S14 Protein kinase annotation among the three genomes of Verticillium dahliae isolates Vd991, JR2 and VdLs.17 Table S15 Annotation of transcription factors among the three genomes of Verticillium dahliae isolates Vd991, JR2, and VdLs.17 Table S16 Percentages of protein‐coding genes with functional annotations in the genomes of the three Verticillium dahliae isolates Vd991, JR2, and VdLs.17.

    Techniques:

    Ortholog gene clusters among the three Verticillium dahliae Vd991, JR 2 and VdLs.17 genomes. The numbers in solid yellow circles represent the total gene families composed of single‐copy genes among the three V. dahliae genomes; the numbers in solid gray circles represent the total gene families composed of multiple copies of genes in the three V. dahliae genomes. Red, green and blue correspond to Vd991, JR 2 and VdLs.17, respectively; the numbers in open gray circles represent the specific single‐copy genes in the Vd991, JR 2 and VdLs.17 genomes.

    Journal: The New Phytologist

    Article Title: Comparative genomics reveals cotton‐specific virulence factors in flexible genomic regions in Verticillium dahliae and evidence of horizontal gene transfer from Fusarium

    doi: 10.1111/nph.14861

    Figure Lengend Snippet: Ortholog gene clusters among the three Verticillium dahliae Vd991, JR 2 and VdLs.17 genomes. The numbers in solid yellow circles represent the total gene families composed of single‐copy genes among the three V. dahliae genomes; the numbers in solid gray circles represent the total gene families composed of multiple copies of genes in the three V. dahliae genomes. Red, green and blue correspond to Vd991, JR 2 and VdLs.17, respectively; the numbers in open gray circles represent the specific single‐copy genes in the Vd991, JR 2 and VdLs.17 genomes.

    Article Snippet: Table S1 Primers used in the study Table S2 PacBio RS II and Illumina raw data of genome sequences Table S3 Key parameters of the genome assembly of the Verticillium dahliae strain Vd991by PacBio RS II biotechnology Table S4 Improvement in genome sequence quality of Verticillium dahliae strain Vd991 with Illumina MiSeq data Table S5 Key parameters of the genome assembly of the Verticillium dahliae Vd991 Table S6 Physical locations of Verticillium dahliae Vd991 genomic regions relative to reference genomes of V. dahliae JR2 and VdLs.17 Table S7 Location of rearrangements in the Verticillium dahliae Vd991 genome compared with JR2 and VdLs.17 genomes Table S8 Comparison of gene models among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S9 Gene synteny among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S10 Analysis and comparisons of specific gene content among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S11 Fungi nonsupervised orthologous groups (fuNOG) annotations of protein coding genes among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S12 Functional annotation of potential pathogenicity and virulence‐related factors among the three genomes of Verticillium dahliae Vd991, JR2, and VdLs.17 Table S13 Classification of the subfamilies of CAZymes in the genomes of the three Verticillium dahliae isolates Vd991, JR2, and VdLs.17 Table S14 Protein kinase annotation among the three genomes of Verticillium dahliae isolates Vd991, JR2 and VdLs.17 Table S15 Annotation of transcription factors among the three genomes of Verticillium dahliae isolates Vd991, JR2, and VdLs.17 Table S16 Percentages of protein‐coding genes with functional annotations in the genomes of the three Verticillium dahliae isolates Vd991, JR2, and VdLs.17.

    Techniques: