Shared projects for user JKourelis

8775117184406291592911047Fig3_FigS3_Nb_PLCPs_ClustalOmega_ML_WAG.newick Supplementary Figure 3 Phylogeny of N. benthamiana PLCPs. The evolutionary history of the PLCP family was inferred using the Maximum Likelihood method based on the Whelan and Goldman model. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the taxa analysed. Shown are percentage bootstrap values. Putative pseudogenes are indicated in grey. 73no datasets no views 2020-06-232020-07-06 16:54
8775117184474291592914779Fig4_Rcr3_ClustalOmega_ML_WAG.newick Fig. 4 Rcr3 is highly polymorphic in Solanaceae. a) The evolutionary history of Rcr3 was inferred using the Maximum Likelihood method based on the Whelan and Goldman model. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history. Shown are percentage bootstrap values. 36no datasets no views 2020-06-232020-07-06 17:02
8775117184350651591307141Fig7_Hcr2_ClustalOmega_FastTree.newick Fig. 7 Cf-2 evolved in a tomato-specific subclade of the Hcr2 gene family. a) Phylogenetic tree of the Hcr2 gene family based on the conserved N-terminal and C-terminal 906 regions (corresponding to residues 1-138 and 713-1112 of Cf-2). Approximately Maximum Likelihood tree was generated using FastTreeMP, based on the LG model. Shown are percentage bootstrap values. Hcr2 family members with known recognition specificity are indicated in bold. 44no datasets no views 2020-06-042020-07-06 17:05
8775117184426881592918418FigS2_Rcr3_Pip1_ClustalOmega_ML_WAG.newick Supplementary Figure 2 Phylogeny of Pip1, Pfp1, Rcr3, Pip1-like PLCPs. The evolutionary history of the Rcr3 clade of proteases was inferred using the Maximum Likelihood method based on the Whelan and Goldman model. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the taxa analysed. Shown are percentage bootstrap values. 121no datasets no views 2020-06-232020-07-06 16:53
877511718457001592919443FigS4_PLCPs_NbAtSl_ClustalOmega_ML_WAG.newick Supplementary Figure 4 Phylogeny of tomato, Arabidopsis, and N. benthamiana PLCPs. The evolutionary history of the PLCP family was inferred using the Maximum Likelihood method based on the Whelan and Goldman model. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the taxa analysed. Shown are percentage bootstrap values. Putative pseudogenes are indicated in grey. 134no datasets no views 2020-06-232020-07-06 16:54
8775117184351131591307143FigS7_Hcr2-Other_ClustalOmega_FastTree.newick Supplementary Figure 7 The C-terminal half of Cf-2 has been repurposed in another RLP family. a) Phylogenetic tree of RLPs containing C-terminal homology to Cf-2. Approximate Maximum Likelihood tree was generated using FastTreeMP (Price et al., 2010), based on the Le Gascuel model (Le and Gascuel, 2008). Shown are percentage bootstrap values. 44no datasets no views 2020-06-042020-07-06 16:55
8775117184351261591307143FigS8_Hcr9_ClustalOmega_ML_WAG.newick Supplementary Figure 8 Hcr9s are conserved in Solanaceae. a) Phylogenetic tree of the Hcr9 protein family. The evolutionary history was inferred by using the Maximum Likelihood method based on the based on the Whelan and Goldman model. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the taxa analysed. Shown are percentage bootstrap values. Hcr9 family members with known recognition specificity are indicated in bold, in light grey those that induce autonecrosis upon agroinfiltration in N. benthamiana. 60no datasets no views 2020-06-042020-07-06 17:01
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  • RefPlantNLR: a comprehensive collection of experimentally validated plant NLRs

    NLRs are the main class of disease resistance genes. Over 300 NLRs have been functionally described to date. Comparative analysis of NLRs may help elucidate function and prioritize candidates. Comparative analysis would be greatly facilitated by a reference list of functionally characterized NLRs. Here we describe a near-comprehensive list of functionally characterized plant NLRs.

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    149155192124458371593014135Figure_4_RefPlantNLR_NBARC_Phylogeny_v415 Figure 4: Phylogenetic diversity of RefPlantNLR sequences. The tree, based on the NB-ARC domain (SUPERFAMILY signature SSF52540), was inferred using the Maximum Likelihood method based on the Jones-Taylor-Thornton (JTT) model (Jones et al., 1992). The tree with the highest log likelihood is shown. Branch labels indicates percentage bootstrap values inferred from 1000 rapid bootstrap replicates (Stamatakis et al., 2008). NLRs with identical NB-ARC domains are collapsed, while for those with multiple NB-ARC domains the NB-ARC are sequentially numbered. The representative sequences of the 90% sequence identity reduced redundancy set are indicated in bold. The TIR-NLR, CC-NLR, CCR-NLR, and CCG10-NLR subclades are indicated. 346no datasets no views 2020-06-242020-12-06 12:08
    149155192124193771628084804Supplemental_dataset_15_RefPlantNLR_v.20210712_481_NBARC_RAxML no description 419no datasets no views 2021-08-04
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