Two NLR immune receptors acquired high-affinity binding to a fungal effector through convergent evolution of their integrated domain
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, United Kingdom
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, United Kingdom
- Division of Genomics and Breeding, Iwate Biotechnology Research Centre, Japan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Japan
Figures
Figure 1 with 6 supplements
The Pik-1/Pik-2 orthologues are distributed across diverse species of grasses.
(A) The maximum likelihood (ML) phylogenetic trees of Pik-1 (left) and Pik-2 (right) orthologues. The trees were calculated from 927- and 1239-nucleotide-long codon-based alignments of the NB-ARC …
-
Figure 1—source data 1
Selection test for Pik-1 vs. Pik-2 orthologues.
- https://cdn.elifesciences.org/articles/66961/elife-66961-fig1-data1-v1.xlsx
Figure 1—figure supplement 1
Pik-1 and Pik-2 orthologues fall into two well-supported clades.
(A) Phylogenetic tree of CC-type NLRs of Zea mays, Sorghum bicolor, Setaria italica, Triticum aestivum, Hordeum vulgare, Brachypodium distachyon, Oryza brachyantha, and Oryza sativa. The maximum like…
Figure 1—figure supplement 2
Genotyping of Oryza brachyantha accession.
(A) Nucleotide alignment of Pikp-2, the ObPik-2 (Ob locus) gene, and the ObPik-2 coding sequence (Ob cds) from the reference genome (Chen et al., 2013), illustrating 46-bp-long deletion and the …
Figure 1—figure supplement 3
Pik-1 and Pik-2 orthologues from Oryza spp. fall into K- and N-type clades.
The phylogenetic tree shown in Figure 1A, illustrating the divide between the N- (dark grey) and K-type (light grey) Pik genes. The trees were manually rooted using the selected clades (marked with …
Figure 1—figure supplement 4
Schematic representation of selected Pik clusters in wheat (T. aestivum), sorghum (S. bicolor), and foxtail millet (S. italica).
The schematic presents gene models and genetic locations of Pik-1 (blue), Pik-2 (grey), and other NLR genes (purple). Non-NLR genes are shown in light green. The coordinates of the regions presented …
Figure 1—figure supplement 5
Random pairwise comparisons of dS rates calculated for the Pik-1 and Pik-2 receptors.
The synonymous (dS) rates were calculated using Yang and Nielsen, 2000 and presented in Figure 1C. The random datasets for dS values were generated by name shuffling in the existing dataset and …
Figure 1—figure supplement 6
Genetically linked Pik-1 and Pik-2 have similar molecular age.
Comparisons of pairwise dS rates calculated for the Pik-1 and Pik-2 receptors. The rates were calculated using Yang and Nielsen, 2000 based on 972- and 1269-nucleotide-long codon-based alignments of …
Figure 2 with 4 supplements
The integrated heavy metal-associated (HMA) domain exhibits elevated rates of ω (dN/dS) compared with the NB-ARC domain of Pik-1.
(A, B) Pairwise comparison of nucleotide substitution rates within the Pik-1 integration clade for the (A) HMA and (B) NB-ARC domains, calculated using Yang and Nielsen, 2000. The diagonal line …
-
Figure 2—source data 1
Selection test for Pik-1-HMA vs. NB-ARC.
- https://cdn.elifesciences.org/articles/66961/elife-66961-fig2-data1-v1.xlsx
Figure 2—figure supplement 1
Multiple sequence alignment illustrating the conservation around the HMA integration site.
The codon-based sequence alignment of the region surrounding the HMA integration site was generated using MUSCLE (Edgar, 2004). The residues are coloured based on percentage sequence identity from …
Figure 2—figure supplement 2
The integrated heavy metal-associated (HMA) domain displays elevated rates of dN compared with the NB-ARC domain of Pik-1.
Pairwise comparison of (A) dS and (B) dN rates between the HMA and NB-ARC domains of Pik-1. Pairwise comparison were calculated using Yang and Nielsen, 2000.
Figure 2—figure supplement 3
Residues within the integrated heavy metal-associated (HMA) domain are likely to have experienced positive selection.
(A) The neighbour joining (NJ) tree of the HMA domain calculated using the JTT substitution model (Jones et al., 1992) and bootstrap method with 100 iterations test (Felsenstein, 1985). Alignment of …
Figure 2—figure supplement 4
Selection test at the amino acid sites within the NB-ARC domain of the K-type Pik-1 genes.
Results from the codon substitution models for heterogeneous selection at amino acid sites (upper panel) and the likelihood ratio test (bottom panel).
Figure 3 with 3 supplements
The integrated heavy metal-associated (HMA) domain of Pikp-1 exhibits stronger association with the AVR-PikD effector than its predicted ancestral state.
(A) Overview of the strategy for resurrection of the ancestral HMA (ancHMA) domain. Following ancestral sequence reconstruction, the gene sequences were synthesised and incorporated into Pikp-1 by …
Figure 3—figure supplement 1
Phylogenetic analyses of the heavy metal-associated (HMA) domain of K-type Pik-1 NLRs.
The phylogenetic trees were built using MEGA X software (Kumar et al., 2018) and bootstrap method based on 1000 iterations (Felsenstein, 1985). Codon-based 249-nucleotide-long alignment was …
Figure 3—figure supplement 2
Ancestral sequence reconstruction yielded multiple plausible ancestral HMA (ancHMA) sequences.
(A) Representative neighbour joining (NJ) phylogenetic tree of the heavy metal-associated (HMA) domain. The tree was built using JTT substitution model (Jones et al., 1992) and bootstrap method with …
Figure 3—figure supplement 3
Replicates of the co-immunoprecipitation (co-IP) experiment between AVR-PikD and the reconstructed ancestral HMA (ancHMA) sequences.
Co-IP experiment between AVR-PikD (N-terminally tagged with FLAG) with Pikp-1 with ancestral sequences of HMA (N-terminally tagged with HA). Wild-type (WT) HA:Pikp-1 and HA:Pikp-1E230R were used as …
Figure 4 with 1 supplement
The IAQVV/LVKIE region of the Pikp-HMA domain determines high-affinity binding to AVR-PikD.
(A) Protein sequence alignment showing the Pikp–ancHMA swap chimeras. The amino acid sequences of ancestral HMA (ancHMA), Pikp-HMA, and chimeras are aligned, with the protein model above …
Figure 4—figure supplement 1
Replicates of the co-immunoprecipitation (co-IP) experiment between AVR-PikD and the Pikp-1:ancHMA chimeras.
Association of AVR-PikD (N-terminally tagged with FLAG) with Pikp-1, Pikp-1E230R, Pikp-1:ancHMA, and Pikp-1:ancHMA chimeras (N-terminally tagged with HA), labelled above, was tested in planta by …
Figure 5 with 5 supplements
The AV-VE substitutions within the IAQVV/LVKIE region of ancestral HMA (ancHMA) increase binding to AVR-PikD.
(A) Schematic representation of a neighbour joining (NJ) phylogenetic tree of the heavy metal-associated (HMA) domain from Oryza spp. (shown in Figure 3—figure supplement 2). The scale bar indicates …
-
Figure 5—source data 1
Raw data of Pikp-ancHMA Rmax SPR.
- https://cdn.elifesciences.org/articles/66961/elife-66961-fig5-data1-v1.xlsx
Figure 5—figure supplement 1
Co-immunoprecipitation experiment between AVR-PikD and the two plausible historical states of the IAQVV/LVKIE region within Pikp-HMA.
In planta association of AVR-PikD (N-terminally tagged with FLAG) Pikp-1, Pikp-1E230R, Pikp-1:ancHMA, and Pikp-1:ancHMA mutants (N-terminally tagged with HA), labelled above. Wild-type (WT) …
Figure 5—figure supplement 2
Replicates of the co-immunoprecipitation (co-IP) experiments between the Pikp-1:ancHMA IAQVV/LVKIE mutants and AVR-PikD.
In planta association of AVR-PikD (N-terminally tagged with FLAG) with Pikp-1, Pikp-1E230R, Pikp-1:ancHMA, and Pikp-1:ancHMA mutants (N-terminally tagged with HA), labelled above. Wild-type (WT) …
Figure 5—figure supplement 3
Purified proteins used in surface plasmon resonance studies.
(A) Coomassie Brilliant Blue-stained SDS-PAGE gel showing purified heavy metal-associated (HMA) proteins used in in vitro experiments. Dashed lines signify different components of the same gel. (B) …
Figure 5—figure supplement 4
Surface plasmon resonance (SPR) results show the effect of the IAQVV-LVKIE mutations on the AVR-PikD binding, as indicated by %Rmax.
(A) Schematic representation of the SPR sensorgrams showcasing the measurements taken to monitor binding dynamics: ‘binding’ and ‘dissociation’. (B) Plots illustrating calculated percentage of the …
Figure 5—figure supplement 5
The AV-VE (Ala-222-Val and Val-230-Glu) substitutions are sufficient to increase binding affinity towards the AVR-PikD effector in co-immunoprecipitation (co-IP).
Co-IP experiments between AVR-PikD (N-terminally tagged with FLAG) and Pikp-1 and Pikp-1:ancHMA constructs (N-terminally tagged with HA), labelled above. Wild-type (WT) HA:Pikp-1 and HA:Pikp-1E230R …
Figure 6 with 6 supplements
Pikp-1:ancHMALVKIE* and Pikp-1:ancHMALAKIE* mediate immune response towards the AVR-PikD effector.
(A) Schematic representation of wild-type Pikp-1 and Pikp-1:ancHMA fusions used in the assay. The mutated regions are presented with arrowheads and listed. (B) Representative images of …
-
Figure 6—source data 1
Hypersensitive response scores for IAQVV to LVKIE mutations in Pikp-HMA.
- https://cdn.elifesciences.org/articles/66961/elife-66961-fig6-data1-v1.xlsx
Figure 6—figure supplement 1
Pikp-1:ancHMA fusions are autoactive in a Pikp-2-dependent manner.
Hypersensitive response (HR) assay after transient co-expression of Pikp-1:HMA variants (N-terminally tagged with HA) with AVR-PikD (N-terminally tagged with FLAG) and Pikp-2 (C-terminally tagged …
-
Figure 6—figure supplement 1—source data 1
Hypersensitive response scores used in Figure 6—figure supplement 1.
- https://cdn.elifesciences.org/articles/66961/elife-66961-fig6-figsupp1-data1-v1.xlsx
Figure 6—figure supplement 2
Statistical analysis of hypersensitive response cell death for the Pikp-1:ancHMA fusions.
The statistical analysis was conducted using an estimation method using besthr R library (MacLean, 2019). (A–G) Each panel corresponds to a different Pikp-1:ancHMA fusion (labelled above), …
Figure 6—figure supplement 3
The AMEGNND mutations within ancestral HMA (ancHMA) abolish autoactivity.
Hypersensitive response (HR) assay after transient co-expression of Pikp-1:HMA mutants (N-terminally tagged with HA) with AVR-PikD (N-terminally tagged with FLAG) and Pikp-2 (C-terminally tagged …
-
Figure 6—figure supplement 3—source data 1
Hypersensitive response scores used in Figure6—figure supplement 3.
- https://cdn.elifesciences.org/articles/66961/elife-66961-fig6-figsupp3-data1-v1.xlsx
Figure 6—figure supplement 4
Statistical analysis of cell death assay for the Pikp-1:ancHMA chimeras.
The statistical analysis was carried out using an estimation method implemented in besthr R library (MacLean, 2019). (A–F) Each panel corresponds to a different chimera of Pikp-1:ancHMA (labelled …
Figure 6—figure supplement 5
Statistical analysis of cell death for the Pikp-1:ancHMA mutants within the IAQVV/LVKIE region.
The statistical analysis was performed using an estimation method implemented in besthr R library (MacLean, 2019). (A–G) Each panel corresponds to a different Pikp-1:ancHMA* mutant co-expressed with …
Figure 6—figure supplement 6
In planta accumulation of the Pikp-1:ancHMA* mutants in the IAQVV/LVKIE region.
Western blot experiments of the Pikp-1:ancHMA* mutants (C-terminally tagged with HF) labelled above. Pikp-2 (C-terminally tagged with HA) was included as a negative control. Proteins were …
Figure 7 with 2 supplements
The MKANK/EMVKE region of the heavy metal-associated (HMA) domain of Pikm-1 determines high-affinity AVR-PikD binding.
(A) Protein sequence alignment between the ancestral HMA (ancHMA), Pikm-HMA, and Pikm–ancHMA chimeras. The protein model above the alignment depicts Pikm-HMA secondary structure. The colour-coded …
Figure 7—figure supplement 1
Protein sequence alignment of the heavy metal-associated (HMA) domain from the Oryza spp.
Sequences of the K-type Pik-1-integrated HMA domains (blue), non-integrated HMAs from O. sativa and O. brachyantha (grey), and I-N2 ancHMA (bold) were aligned using MUSCLE (Edgar, 2004). Regions …
Figure 7—figure supplement 2
Replicates of the co-immunoprecipitation (co-IP) experiment between the Pikm-1:ancHMA chimeras and AVR-PikD.
In planta association of AVR-PikD (N-terminally tagged with FLAG) with Pikp-1, Pikp-1E230R, Pikm-1, Pikm-1:ancHMA, and Pikm-1:ancHMA chimeras (N-terminally tagged with HA), labelled above. Wild-type …
Figure 8 with 5 supplements
The ANK-VKE substitutions are essential for Pikm-HMA adaptation towards high-affinity binding to AVR-PikD.
(A) Schematic representation of the neighbour joining (NJ) tree of the ancestral HMA (HMA) domains from Oryza spp. (shown in Figure 3—figure supplement 2). The scale bar indicates the evolutionary …
-
Figure 8—source data 1
Raw data of Pikm-ancHMA Rmax SPR.
- https://cdn.elifesciences.org/articles/66961/elife-66961-fig8-data1-v1.xlsx
Figure 8—figure supplement 1
Replicates of the co-immunoprecipitation experiment between Pikm-1:ancHMA mutants in the MKANK/EMVKE region and AVR-PikD.
In planta association of AVR-PikD (N-terminally tagged with FLAG) with Pikp-1, Pikp-1E230R, Pikm-1, Pikm-1:ancHMA, and Pikm-1:ancHMA mutants (N-terminally tagged with HA), labelled above. Wild-type …
Figure 8—figure supplement 2
Purified proteins used in surface plasmon resonance studies.
(A) Coomassie Blue-stained SDS-PAGE gel showing purified heavy metal-associated proteins used in in vitro experiments. (B) Table summarising intact masses (monoisotopic) of proteins from (A). *The …
Figure 8—figure supplement 3
Different stoichiometry of the ancHMA–AVR-PikD complexes.
Analytical gel filtration traces depicting the retention volumes of AVR-PikD in complexes with (A) ancHMA and (B) ancHMAEMVKE with 5-amino acid extension, and (C) ancHMA and (D) ancHMALVKIE without …
Figure 8—figure supplement 4
Surface plasmon resonance (SPR) results showing the effect of the step-by-step mutations within the MKANK/EMVKE region on the AVR-PikD binding in vitro, as indicated by %Rmax.
(A) Schematic illustration of the SPR sensorgram and the timepoints corresponding to ‘binding’ and ‘dissociation’, recorded in this study. (B) Plots illustrating calculated percentage of the …
Figure 8—figure supplement 5
The surface plasmon resonance (SPR) sensorgrams for the AVR-PikD–HMA binding.
The SPR sensorgrams from five independent replicates are shown. His-tagged AVR-PikD was immobilised on the sample cell, giving a response level of 99 ± 33 response units (RU).
Figure 9 with 1 supplement
Model of molecular convergence of Pikp-1 and Pikm-1 towards AVR-PikD binding at high affinity.
(A) The heavy metal-associated (HMA) domains of Pikp-1 and Pikm-1 receptors have convergently evolved through distinct evolutionary and biochemical paths to bind AVR-PikD with high affinity. The …
Figure 9—figure supplement 1
The Val-230-Glu mutation within the LVKIE region of ancestral HMA (ancHMA) enhances interaction with AVR-PikD through hydrogen bond formation.
(A) Schematic representation of the structure of ancHMALVKIE complexed with the AVR-PikD effector. The molecules are shown as ribbons with selected side chains presented as sticks and labelled; the …
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Recombinant DNA reagent | pICH41308 | Addgene | No. 47998 | Golden Gate level 0 acceptor |
| Recombinant DNA reagent | pICSL12008 | TSL (The Sainsbury Laboratory) SynBio team | 35S + Ω promoter Golden Gate module | |
| Recombinant DNA reagent | pICH41414 | Addgene | No. 50337 | 35S terminator Golden Gate module |
| Recombinant DNA reagent | pICSL30007 | TSL (The Sainsbury Laboratory) SynBio team | N-terminal 6×HA Golden Gate module | |
| Recombinant DNA reagent | pICH47732 | Addgene | No. 48001 | Level 1 binary vector |
| Recombinant DNA reagent | p41308-PikpN | This paper | Materials and methods: Cloning for in planta assays | |
| Recombinant DNA reagent | p41308-PikpC | This paper | Materials and methods: Cloning for in planta assays | |
| Recombinant DNA reagent | pICSL13004 | TSL (The Sainsbury Laboratory) SynBio team | Mas promoter Golden Gate module | |
| Recombinant DNA reagent | pICSL50001 | TSL (The Sainsbury Laboratory) SynBio team | C-terminal HF Golden Gate module | |
| Recombinant DNA reagent | pICH77901 | TSL (The Sainsbury Laboratory) SynBio team | Mas terminator Golden Gate module | |
| Recombinant DNA reagent | p41308-PikmN | This paper | Materials and methods: Cloning for in planta assays | |
| Recombinant DNA reagent | p41308-PikmC | This paper | Materials and methods: Cloning for in planta assays | |
| Recombinant DNA reagent | pOPIN-M | Addgene | No. 26044 | E. coli expression vector |
| Recombinant DNA reagent | AVR-PikD in pOPIN-S3C | Maqbool et al., 2015 | E. coli expression construct | |
| Commercial assay, kit | Anti-HA Affinity Matrix, from rat IgG1 | Roche | 11815016001 | Materials and methods: Protein–protein interaction studies: co-IP; 20 μL |
| Antibody | HA-probe (F-7) HRP-conjugated; mouse monoclonal IgG2a | Santa Cruz Biotech | sc-7392 | Materials and methods: Protein–protein interaction studies: co-IP; 1:5000 |
| Antibody | Mouse monoclonal ANTI-FLAG M2 | Sigma | F3165 | Materials and methods: Protein–protein interaction studies: co-IP |
| Antibody | A-14 anti-Myc antibody; A-14 anti-Myc antibody | Santa Cruz Biotechnology | Sc-40 | Materials and methods: Protein–protein interaction studies: co-IP; 1:5000 |
| Commercial assay, kit | Pierce ECL Western Blotting Substrate | Thermo Fisher Scientific | 32109 | Materials and methods: Protein–protein interaction studies: co-IP; 1:5000 |
| Commercial assay, kit | SuperSignal West Femto Maximum Sensitivity Substrate | Thermo Fisher Scientific | 34094 | Materials and methods: Protein–protein interaction studies: co-IP; 1:5000 |
| Commercial assay, kit | Pierce Reversible Protein Stain Kit | Thermo Fisher Scientific | 24585 | Materials and methods: Protein–protein interaction studies: co-IP; 1:5000 |
| Software, algorithm | CCP4i2 graphical interface | Potterton et al., 2018 | Materials and methods: Crystallisation, data collection, and structure solution | |
| Software, algorithm | MolProbity | Chen et al., 2010 | Materials and methods: Crystallisation, data collection, and structure solution | |
| Software, algorithm | CCP4MG | McNicholas et al., 2011 | Materials and methods: Crystallisation, data collection, and structure solution | |
| Software, algorithm | SWISS-MODEL | Waterhouse et al., 2018 | Materials and methods: Crystallisation, data collection, and structure solution | |
| Software, algorithm | besthr | MacLean, 2019 | Materials and methods: Cell death assay | |
| Software, algorithm | NLR-Parser | Steuernagel et al., 2015 | ||
| Software, algorithm | HMMER 3.2b2 | Eddy, 1998 | Materials and methods: Identification and phylogenetic analysis of CC-NLRs from grasses | |
| Software, algorithm | MUSCLE v2.8.31 | Edgar, 2004 | Materials and methods: Identification and phylogenetic analysis of CC-NLRs from grasses | |
| Software, algorithm | QKphylogeny | https://github.com/matthewmoscou/QKphylogeny | Materials and methods: Identification and phylogenetic analysis of CC-NLRs from grasses | |
| Software, algorithm | RAxML v8.2.11 | Stamatakis, 2014 | Materials and methods: Identification and phylogenetic analysis of CC-NLRs from grasses | |
| Software, algorithm | iTOL v5.5.1 | Letunic and Bork, 2007 | Materials and methods: Identification and phylogenetic analysis of CC-NLRs from grasses | |
| Software, algorithm | BLAST v2.3.0 | Altschul et al., 1990 | Materials and methods: Identification and phylogenetic analysis of Pik-1 and Pik-2 homologues | |
| Software, algorithm | MEGA X | Kumar et al., 2018 | Materials and methods: Phylogenetic analyses of rice HMA domains and ancestral sequence reconstruction | |
| Software, algorithm | FastML | Ashkenazy et al., 2012 | Materials and methods: Phylogenetic analyses of rice HMA domains and ancestral sequence reconstruction | |
| Software, algorithm | PAML v4.9j | Yang, 1997 | Materials and methods: Testing for selection | |
| Software, algorithm | ggplot2 R v3.6.3 package | Ginestet, 2011 | Materials and methods: Testing for selection | |
| Software, algorithm | SNAP | https://www.hiv.lanl.gov/ | Materials and methods: Testing for selection | |
| Sequence-based reagent | 5′-TGAAGCAGATCCGAGACATAGCCT-3′ | This study | PCR primer | Materials and methods: Identification and cloning of Pik-1 and Pik-2 from Oryza brachyantha |
| Sequence-based reagent | 5′-TACCCTGCTCCTGATTGCTGACT-3′ | This study | PCR primer | Materials and methods: Identification and cloning of Pik-1 and Pik-2 from Oryza brachyantha |
| Sequence-based reagent | 5′-AGGGAGCAATGATGCTTCACGA-3′ | This study | PCR primer | Materials and methods: Identification and cloning of the Pik-1–integrated HMA domains from wild rice relatives |
| Sequence-based reagent | 3′-TTCTCTGGCAACCGTTGTTTTGC-5′ | This study | PCR primer | Materials and methods: Identification and cloning of the Pik-1–integrated HMA domains from wild rice relatives |
| Commercial assay or kit | In-Fusion HD Cloning | Clontech | 639647 | Materials and methods: Cloning for in vitro studies |
| Gene (O. brachyantha) | W0654 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of Pik-1 and Pik-2 from Oryza brachyantha | |
| Gene (O. brachyantha) | W0655 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of Pik-1 and Pik-2 from Oryza brachyantha | |
| Gene (O. brachyantha) | W0656 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of Pik-1 and Pik-2 from Oryza brachyantha | |
| Gene (O. brachyantha) | W1057 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of Pik-1 and Pik-2 from Oryza brachyantha | |
| Gene (O. brachyantha) | W1401 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of Pik-1 and Pik-2 from Oryza brachyantha | |
| Gene (O. brachyantha) | W1402 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of Pik-1 and Pik-2 from Oryza brachyantha | |
| Gene (O. brachyantha) | W1403 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of Pik-1 and Pik-2 from Oryza brachyantha | |
| Gene (O. brachyantha) | W1404 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of Pik-1 and Pik-2 from Oryza brachyantha | |
| Gene (O. brachyantha) | W1405 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of Pik-1 and Pik-2 from Oryza brachyantha | |
| Gene (O. brachyantha) | W1407(B) | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of Pik-1 and Pik-2 from Oryza brachyantha | |
| Gene (O. brachyantha) | W1703 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of Pik-1 and Pik-2 from Oryza brachyantha | |
| Gene (O. brachyantha) | W1705 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of Pik-1 and Pik-2 from Oryza brachyantha | |
| Gene (O. brachyantha) | W1706 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of Pik-1 and Pik-2 from Oryza brachyantha | |
| Gene (O. brachyantha) | W1708 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of Pik-1 and Pik-2 from Oryza brachyantha | |
| Gene (O. brachyantha) | W1711 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of Pik-1 and Pik-2 from Oryza brachyantha | |
| Gene (O. brachyantha) | W1712 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of Pik-1 and Pik-2 from Oryza brachyantha | |
| Gene (O. brachyantha) | W0654 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. australiensis) | W0008 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. australiensis) | W1628 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. barthii) | W1643 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. barthii) | W1605 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. barthii) | W0042 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. barthii) | W0698 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. eichingeri) | W1526 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. glumaepatula) | W1171 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. glumaepatula) | W2203 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. grandiglumis) | W1480(B) | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. granulata) | W0005 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. granulata) | W0067(B) | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. latifolia/O. alta) | W0542 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. latifolia/O. alta) | W1539 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. longiglumis) | W1228 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. longistaminata) | W1504 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. longistaminata) | W1540 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. longistaminata) | W0643 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. meridionalis) | W2081 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. meridionalis) | W2112 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. meyeriana) | W1354 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. minuta) | W1328 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. officinalis) | W0614 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. officinalis) | W1200 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. punctata) | W1408 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. punctata) | W1514 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. rhizomatis) | W1808 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. ridleyi) | W0001 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. ridleyi) | W2035 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. rufipogon) | W2003 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. rufipogon) | W1715 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. rufipogon/ O. meridionalis) | W2117 | Wild Rice Collection ‘Oryzabase’; Kurata and Yamazaki, 2006 | Materials and methods: Identification and cloning of the Pik-1-integrated HMA domains from wild rice relatives | |
| Gene (O. brachyantha) | LOC102699268 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. barthii) | OBART11G23150 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. longistaminata) | KN541092.1 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. punctata) | OPUNC11G19550 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. sativa) | HM035360.1 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. sativa) | HM048900_1 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. sativa) | HQ662330_1 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. sativa) | HQ662329_1 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. sativa) | AB462324.1 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. brachyantha) | LOC102708959 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. brachyantha) | LOC102709146 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. brachyantha) | LOC102714171 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. brachyantha) | LOC102716957 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. brachyantha) | LOC102717220 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. sativa) | LOC_Os04g39360 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. sativa) | LOC_Os04g39370 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. sativa) | Os04g0469000_01 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. sativa) | Os02g0585200 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. sativa) | Os02g0584800_01 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. sativa) | Os02g0584700_01 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. sativa) | Os04g0469300_01 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains and ancestral sequence reconstruction | |
| Gene (O. sativa) | Os02g0585100 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. sativa) | Os02g0584600 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. sativa) | OSJNBa0060P14.7_01 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains and ancestral sequence reconstruction | |
| Gene (O. sativa) | Os04g0464100_01 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction | |
| Gene (O. sativa) | Os02g0582600 | GenBank | Materials and methods: Phylogenetic analyses of rice HMA domains andancestral sequence reconstruction |
Additional files
-
Supplementary file 1
Supplementary tables A–N.
- https://cdn.elifesciences.org/articles/66961/elife-66961-supp1-v1.docx
-
Supplementary file 2
Full list of all Poaceae NLRs and filtering details.
- https://cdn.elifesciences.org/articles/66961/elife-66961-supp2-v1.xlsx
-
Supplementary file 3
Site selection test for K-type HMAs.
- https://cdn.elifesciences.org/articles/66961/elife-66961-supp3-v1.xlsx
-
Supplementary file 4
ancHMA prediction probabilities.
- https://cdn.elifesciences.org/articles/66961/elife-66961-supp4-v1.xlsx
-
Transparent reporting form
- https://cdn.elifesciences.org/articles/66961/elife-66961-transrepform-v1.docx
