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 |