Fig. 2: Functional NLRs are highly expressed in the de novo assembled transcriptome of unchallenged plants of Aegilops, Cajanus, Arabidopsis, Solanum and Hordeum species.

a–f, Known functional NLRs from each species are among the most highly expressed NLR transcripts from unchallenged plant tissue (Supplementary Data 2). Transcript abundance was estimated from self-aligned RNA-seq data and measured in transcripts per million (TPM). Panel a shows transcript abundance of NLRs from the de novo assembled leaf transcriptomes of Hordeum vulgare accessions Golden Promise, CI16153 and CI16147. The expression of the functional resistance gene Rps7 against Bh and Pst is indicated. Panel b shows transcript abundance of NLRs from the de novo assembled leaf transcriptomes of Aegilops tauschii accessions KU2025, KU2075, KU2078, KU2093, KU2124 and PI499262. The expression of the functional resistance genes Sr45, Sr46 and SrTA1662 against Pgt is indicated. Panel c shows transcript abundance of NLRs from the leaf transcriptomes of Arabidopsis thaliana accessions Col-0, Ler-0, Sf-2 and Ws-0. The expression of the functional resistance genes RPP4, RPP5, RPP8 and RPP13 to downy mildew (caused by Hyaloperonospora arabidopsidis); WRR4 against white rust (Albugo candida); ZAR1 against Pseudomonas syringae and Xanthomonas campestris pv. campestris; RPS2 and RPM1 against Pseudomonas syringae; RCY1 against cucumber mosaic virus; and alleles of RLM3 against grey mould (Botrytis cinerea), dark leaf spot of cabbage (Alternaria brassicicola) and dark spot of crucifers (Alternaria brassicae) is indicated. Panel d shows transcript abundance of NLRs from the Cajanus cajan accession G119-99 leaf transcriptome. The expression level of CcRpp1, which confers resistance to Asian soybean rust (Phakopsora pachyrhizi)⁵⁸, is indicated. Panel e shows transcript abundance of NLRs from the de novo assembled leaf transcriptome of Solanum americanum accession SP2273. The expression of the functional resistance genes Rpi-amr1 and Rpi-amr3 to late blight (Phytophthora infestans) is indicated. An allele of Ptr1, which recognizes Pseudomonas syringae pv. tomato and Ralstonia pseudosolanacearum in Solanum lycopersicoides, is also shown. Helper NLRs are annotated as NRC1, NRC2, NRC3, NRC4 and NRC0 as defined by Kourelis et al.¹⁴⁰. NRC6 is not present in the dataset. Panel f shows transcript abundance of NLRs from Solanum lycopersicum cultivars VFNT Cherry and Motelle carrying Mi-1 with resistance to root-knot nematodes (Meloidogyne spp.), the potato aphid (Macrosiphum euphorbiae) and the sweet potato whitefly (Bemisia tabaci). Mi-1 is highly expressed in both cultivars in both leaf and root tissue. The expression levels of additional known functional NLRs Tm-2 for resistance to tobamoviruses including tomato mosaic virus and tobacco mosaic virus, Prf for resistance to Pseudomonas syringae pv. tomato, Sw5 for resistance to a broad range of viruses across paralogues and Ph-3 for resistance to P. infestans are indicated. Helper NLRs are annotated as NRC1, NRC2, NRC3, NRC4, NRC6 and NRC0 as defined by Kourelis et al.¹⁴⁰.