Table 1.

Examples of plant pan-genome or pan-NRLome studies and key observations on NLRs or R genes

Plant pan-genome or pan-NLRome studies
Organism (s)	N	Sequencing technology	Assembly strategy	Reference	Key observations on NLR or R genes
Brassica rapa	3	Short reads	De novo assemblies	Lin et al. (2014)	– NLRs enriched in dispensable genome.
Glycine soja	7	Short reads	De novo assemblies	Li et al. (2014)	– CNVs common in NLRs: candidates of resistance differences between wild and cultivated accessions.   – NLRs numbers and domain architectures varying between species.   – NLRs enriched in dispensable genome.
Zea mays	503	Short reads	De novo transcriptome	Hirsch et al. (2014)
Oryza sativa	3	Short reads	De novo assemblies	Schatz et al. (2014)	− NLRs enriched in dispensable genome, e.g. 12% shell versus 0.35% core genes are NLRs.
O. sativa	1483	Short reads	Iterative assembly	Yao et al. (2015)	– NLRs enriched in dispensable genome.
Populus clade	7	Short reads	Map to reference	Pinosio et al. (2016)	− CNVs and SVs enriched for NLRs.
Brassica oleraceae	10	Short reads	Iterative assembly	Golicz et al. (2016)	– NLRs enriched in genes showing PAV.   – 43% of NLRs dispensable, 45% in clusters, and 60% absent from reference.
Brachypodium distachyon	54	Short reads	De novo assemblies	Gordon et al. (2017)	− NLRs enriched in genes showing PAV, likely underlying variation in disease resistance.
Triticum aestivum	19	Short reads	Iterative assembly	Montenegro et al. (2017)	– NLRs enriched in genes showing PAV.
Medicago truncatula	15	Short reads	De novo assemblies	Zhou et al. (2017)	− NLRs enriched in dispensable genome show high nucleotide and protein diversity, large effect SNPs, often with PAV, CNVs and differences in domain architectures.
Capsicum clade	383	Short reads	Iterative assembly	Ou et al. (2018)
Oryza clade	66	Short reads	De novo assemblies	Zhao et al. (2018)	− NLRs enriched in dispensable genome.
O. sativa	3010	Short reads	Map to reference	Wang et al. (2018)	– NLRs enriched in dispensable genome.
Brassica napus	53	Short reads	Iterative assembly	Hurgobin et al. (2018)	– NLR enriched in genes showing PAV.   – 30.6% core NLRs, 69.4% variable, and ∼50% absent from reference.
Juglans clade	6	Short reads (long reads for J. regia)	De novo assemblies	Stevens et al. (2018)/Trouern-Trend et al. (2020)	– Overrepresentation of disease resistance genes in rapidly evolving, contracting, and expanding gene families.
Helianthus clade	493	Short reads	Iterative assembly	Hübner et al. (2019)	− NLRs overrepresented in regions introgressed from wild into cultivated species.
Sesamum clade	5	Short reads	De novo assemblies	Yu et al. (2019)	– Defense response genes expanded (e.g. RPM1), positively selected for and fast evolving.
Lycopersicon clade	725	Short reads	Iterative assembly	Gao et al. (2019)	– Disease resistance genes enriched in genes lost or selected against during domestication and improvement.   – Defense response genes show high PAV.
Hordeum vulgare	63	Short reads	De novo transcriptome	Ma et al. (2019)	– Higher proportion of NLRs genes in wild versus cultivated genotypes.   – NLRs under high selective pressures during domestication, e.g. Mla genes.
Zea mays	4	Short reads	De novo assemblies	Haberer et al. (2020)
Arabidopsis thaliana	8	Short and long reads	De novo assemblies	Jiao and Schneeberger (2020)	– Low collinearity between accessions in NLR-rich regions.   – SVs in NLRs suppressing meiotic recombination.
Solanum clade	14	Short and ultra-long reads	De novo assemblies	Alonge et al. (2020)	− SV hotspots introgressed from wild into domesticated species enriched for R genes.
P. persica and relatives	4	Short reads (long reads and Hi-C for P. mira)	De novo assemblies	Cao et al. (2020)	– NLRs enriched in dispensable genome.   – Cross-species SV underlying nematode resistance.   – NLR numbers range from 310 to 339 across species.
O. sativa	12	Short and long reads and optical map	De novo assemblies	Zhou et al. (2020)
B. napus	9	Short and long reads (Hi-C and optical map for some)	De novo assemblies	Song et al. (2020)	– Defense response genes enriched for PAV.
Glycine clade	29	Short and long reads, Hi-C and optical map	De novo assemblies and graph	Liu et al. (2020b)	− NLRs enriched in dispensable genome.
A. thaliana	64	RenSeq: short and long reads	Map to reference	Van de Weyer et al. (2019)	– NLR diversity saturation point reached after 40 accessions.   – In 64 accessions, four times higher diversity in NLR architecture than in reference.
Solanum/N. benthamiana/C. annum	18	RenSeq: short and long reads	Map to reference	Seong et al. (2020)	– 128 of 314 NLR annotations improved.   – Preferential expansion of the extended CC-NLR N terminal region.