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. 2021 Feb 2;33(4):814–831. doi: 10.1093/plcell/koaa002

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.