Tomato relatives reveal shared immune genes depend on how widely scientists look

A new genome-scale study has mapped the shared and variable components of the immune-receptor repertoire across the tomato group and its wild relatives. An analysis of 76 chromosome-level genome assemblies from the tomato group and its closest wild relatives shows that the set of immune receptors shared by all sampled plants shrinks or expands dramatically depending on how much of the wild diversity researchers include. The work also reveals that the rarer genes in the pan-genome carry most of the copy-number and sequence variation, and it prioritises upstream structural states for functional testing.

The study, published in Theoretical and Applied Genetics, focused on intracellular nucleotide-binding leucine-rich repeat receptors, or NLRs. NLR repertoires differ between plants in gene content, genomic organisation and sequence, but the extent of that diversity across the tomato group and allied wild relatives had remained unresolved.

The curation identified 14,582 NLR loci, which formed 291 orthogroups. Of these, shell orthogroups accounted for 10,893 loci, or 74.7 percent of the total. Discovery of low-frequency orthogroups remained unsaturated.

When the analysis included all 76 accessions spanning the full taxonomic breadth, only five orthogroups were universally present. Restricting the sample to the 53 accessions of cultivated Solanum lycopersicum, S. lycopersicum var. cerasiforme and S. pimpinellifolium raised the count to 34. Narrowing further to just 25 cultivated S. lycopersicum accessions increased it to 68. The scope-associated pattern was retained in equal-sized subsamples.

The researchers state that these results define shared and variable components of the pan-NLRome of section Lycopersicon and allied wild Solanum taxa.

The two RPW8-like orthogroups were associated almost exclusively with whole-genome duplication.

Among retained sequence units, nucleotide diversity decreased from S. pimpinellifolium through S. lycopersicum var. cerasiforme to cultivated S. lycopersicum, and increased from core to shell orthogroups.

Structural variation affected the occupancy classes of NLR loci approximately in proportion to their genomic abundance. The analysis also found that strict head-to-head arrangements of NLR genes did not overlap integrated-domain loci.

The CNL066 orthogroup was single-copy in 61 accessions and retained highly similar coding sequences. Three upstream structural states showed distinct accession-group distributions and predicted cis-element compositions. The researchers state that these results prioritise upstream structural states for functional testing.

Subject of Research: Pan-genome diversity of NLR immune receptor genes across tomato and allied wild Solanum species

Article Title: The pan-NLRome of section Lycopersicon and allied wild Solanum taxa reveals taxonomic-scope dependence of shared receptors and shell-enriched copy and sequence diversity

Article References: Zhang, B., Jiang, T., Yang, W., Ao, N., Tang, B., Mo, C., Wang, Q., & Deng, Y. (2026). The pan-NLRome of section Lycopersicon and allied wild Solanum taxa reveals taxonomic-scope dependence of shared receptors and shell-enriched copy and sequence diversity. Theoretical and Applied Genetics, 139(11), Article 322. https://doi.org/10.1007/s00122-026-05435-y

Image Credits: AI Generated

DOI: 10.1007/s00122-026-05435-y

Keywords: NLR receptors, pan-genome, tomato, Solanum, orthogroups, gene copy number, nucleotide diversity, structural variation, disease resistance, RPW8, domestication, cis-regulatory elements