Fig. 4: NLR gene profiles and expressions patterns in the cointree genome.

A UMAP clustering of NLR genes based on sequence similarity, showing relationships among CNL, TNL, NL, and RNL subfamilies. B Distribution of NLRs in both haplotypes across different FPKM intervals for three tissues. C Ternary plot of expression levels for 853 NLRs across all transcriptome samples. Each dot represents a gene triad with R, S, and L coordinates. Genes near vertices are dominant, those along edges are suppressed, and grey dots near the center indicate balanced triads. D Venn diagram of highly expressed NLR genes (FPKM > 5.46) across three tissues. E Ratio of TE insertions in the four NLR types across two haplotypes. F Boxplot of total TE numbers in each NLR type with Student’s t-test statistical comparisons. The sample size used to derive statistics for each NLR type are indicated below each plot: CNL (n = 146), NL (n = 183), RNL (n = 6), and TNL (n = 96) in HapA; and CNL (n = 131), NL (n = 191), RNL (n = 6), and TNL (n = 98) in HapB. G Boxplot showing FPKM distributions of allelic versus non-allelic genes within the CNL (n = 240 vs. n = 36), NL (n = 290 vs. n = 87), and TNL (n = 170 vs. n = 25) families, with Student’s t-test statistical comparisons. Non-allelic genes were not present in the RNL family and are therefore excluded. H Venn diagram of NLRs exhibiting ASE across three tissues. I Collinearity analysis showing a ~ 246 kb deletion on chromosome 9 of HapA, with associated simple repeats (SRs) and transposable elements (TEs). J Ultra-long ONT read alignments confirming the ~250 kb deletion, supported by approximately half the read depth. K Distribution of NLR gene types across four Rhamnaceae species. L Maximum-likelihood phylogenetic tree of RNLs from four Rhamnaceae species.