Fig. 3: Ultra-long genes display unique transcriptional and epigenomic regulation.

a The distribution of gene length in L. regale. b The intron/exon ratio of each gene between different length categories of full-length genes (n = 15,667 ( < 1 kb), 34,295 (1–10 kb), 11,963 (10–100 kb), 952 ( > 100 kb) genes). Genes without introns were regarded as “0”. c The GC content (%) of different length genes in full genes/exons/introns. The intron/exon ratio of each gene between different length genes (n = 15,667 ( < 1 kb), 34,295 (1–10 kb), 11,963 (10–100 kb), 952 ( > 100 kb) genes). Genes without introns were regarded as “0”. d The TPM of different length genes (n = 5369 ( < 1 kb), 14,262 (1–10 kb), 12,668 (10–100 kb), 3171 ( > 100 kb) genes) in four tissues. e The DNA Methylation ratio (The proportion of 5mC at the given site) of gene bodies, exons and introns between their upstream and downstream (±2 Kb) in flower tissue. Colors represent different lengths of genes. f With many TE insertions, LregChr03G072890 expression under the control of methylation. The gene structure, TE insertions, intact LTR with its insertion time (year), methylation levels (CG, red; CHG, yellow; and CHH, blue; methylation level represent the proportion of 5mC at the given site), gene expression in four tissues (flower, orange; bulb, canary; leaf, cyan; and stem, purple) were plotted from the top to bottom successively. The shaded gray areas represent exon regions. b–d Groups labeled with different lowercase letters indicate significant differences (P < 0.05) based on LSD comparisons following one-way ANOVA, box plots denote the 25th percentile, the median and the 75th percentile, with minimum to maximum whiskers. Source data are provided as a Source Data file. In b, c gene outliers based on GC content are filtered out from total genes.