Fig. 2: Phylogeny and hybridization patterns of Lilium.
From: The giant genome of lily provides insights into the hybridization of cultivated lilies
a The phylogenetic tree of the wild Lilium species and cultivated lilies was inferred from combined RNA-seq data of wild Lilium species and Lilium cultivars. The blue numbers labeled on the tree represent the classified clades. Bootstrap values for important branches were labeled above branches. b Heatmap showing shared genomic haplotype patterns among different lily species. Each cell represents the ratio of the number of transcripts with the highest gene similarity (identity >95%) between two species to the total number of transcripts within the corresponding species in that row (excluding self-aligning transcripts). The intensity of the box color reflects the proportion of gene similarity (best match ratio, BMR), with redder shades indicating higher similarity. The yellow rectangle highlights shared genomic haplotypes between clades, while boxes of species within the same clade are delineated by black rectangles. The order of species represented vertically (from top to bottom) and horizontally (from left to right) in the heatmap corresponds to the order of species in the phylogenetic tree represented in (a). c The ratios of the number of gene clusters obtained through Orthofinder to the number of genes within a cluster were depicted for different lilies within Clade 1-1 (upper panel) and Clade 1-2 (lower panel). Source data are provided as a Source Data file.
