Fig. 2: Evolution of the allotetraploid Perilla.
From: Incipient diploidization of the medicinal plant Perilla within 10,000 years
a Distribution of synonymous nucleotide substitutions (dS) between the four perilla sequences. The dS = 0 signal between PFA-PC02 (n = 8939) was not displayed. b Chromosomal synteny between PF and PC genomes. Each dot represented syntenic gene relationship between PFA-PC02 (19,412 gene pairs, in red) or PFB-PC02 (15,422 gene pairs, in blue). Scattered segmental duplications not related to polyploidization were shown by magenta dots. PF chromosomes underlined were reversed for visual consistence. c Patterns and statistics of nucleotide mutational signatures of PFA and PC02 since polyploidization. The signatures are displayed according to the 96-substitution classification defined by substitution class and sequence context immediately 5′ and 3′ to the mutated base, and displayed alphabetically from ANA to TNT. d Subgenome expression dominance as calculated by log2 transformed TPM (Transcripts Per Million) ratio of PFA to PFB syntenic genes (n = 15,484). Solid lines represented RNA-seq data of PF40 from flower and leaf with three replicates each. For any paired TPM values of <1, a pseudo-count of 1 was added to both PFA and PFB values before log2 ratio calculation. Enlarged inset showed expression bias toward PFA with a minor peak around 0.2 (red downward arrowhead). Source data underlying Fig. 2c are provided as a Source data file.
