Fig. 2
Comparative genomics analyses between Cinnamomum camphora and C. kanehirae. a Top 20 significant Pfam gains in C. camphora sorted by the ratio of domain counts between C. camphora and C. kanehirae. The cold shock domain (CSD) had the greatest gain in Pfam in C. camphora compared with C. kanehirae. For every Pfam, a z score was calculated for the corresponding abundance in each species. Only z scores greater than 1.50 or less than −1.50 are considered to be significant. b GO enrichment of gene pairs between C. camphora and C. kanehirae showing that genes related to circadian rhythm were positively selected. The x-axis represents the average Ka/Ks ratios of genes in each GO term, and the y-axis represents the enrichment score. GO terms with an average Ka/Ks ratio greater than 0.4 and enrichment score greater than 1.5 are highlighted. c Tandemly duplicated genes in C. camphora compared with C. kanehirae. The left panel shows enriched GO terms related to the stress response of the most tandemly duplicated gene families. The bottom and upper panels show the gene name and number of these tandem-duplicated genes. The dots indicate gene enrichment in corresponding GO terms. d Phylogenetic and tandem duplication analyses of CYP450 genes in C. camphora. Branches of the phylogenetic tree are colour-coded according to CYP450 subgroups. The right panels indicate dense tandem arrays of members from the CYP450 72 or 85 clan. These CYP450 genes formed gene clusters with genes (names in purple) responding to abiotic stress on Chr 7, 12, 1, and 2