Deducing trajectories of S. rosmarinus.
Angiosperms have been proposed to derive from an ancestral eudicot karyotype (AEK) structured with seven protochromosomes. AEK experienced a known whole-genome triplication (WGT γ event) generating a 21-chromosome intermediate for the formation of the modern chromosomes of most eudicots (Bowers, Chapman, Rong, & Paterson, 2003; Jaillon et al., 2007). To infer the chromosome evolution of rosemary, we identified collinearity blocks across S. rosmarinus , S. miltiorrhiza ,S. splendens and V. vinifera genomes (Figure S8), withV. vinifera used as the reference and to represent the ancestral eudicot karyotype (AEK) genome due to its stable structure among core eudicots (Jaillon et al., 2007; Murat et al., 2017). S. miltiorrhiza and S. splendens have the closest relationships with rosemary among species with whole genome sequenced, therefore,S. miltiorrhiza and S. splendens were used for infering the evolutionary trajectory of rosemary chromosomes. The complexity of rosemary chromosome evolution was demonstrated by collinearity analysis, which revealed that the integrities of grape chromosomes were not preserved in rosemary, (Figure S8). To investigate the possible source of rosemary chromosomes, we analyzed the collinearity relationship between the genomes of rosemary and S. miltiorrhiza. Our analysis showed that the orthologous regions of S. miltiorrhiza chromosome Chr8 with rosemary genome were distributed on rosemary chromosomes Chr2, Chr3, Chr4 and Chr12, indicating that Sm8 was scattered in these rosemary chromosomes after the divergence of rosemary and S. miltiorrhiza (Figure S8). The remaining main part of Chr2, Chr3, Chr4, Chr12 were merged from other S. miltiorrhiza chromosomes. Chr12 had orthologous regions with S. miltiorrhiza chromosome Chr2, Chr4 and Chr7, and the corresponding orthologous regions in grape genome were obtained by using the homologous relationship between S. miltiorrhiza and grape, then evolutionary trajectory of chromosome Chr12 was obtained. The proto‐chromosomes of rosemary and S. miltiorrhiza were the orthologous regions shared between them (Figure 2d). We inferred the chromosomal evolution trajectories of rosemary andS. miltiorrhiza , and showed traces of 26 proto‐chromosomes in extant chromosomes.