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.