Comparative Chloroplast Genomics, Phylogenomics, and Divergence Times of (Lauraceae).

In the traditional classification system of the Lauraceae family based on morphology and anatomy, the phylogenetic position of the genus has long been controversial. Chloroplast (cp) evolution of has not yet been illuminated. In this study, we first sequenced and assembled the complete cp genomes of , and conducted the comparative cp genomics, phylogenomics, and divergence time estimation of this ecological and economic important genus. The whole length of cp genomes of the 10 ranged from 151,970 bp to 154,011 bp with typical quadripartite structure, conserved gene arrangements and contents. Variations in length of cp were observed in the inverted repeat regions (IRs) and a relatively high usage frequency of codons ending with T/A was detected. Four hypervariable intergenic regions (A-D, H-A, 15-1, and A-J) and 672 cp microsatellites were identified for . Phylogenetic analysis based on 106 cp genomes from 30 genera within the Lauraceae family demonstrated that constituted a monophyletic clade and grouped a sister branch with the sect. within the tribe Cinnamomeae. Divergence time between and its East Asian siblings was estimated at the Middle Miocene (16.98 Mya), diverged from at the Pleistocene epoch (3.63 Mya). Combined with fossil evidence, our results further revealed the crucial role of the Bering Land Bridge and glacial refugia in the speciation and differentiation of . Overall, our study clarified the evolution pattern of cp genomes and elucidated the phylogenetic position and divergence time framework of .