Comparative Chloroplast Genomics, Phylogenomics, and Divergence Times of <i>Sassafras</i> (Lauraceae)

In the traditional classification system of the Lauraceae family based on morphology and anatomy, the phylogenetic position of the genus <i>Sassafras</i> has long been controversial. Chloroplast (cp) evolution of <i>Sassafras</i> has not yet been illuminated. In this study, we first sequenced and assembled the complete cp genomes of <i>Sassafras</i>, 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 <i>Sassafras</i> 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 (<i>ccs</i>A-<i>ndh</i>D, <i>trn</i>H-<i>psb</i>A, <i>rps</i>15-<i>ycf</i>1, and <i>pet</i>A-<i>psb</i>J) and 672 cp microsatellites were identified for <i>Sassafras</i>. Phylogenetic analysis based on 106 cp genomes from 30 genera within the Lauraceae family demonstrated that <i>Sassafras</i> constituted a monophyletic clade and grouped a sister branch with the <i>Cinnamomum</i> sect. <i>Camphora</i> within the tribe Cinnamomeae. Divergence time between <i>S. albidum</i> and its East Asian siblings was estimated at the Middle Miocene (16.98 Mya), <i>S. tzumu</i> diverged from <i>S. randaiense</i> 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 <i>Sassafras</i>. Overall, our study clarified the evolution pattern of <i>Sassafras</i> cp genomes and elucidated the phylogenetic position and divergence time framework of <i>Sassafras</i>.