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

TL;DR

This study analyzes the chloroplast genomes of Sassafras to clarify its evolutionary history and phylogenetic position within the Lauraceae family.

Contribution

The study provides the first complete chloroplast genome analysis of Sassafras, revealing its divergence times and phylogenetic relationships.

Findings

Sassafras chloroplast genomes show conserved structure but variation in inverted repeat regions and codon usage.

Phylogenetic analysis places Sassafras as a sister group to Cinnamomum sect. Camphora.

Divergence times suggest the Bering Land Bridge and glacial refugia influenced Sassafras speciation.

Abstract

In the traditional classification system of the Lauraceae family based on morphology and anatomy, the phylogenetic position of the genus Sassafras has long been controversial. Chloroplast (cp) evolution of Sassafras has not yet been illuminated. In this study, we first sequenced and assembled the complete cp genomes of Sassafras, 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 Sassafras 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 (ccsA-ndhD, trnH-psbA, rps15-ycf1, and petA-psbJ) and 672 cp microsatellites were identified for Sassafras. Phylogenetic analysis based on 106 cp genomes from 30 genera within the Lauraceae family demonstrated that Sassafras constituted a monophyletic clade and grouped a sister branch with the Cinnamomum sect. Camphora within the tribe Cinnamomeae. Divergence time between S. albidum and its East Asian siblings was estimated at the Middle Miocene (16.98 Mya), S. tzumu diverged from S. randaiense 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 Sassafras. Overall, our study clarified the evolution pattern of Sassafras cp genomes and elucidated the phylogenetic position and divergence time framework of Sassafras.

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