Differential plastome diversification of the Lauraceae between tropical regions of Asia and America

ABSTRACT The Lauraceae, a diverse family with over 50 genera and 3000 species, exhibit exceptional species richness in tropical regions of Asia and America. However, the diversification history of the family remains poorly understood due to biased sampling, i.e. the plastome data of the American genera are poorly represented in particular. In this study, we newly sequenced plastomes of 16 genera, and significantly improved the representativeness of the American genera. We reconstructed a robust phylogenomic tree of the Lauraceae covering 82% of the total genera, and identified two novel plastome types. Our analysis of plastome structural variation reveals divergent spatial patterns: the America-diversified (AMD) genera display greater structural variability than the Asia-diversified (ASD) genera. Specifically, the AMD genera display more plastome types, higher pairwise similarity, and higher nonsynonymous substitution rates. Long repeats play a significant role in shaping the plastome variations. Furthermore, we identified 14 positively selected genes and observed niche differentiation within the AMD genera. Our molecular clock-based age analysis suggests the potential association between the diversification of the AMD genera and Andean uplift in the late Neogene, providing new insights into the diversification of Lauraceae in America.