| Summary: | The taxonomy of an ancient gymnosperm genus <i>Taxus</i>, with high value in horticulture and medicine, is perplexing because of few reliable morphological characters for diagnosing species. Here, we performed a comprehensive investigation of the evolutionary dynamics of <i>Taxus</i> chloroplast genomes and estimated phylogenetic relationships, divergence times, and ancestral distributions of <i>Taxus</i> species by comparing 18 complete chloroplast genomes. The variations across the chloroplast genome of different <i>Taxus</i> species indicated that remarkably varied genome variations across lineages have reshaped the genome architecture. Our well-resolved phylogeny supported that <i>T. brevifolia</i> Nutt. was basal lineages followed by the other North America lineages. Divergence time estimation and ancestral range reconstruction suggested that the <i>Taxus</i> species originated in North America in the Late Cretaceous and revealed that extant <i>Taxus</i> species shared a common ancestor whose ancestral distribution area was probably in North America and afterwards the earliest members expanded to Southeast Asia from where Chinese <i>Taxus</i> species originated. The predominant European species have more closer relationship with the Eastern Asian species and the speciation of Eurasia species arose from several dispersal and vicariance events in the Miocene. Genome-wide scanning revealed 18 positively selected genes that were involved in translation and photosynthesis system in <i>Taxus</i>, which might be related to the adaptive evolution of <i>Taxus</i> species. The availability of these complete chloroplast genomes not only enhances our understanding of the elusive phylogenetic relationships and chloroplast genome evolution such as conservation, diversity, and gene selection within <i>Taxus</i> genus but also provides excellent templates and genetic bases for further exploration of evolution of related lineages as well as for plant breeding and improvement.
|
|---|