The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution

Abstract

AbstractBackgroundTheFerulagenus encompasses 180–185 species and is one of the largest genera in Apiaceae, with many ofFerulaspecies possessing important medical value. The previous studies provided more information forFerula, but its infrageneric relationships are still confusing. In addition, its genetic basis of its adaptive evolution remains poorly understood. Plastid genomes with more variable sites have the potential to reconstruct robust phylogeny in plants and investigate the adaptive evolution of plants. Although chloroplast genomes have been reported within theFerulagenus, few studies have been conducted using chloroplast genomes, especially for endemic species in China.ResultsComprehensively comparative analyses of 22 newly sequenced and assembled plastomes indicated that these plastomes had highly conserved genome structure, gene number, codon usage, and repeats type and distribution, but varied in plastomes size, GC content, and the SC/IR boundaries. Thirteen mutation hotspot regions were detected and they would serve as the promising DNA barcodes candidates for species identification inFerulaand related genera. Phylogenomic analyses with high supports and resolutions showed thatTalassia transiliensisandSoranthus meyeriwere nested in theFerulagenus, and thus they should be transferred into theFerulagenus. Our phylogenies also indicated the monophyly of subgeneraSinoferulaand subgeneraNarthexinFerulagenus. Twelve genes with significant posterior probabilities for codon sites were identified in the positively selective analysis, and their function may relate to the photosystem II, ATP subunit, and NADH dehydrogenase. Most of them might play an important role to helpFerulaspecies adapt to high-temperatures, strong-light, and drought habitats.ConclusionPlastome data is powerful and efficient to improve the support and resolution of the complicatedFerulaphylogeny. Twelve genes with significant posterior probabilities for codon sites were helpful forFerulato adapt to the harsh environment. Overall, our study supplies a new perspective for comprehending the phylogeny and evolution ofFerula.