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

Abstract

Background The Ferula genus encompasses 180–185 species and is one of the largest genera in Apiaceae, with many of Ferula species possessing important medical value. The previous studies provided more information for Ferula, 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 the Ferula genus, few studies have been conducted using chloroplast genomes, especially for endemic species in China. Results Comprehensively 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 in Ferula and related genera. Phylogenomic analyses with high supports and resolutions showed that Talassia transiliensis and Soranthus meyeri were nested in the Ferula genus, and thus they should be transferred into the Ferula genus. Our phylogenies also indicated the monophyly of subgenera Sinoferula and subgenera Narthex in Ferula genus. 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 help Ferula species adapt to high-temperatures, strong-light, and drought habitats. Conclusion Plastome data is powerful and efficient to improve the support and resolution of the complicated Ferula phylogeny. Twelve genes with significant posterior probabilities for codon sites were helpful for Ferula to adapt to the harsh environment. Overall, our study supplies a new perspective for comprehending the phylogeny and evolution of Ferula.

Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses

“…The incongruences between ITS-based and plastome-based phylogenies are a common phenomenon in Apiaceae [ 31 , 33 , 35 , 36 , 67 ], and our results are no exception. These incongruences are mainly caused by hybridization/introgression, incomplete lineage sorting (ILS) and chloroplast capture events [ 20 ], as well as the maternal inheritance of plastid and biparental inheritance of ITS, which may also be an important factor [ 30 ].…”

“…The plastome is uniparental inheritance, lacks recombination, and has highly variable loci; thus, it has been widely used in phylogenetic studies of angiosperms, especially at the low taxonomic levels of Apiaceae [ 20 , 30 – 32 , 35 – 40 , 66 , 67 ]. In the present study, the plastome data generated a well-resolved phylogenetic tree for Sanicula .…”

Sesquiterpenes and Sesquiterpene Derivatives from Ferula: Their Chemical Structures, Biosynthetic Pathways, and Biological Properties

“…Several Ferula species have a long history of use in traditional medicine due to their potential therapeutic properties in treating various health conditions, such as gastrointestinal disorders, respiratory issues, and inflammatory diseases. In recent years, due to its important edible and medicinal values, extensive research has been conducted on every aspect of Ferula, such as its geographical distribution, physiological ecology, genomics, metabolomics, taxonomy, phytoconstituents, biosynthesis, pharmacological activity, traditional uses, clinical efficacy, and industrial applications [250][251][252][253][254].…”

Table_3.doc

“…The fruit characteristics, as one of the most important morphological characters in the classification system of the Apiaceae, have been widely used in taxonomic studies of many genera of Apiaceae (Xiao et al, 2021;Cai et al, 2022;Lei et al, 2022;Qin et al, 2023). In the present study, we collected mature fruits from eight taxa (three varieties and three type varieties, and two new species) of Sanicula in the field and fixed them in formaldehyde-acetic acid-ethanol (FAA) solution.…”

“…In most angiosperms, plastids are usually considered to be inherited from the maternal parent and have low nucleotide substitution rates (Wicke et al, 2011;Wataru and Tsuneaki, 2023). Thus, the plastid genomes (plastomes) have been widely and successfully used for plant phylogenetic analyses (Duminil et al, 2012;Miller et al, 2014;Razafimandimbison et al, 2014;Zhang et al, 2018;Schneider et al, 2021;Xu and Hong., 2021;Ji et al, 2022;Scatigna et al, 2022;Xiang et al, 2022;Baldwin et al, 2023;Fu et al, 2023), especially for those taxonomically controversial taxa within the family Apiaceae (Gou et al, 2020;Ren et al, 2020Ren et al, , 2022Cai et al, 2022;Liu et al, 2022;Guo et al, 2023;Liu et al, 2023a;Lei et al, 2022;Gui et al, 2023;Peng et al, 2023;Qin et al, 2023;Song et al, 2023;Tian et al, 2023;Song et al, 2024). For example, Song et al (2023) transferred Peucedanum franchetii C.Y.Wu & F.T.Pu under the genus Ligusticopsis Leute based on phylogenetic analysis of ten plastomes.…”