The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution.
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.
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.
- NCBI accession OP324722; Ferula sinkiangensis chloroplast, complete genome.
- NCBI accession OP324723; Ferula leiophylla chloroplast, complete genome.
- NCBI accession OP324724; Ferula teterrima chloroplast, complete genome.
- NCBI accession OP324725; Ferula akitschkensis chloroplast, complete genome.
- NCBI accession OP324726; Ferula feruloides chloroplast, complete genome.
- NCBI accession OP324727; Ferula songarica chloroplast, complete genome.
- NCBI accession OP324728; Ferula gracilis chloroplast, complete genome.
- NCBI accession OP324729; Ferula lehmannii chloroplast, complete genome.
- NCBI accession OP324730; Ferula canescens chloroplast, complete genome.
- NCBI accession OP324731; Ferula caspica chloroplast, complete genome.
- NCBI accession OP324732; Ferula bungeana chloroplast, complete genome.
- NCBI accession OP324733; Ferula licentiana chloroplast, complete genome.
- NCBI accession OP324734; Ferula dissecta chloroplast, complete genome.
- NCBI accession OP324735; Ferula hexiensis chloroplast, complete genome.
- NCBI accession OP324736; Ferula conocaula chloroplast, complete genome.
- NCBI accession OP324737; Ferula transiliensis chloroplast, complete genome.
- NCBI accession OP324738; Ferula meyeri chloroplast, complete genome.
- NCBI accession OP324739; Ferula syreitschikowii chloroplast, complete genome.
- NCBI accession OP324740; Ferula kirialovii chloroplast, complete genome.
- NCBI accession OP324741; Ferula olivacea chloroplast, complete genome.
- NCBI accession OP324742; Ferula sp. XM-2019a chloroplast, complete genome.
- NCBI accession OP324743; Ferula kingdon-wardii chloroplast, complete genome.