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.

Keywords: Apiaceae; DNA barcoding; Ferula; Phylogenetic relationships; Plastome evolution; Talassia and Soranthus.

Fig. 1

Plastome maps of twenty-two species. Genes shown outside of outward layer circle are transcribed clockwise, while those insides are transcribed counterclockwise. The genes belonging to different functional groups are color-coded. The green area of the inner circle denotes the GC content of plastome

Fig. 2

Analysis of simple sequence repeats (SSRs) and repeat sequences in 22 species plastomes. A Total numbers of various repeat types. B Total Numbers of different repeat types. C Number of repeats divided by length

Fig. 3

The RSCU values of all concatenated protein-coding genes for 22 species plastomes. Color key: the red values mean higher RSCU values and the blue values mean lower RSCU values. (*) to mark the terminator codons

Fig. 4

Comparison of the border of the LSC, SSC, and IR regions among twenty-two species plastomes

Fig. 5

Sequence identity plots of the 22 species plastomes using F. sinkiangensis as a reference

Fig. 6

Comparative analysis of the nucleotide diversity (Pi) values among the twenty-two species plastomes: A coding regions; B non-coding regions

Fig. 7

Phylogenetic tree reconstruction of 42 taxa inferred from Maximum likelihood (ML) and Bayesian inference (BI) analyses based on the single-copy CDs. Numbers indicate Bayesian posterior probabilities (PP) and maximum likelihood bootstrap values (BS), and (*) indicates maximum support in both two analyses

Fig. 8

Combination of mericarps and partial plastome CDSs phylogenetic tree from twenty-two species in the black box, with arrows indicating correspondence. Scale bars: dorsal side views = 1 mm, transverse sections = 1 mm

Fig. 9

Partial alignment of three out of twelve positively selected genes. A Partial aligned amino acids sequences of the rpoC2 gene; B partial aligned amino acids sequences of the atpF gene; C partial aligned amino acids sequences of the ndhK gene. The red blocks indicate the amino acids in Ferula, Talassia, and Soranthus with a high BEB posterior probability