Fig 1.
Graphic representation of features identified in the plastome of three Atractylodes species by using CPGAVAS2.
The map contains four rings. From the center going outward, the first circle shows the forward and reverse repeats connected with red and green arcs, respectively. The next circle shows the tandem repeats marked with short bars. The third circle shows the microsatellite sequences identified using MISA. The fourth circle is drawn using drawgenemap and shows the gene structure on the plastome. The genes were colored based on their functional categories, which are shown at the left corner.
Table 1.
Summary of the plastome features for the three Atractylodes species.
Table 2.
Gene contents of the three Atractylodes plastomes.
Fig 2.
Sequence identity plot comparing the three plastomes with A. lancea as the reference by using mVISTA.
Gray arrows above the alignment indicate genes and their orientation, with their names labeled on top of the arrows. A cut-off of 70% identity was used to make the plots. The x-axis indicates the position of the plastomes, and the y-axis represents the percent identity ranging from 50% to 100%. Regions colored differently represent gene, exon, tRNA, and CNS. CNS: conserved noncoding sequences.
Fig 3.
Molecular phylogenetic analyses.
Plastome sequences of 64 common proteins present from 40 species (Ageratina adenophora, Anaphalis sinica, Atractylodes chinensis, Atractylodes lancea, Atractylodes macrocephal, Aztecaster matudae, Baccharis genistelloides, Carthamus tinctorius, Centaurea diffusa, Chrysanthemum indicum, Conyza bonariensis, Cynara baetica, Cynara cornigera, Diplostephium alveolatum, Echinacea angustifolia, Eclipta prostrata, Floscaldasia hypsophila, Galinsoga quadriradiata, Guizotia abyssinica, Helianthus annuus, Heterothalamus alienus, Hinterhubera ericoides, Jacobaea vulgaris, Lactuca sativa, Laennecia sophiifolia, Laestadia muscicola, Lagenophora cuchumatanica, Leontopodium leiolepis, Llerasia caucana, Menyanthes trifoliate, Mikania micrantha, Oritrophium peruvianum, Parastrephia quadrangularis, Pericallis hybrida, Praxelis clematidea, Saussurea chabyoungsanica, Scaevola taccada, Soliva sessilis, Taraxacum amplum, and Westoniella kohkemperi) were used to construct the phylogenetic tree with the maximum likelihood method implemented in the RAxML. Two taxa, namely, Menyanthes trifoliata and Nymphoides coronata, which were the closest relatives based on the APG IV system, were used as outgroups. Tribes to which each species belongs are shown on the right side of the tree. Bootstrap supports were calculated from 1000 replicates.
Fig 4.
Alignment of the cz11 sequences from 15 individual plant samples of the three Atractylodes species.
Arabic numerals represent different individuals. Letters a, b, and c represent duplicated Sanger sequencing results, and the red bases indicate different bases among the three species. The two regions (A and B) that can be used to distinguish the three species are highlighted with squares.
Table 3.
The information for the samples collected from the field and their validation results.
Table 4.
Types and frequencies of individual allele sequence of the cz11 marker loci among the three Atractylodes species.
Fig 5.
Multiple sequence alignment and phylogenetic analysis of nuclear gene SLD5 from three Atractylodes species.
(A) Alignment of two sequences from A. macrocephala and one sequence from A. lancea and A. chinensis each. The sequence from Arabidopsis thaliana was provided as outer group. (B) Phylogenetic tree was constructed with the maximum likelihood method implemented in the RAxML. The A. thaliana, was used as the outgroup. Bootstrap supports were calculated from 1000 replicates.