Figure 1.
The map of the chloroplast genome of Artemisia frigida.
IR, inverted repeat; LCS, large single copy region; SSC, small single copy region; Inv1, inverted sequence region 1; Inv2, inverted sequence region 2. Genes containing introns are marked with *.
Table 1.
Genes present in Artemisia frigida chloroplast genome.
Figure 2.
Sequence alignment of seven sequenced cp genomes in the Asteraceae family.
Sequences of chloroplast genomes were aligned and compared using mVISTA program. A cut-off of 70% identity was used for the plot and the Y-scale represents the percent identity ranging from 50–100%. Blue represents exons, green-blue represents tRNA and rRNA genes, and pink represents conserved non-coding sequences (CNS). Grey arrows the direction of transcription; horizontal blue lines indicate the position of IRa and IRb; horizontal red lines indicate the position of Inv1 and Inv2.
Figure 3.
Comparison of the SSC region among different Asteraceae species.
Gene sequences in the SSR region were annotated and indicated along the green lines. Genes above the green lines indicate their transcriptions in forward direction and genes below the green lines represent their transcriptions in reverse direction.
Figure 4.
Analyses of SSC inversions in the Asteraceae family.
A. Primer design to amplify junction regions between IR and SSC regions. The positions of ndhF and ycf1 genes in relation to IRa and IRb regions are drawn based on the sequence assembly results of A. frigida in this study and H. annuus and L. sativa from published data [38]. To design primers that amplify the junction region between IRa and left border of the SSC, the forward primer P1F contains the sequence with half of length from IRb and the other half from the SSC region. The sequence of the reverse primer (P1R) is located in the ndhF gene. The same strategy was employed in primer design to amplify the other junction region between ycf1 and IRa regions as indicated. The same strategy was also used to examine the junctions in H. annuus and L. sativa based on their assembled sequences as indicated in the diagram. B. PCR amplification of IR and SSC junction regions in Artemisia frigida, Helianthus annuus and Lactuca sativa. M:Promega 1 kb ladder; lane 1, primer pair P1F and P1R, lane 2, primer pair P2F and P2R, lane 3, primer pair P1F and P2F, and lane 4, primer pair P1R and P2R. C. PCR amplification of IR and SSC junction regions in different accessions of Artemisia frigida. Four Artemisia frigida accessions were used in PCR reactions; CN: cp sequenced accession in this study and originated from China, AG:AG258 from Alaska, USA, W6: W6 30042 from Colorado, USA, and PI: PI 639180 from Mongolia. Lane 1, primer pair P1F and P1R, Lane 2, primer pair P2F and P2R.
Figure 5.
Repeat sequence analysis in seven sequenced Asteraceae chloroplast genomes.
REPuter was used to identify repeat sequences with length ≥30 bp long and sequence identity ≥90% in the cp genomes. F, P, R, and C indicate that the repeats matching in forward, palindrome, reverse, and complement orientations, respectively. Different repeat unit lengths are indicted with different color.
Table 2.
Repeat sequences in the Artemisia frigida chloroplast genome.
Figure 6.
The distribution and frequency of simple sequence repeats in the Artemisia frigida cp genome.
The SSR length is implied by the number of repeat for each SSR type in the Y-axes The percentage of a repeat with specific length from the total number of repeats is indicated above the bars.
Table 3.
Simple sequence repeat in Artemisia frigida chloroplast genome.
Figure 7.
Phylogenetic tree reconstruction of 59 taxa using maximum likelihood (ML) based on concatenated sequence from 61 chloroplast protein-coding genes.
The position of Artemisia frigida is indicated by a red arrow.