Characterization of the Chloroplast Genome of Argyranthemum frutescens and a Comparison with Other Species in Anthemideae

Abstract

Argyranthemum frutescens, which belongs to the Anthemideae (Asteraceae), is widely cultivated as an ornamental plant. In this study, the complete chloroplast genome of A. frutescens was obtained based on the sequences generated by Illumina HiSeq. The chloroplast genome of A. frutescens was 149,626 base pairs (bp) in length, containing a pair of inverted repeats (IR, 24,510 bp) regions separated by a small single-copy (SSC, 18,352 bp) sequence and a large single-copy (LSC, 82,254 bp) sequence. The genome contained 132 genes, consisting of 85 coding DNA sequences, 37 tRNA genes, and 8 rRNA genes, with nineteen genes duplicated in the IR region. A comparison chloroplast genome analysis among ten species from the tribe of Anthemideae revealed that the chloroplast genome size varied, but the genome structure, gene content, and oligonucleotide repeats were highly conserved. Highly divergent regions, e.g., ycf1, trnK-psbK, petN-psbM intronic, were detected. Phylogenetic analysis supported Argyranthemum as a separate genus. The findings of this study will be helpful in the exploration of the phylogenetic relationships of the tribe of Anthemideae and contribute to the breeding improvement of A. frutescens.

Keywords: Anthemideae; Argyranthemum frutescens; chloroplast genome; ornamental plant; phylogenetic relationship.

Figure 1

Circular chloroplast genome of the A. frutescens. Genes presented inside the circle were transcribed counter-clockwise, and those drawn outside were transcribed clockwise. Color-coding represents different gene functional groups.

Figure 2

The long repetitive sequences of 10 chloroplast genomes. (A) Number of identified repeats. F, forward repeats; P, palindromic repeats; R, reverse repeats; C, complementary repeats. (B) Number of different repeat types of different lengths in 10 chloroplast genomes.

Figure 3

Simple-sequence repeats (SSRs) in ten different Anthemideae chloroplast genomes. Mono- represents mononucleotide SSRs, and Di- represents dinucleotide SSRs, etc. The vertical axis represents the number of different SSR types.

Figure 4

The junctions of IR/SC comparison among 10 species in the tribe of Anthemideae. Arrows indicated the distance of the gene to the junctions, and the I-shaped line represented the length of the gene on either side of the junctions.

Figure 5

Maximum likelihood (ML) tree of 19 species in different genera of Anthemideae based on the whole chloroplast genomes.