Characterization of the complete chloroplast genome of Sinosenecio oldhamianus (Compositae).

The complete chloroplast (cp) genome sequence of Sinosenecio oldhamianus, a common medicinal plant is widely distributed in South China. The plastome is 150,926 bp in length, with one large single-copy region of 94,588 bp, one small single-copy region of 18,130 bp, and two inverted repeat (IR) regions of 24,852 bp. It contains 134 genes, including 87 protein-coding genes, 8 ribosomal RNA, and 37 transfer RNA. The phylogenetic tree shows that this species is a sister to the genus Ligularia. The published plastome within Sinosenecio provides significant insight for elucidating the phylogenetic relationship of taxa within tribe Compositae.

Sinosenecio oldhamianus (Maxim.) B. Nord., a common medicinal plant (Wu and Wu 2003; Liang and Ye 2006; Yang et al. 2014), belongs to the genus Sinosenecio (Compositae), consisting of ∼40 species (Chen et al. 2011). and is widely distributed in South China. Because of the complexity of their inter- and intraspecific morphological variations, species delimitation is sometimes quite difficult. However, no information is available about its molecular biology and no genomic study has been performed on S. oldhamianus. In our study, we characterized the complete chloroplast (cp) genome sequence of S. oldhamianus for further physiological, molecular, and phylogenetical study of this medicinal species.

Fresh leaves of S. oldhamianus were collected from Xiaozhaizigou National Reserve (Mianyang, Sichuan, China; coordinate: 103°45′E, 31°50′N), dried and kept in silica gel for DNA extraction, and then stored in the College of Life Science, Sichuan University. Total genomic DNA was extracted with a modified CTAB method (Doyle and Doyle 1987). First, we obtained 10 million high-quality pair-end reads for S. oldhamianus, and after removing the adapters, the remaining reads were used to assemble the complete cp genome by NOVOPlasty (Dierckxsens et al. 2017). The complete cp genome sequence of Sinosenecio polylepis was used as a reference. Plann v1.1 (Huang and Cronk 2015) and Geneious v11.0.3 (Kearse et al. 2012) were used to annotate the cp genome and correct the annotation.

The S. oldhamianus cp genome is 150,926 bp in length, exhibits a typical quadripartite structural organization, consisting of a large single-copy (LSC) region of 83,092 bp, two inverted repeat (IR) regions of 24,852 bp each, and a small single-copy (SSC) region of 18,130 bp. The cp genome contains 134 complete genes, including 87 protein-coding genes (87 PCGs), 8 ribosomal RNA genes (4rRNAs), and 37 tRNA genes (37 tRNAs). Most genes occur in a single copy, while 17 genes occur in double, including 4 rRNAs (4.5S, 5S, 16S, and 23S rRNA), 7 tRNAs (trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, and trnV-GAC), and 6 PCGs (rps7, rpl2, rpl23, ndhB, ycf2, and ycf15), while a partial ycf1 and rps19 genes were identified at the IRb/SSC junction as a pseudogene. The overall AT content of cp DNA is 62.7%, while the corresponding values of the LSC, SSC, and IR regions are 64.6, 69.4, and 57.0%.

In order to further clarify the phylogenetic position of S. oldhamianus, the plastomes of five representative Compositae species were obtained from NCBI to construct the plastome phylogeny, with Sonchus boulosii as an outgroup. All the sequences were aligned using MAFFT v.7.313 (Katoh and Standley 2013) and maximum-likelihood phylogenetic analyses were conducted using RAxML v.8.2.11 (Stamatakis 2014). The phylogenetic tree shows that S. oldhamianus clustered together with Ligularia hodgsonii, the Artemisia selengensis clustered together with Opisthopappus taihangensis and Chrysanthemum lucidum, forming one clade within the Compositae (Figure 1).

Figure 1.

Phylogenetic relationships of Compositae species using whole chloroplast genome. GenBank accession numbers: Artemisia selengensis (NC_039647), Chrysanthemum lucidum (NC_040920), Ligularia hodgsonii (NC_039381), Opisthopappus taihangensis (MK552323), Sonchus boulosii (NC_042244).