The complete chloroplast genome of Aruncus dioicus var. kamtschaticus (Rosaceae)

Abstract Aruncus dioicus var. kamtschaticus is an economically important herb in the cold temperate regions of East Asia, and displays highly variable morphological features. Completed chloroplast genome of A. dioicus var. kamtschaticus isolated in Korea is 157,859 bp long with four subregions: 85,972 bp of large single copy and 19,185 bp of small single-copy regions separated by 26,351 bp of inverted repeat regions. The genome includes 131 genes (86 protein-coding genes, eight rRNAs, and 37 tRNAs). Phylogenetic analyses show that our chloroplast genome was clustered with two partial chloroplast genomes of A. dioicus.

Chloroplast genome of A. dioicus var. kamtschaticus (GenBank accession is MW115132) is 157,859 bp long (GC ratio is 36.4%) and has four subregions: 85,972 bp of large single copy (LSC; 34.2%) and 19,185 bp of small single copy (SSC; 30.0%) regions are separated by 26,351 bp of inverted repeat (IR; 42.4%). It contains 131 genes (86 protein-coding genes, eight rRNAs, and 37 tRNAs); 19 genes (eight proteincoding gene, four rRNAs, and seven tRNAs) are duplicated in IR regions. No structural variation was found among the genomes of the species of tribe Spiraeeae examined.
Two partial chloroplasts (KY419932 and KY419926) were used for identifying intraspecific variations: 180 SNPs and 69 INDELs against KY419932 and 299 SNPs and 84 INDELs against KY419926 in LSC, SSC, and IRb regions. Numbers of intraspecific variations are relatively large based on the intraspecific variation analysis of chloroplast genomes . High levels of intraspecific variations were found in many plant species, such as some species in Orchidaceae (Oh et al. 2019a(Oh et al. , 2019bPark, Suh, et al. 2020;Kang et al. 2020) and Rosaceae (Cho et al. 2019;Heo et al. 2020), Camellia japonica , Euscaphis japonica (Oh and Park 2020), Selaginella tamariscina , and Marchantia polymorpha subsp. ruderalis (Kwon et al. 2019).
Thirteen chloroplast genomes to represent the major lineages of tribe Spiraeeae (Potter et al. 2007) were used in phylogenetic analysis of the maximum likelihood (ML) and Bayesian inference (BI). Seventy-eight genes of LSC, SSC, and IRb regions were included in the analyses. A heuristic search was used with nearest-neighbor interchange branch swapping, the Tamura-Nei model, and uniform rates among sites to construct ML phylogenetic tree with default values for other options using MEGA X (Kumar et al. 2018). Bootstrap analysis with 1000 pseudoreplicates was also conducted. BI tree was constructed by MrBayes version 3.2.7a (Ronquist et al. 2012). The GTR model with gamma rates was used as a molecular model. A Markov-chain Monte Carlo (MCMC) algorithm was employed for 10,000,000 generations, sampling trees every 200 generations, with four chains running simultaneously.
The phylogenetic tree shows that A. dioicus var. kamtschaticus clustered with two previously sequenced chloroplasts of A. dioicus forming a strongly supported clade (Figure 1). Our new chloroplast genome sequences are determined from the Korean sample. Geographic origin of the two A. dioicus published chloroplast genomes (Zhang SD et al. 2017) is unknown, but it is unlikely to be from Korea. The high level of intraspecific variation suggests that the chloroplast genome can be utilized to understand phylogeographic pattern of A. dioicus across the whole distribution range as well as relationships among the several varieties of the species.

Disclosure statement
No potential conflict of interest was reported by the author(s).  Phylogenetic tree was drawn based on maximum likelihood tree. The numbers above branches indicate bootstrap support values of maximum likelihood and posterior probability from the BI inference, respectively.