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

Spiraea prunifolia f. simpliciflora Nakai is a perennial shrub widely used for horticultural and medicinal purposes. We simultaneously obtained the complete plastid genome (plastome) and nuclear ribosomal gene transcription units, 45S nuclear ribosomal DNA (nrDNA) and 5S nrDNA of S. prunifolia f. simpliciflora, using Illumina short-read data. The plastome is 155,984 bp in length with a canonical quadripartite structure consisting of 84,417 bp of a large single-copy region, 18,887 bp of a short single-copy region, and 26,340 bp of two inverted repeat regions. Overall, a total of 113 genes (79 protein-coding genes, 30 tRNAs, and four rRNAs) were annotated in the plastome. The 45S nrDNA transcription unit is 5,848 bp in length: 1,809 bp, 161 bp, and 3,397 bp for 18S, 5.8S, and 26S, respectively, and 261 bp and 220 bp for internal transcribed spacer (ITS) 1 and ITS 2 regions, respectively. The 5S nrDNA unit is 512 bp, including 121 bp of 5S rRNA and 391 bp of intergenic spacer regions. Phylogenetic analyses showed that the genus Spiraea was monophyletic and sister to the clade of Sibiraea angustata, Petrophytum caespitosum and Kelseya uniflora. Within the genus Spiraea, the sections Calospira and Spiraea were monophyletic, but the sect. Glomerati was nested within the sect. Chamaedryon. In the sect. Glomerati, S. prunifolia f. simpliciflora formed a subclade with S. media, and the subclade was sister to S. thunbergii and S. mongolica. The close relationship between S. prunifolia f. simpliciflora and S. media was also supported by the nrDNA phylogeny, indicating that the plastome and nrDNA sequences assembled in this study belong to the genus Spiraea. The newly reported complete plastome and nrDNA transcription unit sequences of S. prunifolia f. simpliciflora provide useful information for further phylogenetic and evolutionary studies of the genus Spiraea, as well as the family Rosaceae.

Section: Resultssupporting

confidence: 90%

The complete plastid genome and nuclear ribosomal transcription unit sequences of Spiraea prunifolia f. simpliciflora (Rosaceae)

CHOI

KIM

PARK

et al. 2023

“…Geneious Prime v2020.2.4 (Biomatters Ltd., Auckland, New Zealand) was used for annotation based on the A. dioicus var. kamtschaticus chloroplast (MW115132) (Suh et al, 2021). A circular map of A. aethusifolius chloroplast genome was drawn using OGDRAW v1.31 (Greiner et al, 2019).…”

Section: Methodsmentioning

confidence: 99%

The complete chloroplast genome of Aruncus aethusifolius (Rosaceae), a species endemic to Korea

Park¹,

Suh

2022

Self Cite

Aruncus aethusifolius (H. Lév.) Nakai is an endemic species in Korea and is economically important as an ornamental herb. The complete chloroplast genome of A. aethusifolius is 157,217 bp long with four subregions consisting of 85,207 bp of large singlecopy and 19,222 bp of small single-copy regions separated by 26,394 bp of inverted repeat regions. The genome includes 131 genes (86 protein-coding genes, eight rRNAs, and 37 tRNAs). Phylogenetic analyses demonstrates that the chloroplast genome of A. aethusifolius was sister to A. dioicus var. kamtschaticus, forming the strongly supported clade of Aruncus. This is the first report of the chloroplast genome of A. aethusifolius.

“…After obtaining the first draft of the chloroplast genome sequences, gaps were filled with GapCloser v1.12 (Zhao et al, 2011) and all bases from the assembled sequences were confirmed by checking each base in the alignment (tview mode in SAMtools v1.9) (Li et al, 2009) against the assembled chloroplast genome generated with BWA v0.7.17 (Li, 2013). All of these processes were conducted under the environment of Genome Information System (GeIS; http://geis.infoboss.co.kr/), which has been utilized in a range of studies (Kim et al, 2021b(Kim et al, , 2021c, including work on plant organelle genomes (Suh et al, 2021;Park et al, 2022aPark et al, , 2022cYoo et al, 2023).…”

Section: Genome Sequencing and De Novo Assembly Of The Two Agrimonia ...mentioning

confidence: 99%

Comparative analyses of Agrimonia complete chloroplast genomes with newly assembled chloroplast genomes of A. coreana and A. nipponica (Rosaceae)

PARK,

SUH,

2024

Self Cite

The genus Agrimonia L. (1753) is a small group consisting of 19 species and three varieties. We completed two Agrimonia chloroplast genomes, Agrimonia coreana Nakai and Agrimonia nipponica Koidz, collected in Korea and conducted comprehensive analyses of six Agrimonia chloroplast genomes. Two of the Agrimonia chloroplasts genomes have a typical quadripartite structure with lengths ranging from 155,161 bp to 151,362 bp, similar to the remaining AAgrimonia chloroplast genomes. High nucleotide diversity was detected in the ycf1 gene, which can serve as a molecular marker. Intraspecific variations of four A. pilosa chloroplast genomes and interspecific variations of three Agrimonia species revealed that KY419942 is distinct to the other three A. pilosa chloroplast genomes. A phylogenetic analysis demonstrated that KY419942 was clustered with A. nipponica, requiring further analyses to understand Agrimonia species in East Asia. A comparison of simple sequence repeats identified from the six Agrimonia chloroplast genomes suggests potential molecular markers to distinguish species or populations of the same species. Our results define the phylogenetic relationship of three Agrimonia species and provide insight into the intraspecific features of Agrimonia chloroplast genomes with which to gain a better understanding of the genetic structure of Agrimonia species.