The complete chloroplast genome of Campanula takesimana Nakai from Dokdo Island in Korea (Campanulaceae)

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The complete chloroplast genome of Zoysia macrostachya Franch. & Sav. isolated in Korea is 135,902 bp long (GC ratio is 38.4%) and has four subregions; 81,546 bp of large single-copy (36.3%) and 12,586 bp of small single-copy (32.7%) regions are separated by 20,885 bp of inverted repeat (44.1%) regions, including 130 genes (83 protein-coding genes, eight rRNAs, and 39 tRNAs). Thirty-nine single nucleotide polymorphisms and 11 insertions and deletion (INDEL) regions were identified from two Z. macrostachya chloroplast genomes, the smallest among other Zoysia species. Phylogenetic trees show that two Z. macrostachya chloroplast genomes are clustered into a single clade. However, we found some incongruency with regard to the phylogenetic position of the Z. macrostachya clade. Our chloroplast genome provides insights into intraspecific variations and species delimitation issues pertaining to the Zoysia species.

Section: Resultsmentioning

confidence: 84%

mentioning

confidence: 99%

The complete chloroplast genome of Zoysia macrostachya (Poaceae): Insights into intraspecific variations and species delimitation of the Zoysia species

Lee

Yun

et al. 2021

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“…(121 SNPs, 0.076% and 789 INDELs, 0.49%) (Cho et al, 2019), Agrimonia pilosa Ledeb. (258 SNPs, 0.20% and 542 INDELs, 0.42%) (Heo et al, 2020), Camellia japonica L. (78 SNPs, 0.050% and 643 INDELs, 0.41%) (Park et al, 2019), Campanula takesimana Nakai (33 SNPs, 0.019% and 662 INDELs, 0.39%) (Park et al, 2021b), and Marchantia polymorpha L. (69 SNPs, 0.057% and 660 INDELs, 0.55%) (Kwon et al, 2019). However, the variations in these cases are less than those of Goodyera schlechtendaliana Rchb.…”

Section: Resultsmentioning

confidence: 99%

Phylogenetic position of Daphne genkwa (Thymelaeaceae) inferred from complete chloroplast data

YOO

Park³

2021

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Daphne genkwa (Thymelaeaceae) is a small deciduous shrub widely cultivated as an ornamental. The complete chloroplast genome of this species is presented here. The genome is 132,741 bp long and has four subregions: 85,668 bp of large single-copy and 28,365 bp of small single-copy regions are separated by 9,354 bp of inverted repeat regions with 107 genes (71 protein-coding genes, four rRNAs, and 31 tRNAs) and one pseudogene. The phylogenetic tree shows that D. genkwa is nested within Wikstroemia and is not closely related to other species of Daphne, suggesting that it should be recognized as a species of Wikstroemia.

“…3A). In addition, 78 out of 292 SNPs and two INDELs were found in 36 of 84 PCGs (42.85%), which is a large number in comparison with other intraspecific variations of Arabidopsis thaliana L. (11 PCGs) (Park et al, 2020f), C. album (nine PCGs) (Park et al, 2021d), and Campanula takesimana Nakai (eight PCGs) (Park et al, 2021a). It is remarkable that only three synonymous SNPs identified in three PCGs were from MT040192; two synonymous SNPs were from MT415946 and no variations were found in A. pilosa var.…”

Section: Intraspecific Variations Identified From the Four Complete C...mentioning

confidence: 93%

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

PARK,

SUH,

2024

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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.