The second complete chloroplast genome sequence of Pseudostellaria palibiniana (Takeda) Ohwi (Caryophyllaceae): intraspecies variations based on geographical distribution

Abstract

Pseudostellaria palibiniana which belongs to subseries Verticilatae is one of the species in Pseudostellaria palibiniana species complex (PPSC). To uncover intraspecies variation of P. palibiniana, we presented its second complete chloroplast genome which is 149,639 bp long and has four subregions: 81,286 bp of large single copy and 16,977 bp of small single copy regions are separated by 25,688 bp of inverted repeat regions including 126 genes (81 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content is 36.5% and those in the LSC, SSC, and IR regions are 34.3%, 29.4%, and 42.4%, respectively. Eighty-four single nucleotide polymorphisms and 125 insertions and deletions are identified between two individuals of P. palibiniana. Phylogenetic tree presents that P. palibiniana isolated from the same place of Pseudostellaria longipedicellata is clustered with another P. palibiniana, showing that PPSC can be solved using complete chloroplast genomes. ARTICLE HISTORY

The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana

“…This is also caused by the inserted region of the Tsu0 chloroplast genome. Other plant chloroplasts of which intraspecific variations of the GC contents are identical to those of A. thaliana are Goodyera schlechtendaliana (37.1% and 37.2%) [ 53 – 55 ] and Gastrodia elata (26.7% and 26.8%) [ 56 – 58 ] which are same to those of Arabidopsis thaliana , while Coffea arabica [ 50 , 59 – 63 ], Viburnum erosum [ 64 , 65 ], Duchesnea chrysantha [ 20 , 21 ], Salix koriyanagi [ 66 , 67 ], Pseudostellaria palibiniana [ 23 , 25 ], and Pyrus ussuriensis [ 68 , 69 ] present no difference in the intraspecific GC contents.…”

The complete chloroplast genome of candidate new species from Rosa rugosa in Korea (Rosaceae)

“…Pair-wise alignment between R. rugosa and R. angusta chloroplast genomes was conducted under the Plant Chloroplast Database (PCD; Park et al, in preparation), resulting 40 single nucleotide polymorphisms and 224 insertions and deletions. They present enough differences between two neighbor species supported by various researches showing less number of intraspecies variations on chloroplast genomes (Kim et al 2019;Min et al 2019;Park, Kim, Lee 2019;Park et al 2019bPark et al , 2019a.…”

“…Phylogenetic trees show that R. augusta is similar to R. rugosa with reasonable number of sequence varaitions ( Figure 1C). Chloroplast genome of candidate new species (Heo et al 2019;Kim et al 2019;Oh et al 2019)…”

The complete chloroplast genome sequence of rose-gold pussy willow, Salix gracilistyla Miq. (Salicaceae)

“…Phylogenetic trees show phylogenetic position of S. gracilistyla clustered with two chloroplast genomes of S. koryianagi and separated from those of three Salix species originated from China (Figure 1). In addition, numbers of single nucleotide polymorphisms and insertions and deletions between S. gracilistyla and S. koriyanagi are 40 and 139, respectively, which is lower than intraspecies variations of Marchantia polymorpha (Kwon et al 2019), Camellia japonica , Pseudostellaria palibiniana (Kim, Heo, et al 2019), Pyrus ussuriensis (Cho et al under review), Rehmannia glutinosa (Jeon et al 2019), and Eucommia ulmoides (Wang et al 2016).…”