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

Abstract

Arabidopsis thaliana (L.) Heynh. is a model organism of plant molecular biology. More than 1,700 whole genome sequences have been sequenced, but no Korean isolate genomes have been sequenced thus far despite the fact that many A. thaliana isolated in Japan and China have been sequenced. To understand the genetic background of Korean natural A. thaliana (named as 180404IB4), we presented its complete chloroplast genome, which is 154,464 bp long and has four subregions: 85,164 bp of large single copy (LSC) and 17,781 bp of small single copy (SSC) regions are separated by 26,257 bp of inverted repeat (IRs) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). Fifty single nucleotide polymorphisms (SNPs) and 14 insertion and deletions (INDELs) are identified between 180404IB4 and Col0. In addition, 101 SSRs and 42 extendedSSRs were identified on the Korean A. thaliana chloroplast genome, indicating a similar number of SSRs on the rest five chloroplast genomes with a preference of sequence variations toward the SSR region. A nucleotide diversity analysis revealed two highly variable regions on A. thaliana chloroplast genomes. Phylogenetic trees with three more chloroplast genomes of East Asian natural isolates show that Korean and Chinese natural isolates are clustered together, whereas two Japanese isolates are not clustered, suggesting the need for additional investigations of the chloroplast genomes of East Asian isolates.

Complete Chloroplast Genome of Clethra fargesii Franch., an Original Sympetalous Plant from Central China: Comparative Analysis, Adaptive Evolution, and Phylogenetic Relationships

“…Most of the SSRs types are mononucleotide and dinucleotide repeats, while the other complex SSRs are at lower frequencies in the two-chloroplast genome sequences, and these results conform with previous studies [65][66][67]. It is a particular case that the number of dinucleotide SSRs is significantly greater than mononucleotide SSRs and A/T (no C/G) is the only mononucleotide SSRs type in the two species (Figures 6A and 7), which are rarely found in other species [68][69][70][71][72]. Of the four copy regions of two species chloroplast genomes, the SSRs mainly in the LSC regions (64.4% and 67.9%) and the proportion close to two-thirds of the total are largely beyond the corresponding proportion of LSC length occupying the whole chloroplast genomes (Figure 6B).…”

The Comparative Analyses of Six Complete Chloroplast Genomes of Morphologically Diverse Chenopodium album L. (Amaranthaceae) Collected in Korea

“…Based on the conventional definition of an SSR on the chloroplast genome, monoSSR (1 bp) to hexaSSR (6 bp), the total length of SSRs on the chloroplast genome exceeds 10 bp. Owing to the different criteria of SSRs on chloroplast genomes, we adopted the criteria used in chloroplast genomes of Dysphania [ 47 ] and Arabidopsis thaliana [ 53 ] and mitochondrial genome of Rosa rugosa [ 54 ] as follows: the monoSSR (unit sequence length of 1 bp) to hexaSSR (6 bp) are used as normal SSRs, and heptaSSR (7 bp) to decaSSR (10 bp) are defined as extended SSRs. Among the normal SSRs, pentaSSRs and hexaSSRs for which the repeat number of unit sequences is 2 are classified as potential SSRs.…”

“…SSRs identified from seven C. album chloroplast genomes were compared based on their flanking sequences under the environment of the SSRDB ( http://ssrdb.infoboss.co.kr/; Park et al, in preparation). The pipeline of the SSR comparison implemented in the SSRDB used in various organelle genome studies [ 53 , 55 ] was used with the following conditions: a cut-off e value of 1 e − 10 and a maximum flanking sequence for the comparison of 60 bp.…”

“…Nucleotide diversity was calculated using the method proposed by Nei and Li [ 56 ] based on the multiple sequence alignment of Chenopodium chloroplast genomes using a Perl script used in previous studies [ 47 , 53 , 57 ]. The window size was set to 500 bp, and the step size was 200 bp when using the sliding-window method.…”

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

“…Numbers of intraspecific variations are relatively large based on the intraspecific variation analysis of chloroplast genomes (Park, Xi, et al. 2020 ). High levels of intraspecific variations were found in many plant species, such as some species in Orchidaceae (Oh et al.…”