The second complete chloroplast genome of <i>Dysphania pumilio</i> (R.Br.) mosyakin &amp; clemants (Amranthaceae): intraspecies variation of invasive weeds

Park, Jongsun; Kim, Yongsung

doi:10.1080/23802359.2019.1598807

Cited by 14 publications

(9 citation statements)

References 17 publications

(17 reference statements)

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“…In addition, A. thaliana and Arabidopsis suecica are clustered because the maternal origin of A. suecica is A. thaliana [ 101 ] ( Figure 7 ). Moreover, the topology of BI tree for the remaining Arabidopsis species, except for A. thaliana and A. suecica , is somewhat inconsistent to those of NJ and ML trees ( Figure 7 ), which has also been found in various plant chloroplast genomes [ 15 , 20 , 28 , 51 , 67 , 69 , 72 , 79 , 91 , 92 , 102 – 109 ]. This suggests that detailed investigations of phylogenetic relationships among Arabidopsis species with various methods should be done in near future.…”

Section: Resultsmentioning

confidence: 92%

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

Park¹,

Xi²,

Kim³

2020

International Journal of Genomics

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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.

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Section: Resultsmentioning

confidence: 92%

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

Park¹,

Xi²,

Kim³

2020

International Journal of Genomics

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“… 2019 ; Min et al. 2019 ; Park and Kim 2019 ; Park, Kim, Kwon, et al. 2019 ; Park, Kim, Lee 2019 ; Park, Kim, Xi 2019 ; Park, Kim, Xi, Heo 2019 ; Park, Kim, Xi, Nho, et al.…”

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confidence: 99%

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

Kim¹,

Heo²,

Nam

et al. 2019

Mitochondrial DNA Part B

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Complete chloroplast genome of candidate new species from Rosa rugosa, named as Rosa angusta, is 156,989 bp long and has four subregions: 86,227 bp of large single copy (LSC) and 18,816 bp of small single copy (SSC) regions are separated by 25,793 bp of inverted repeat (IR) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC content of this chloroplast genome is 37.2% and in the LSC, SSC, and IR regions are 35.2%, 31.1%, and 42.8%, respectively. Phylogenetic trees show that R. angusta is close to R. rugosa with enough number of sequence variations.

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“… 2019 ), Artemisia fukudo (Min et al. 2019 ), and Dysphania pumilio (Park and Kim 2019 ). Interestingly, numbers of SNPs and INDELs between V. erosum (Park, Choi, et al.…”

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confidence: 99%

The second complete chloroplast genome sequence of the Viburnum erosum (Adoxaceae) showed a low level of intra-species variations

Choi

Yun

Park³

et al. 2019

Mitochondrial DNA Part B

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2020) The second complete chloroplast genome sequence of the Viburnumerosum (Adoxaceae) showed a low level of intra-species variations, Mitochondrial DNA Part B, 5:1, 271-272, ABSTRACT We presented the second complete chloroplast genome of the plant. The length of chloroplast genome is 158,587 bp, consisting of four subregions: 87,050 bp of LSC and 18,503 bp of SSC regions separated by a pair of 26,517 bp IR regions. It includes 129 genes (84 protein-coding genes, 8 rRNAs, and 37 tRNAs). A low-level of molecular variation within Viburnum erosum was found with 16 SNPs and 49 indels. The phylogenetic tree shows that the two accessions of V. erosum are clustered with Viburnum japonicum with no resolution between the species, suggesting that chloroplast genome in these species evolve slowly. ARTICLE HISTORY

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The second complete chloroplast genome of Dysphania pumilio (R.Br.) mosyakin & clemants (Amranthaceae): intraspecies variation of invasive weeds

Abstract: View related articles View Crossmark data Citing articles: 5 View citing articles MITOGENOME ANNOUNCEMENT The second complete chloroplast genome of Dysphania pumilio (R.Br.) mosyakin & clemants (Amranthaceae): intraspecies variation of invasive weeds

Cited by 14 publications

References 17 publications

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

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

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

The second complete chloroplast genome sequence of the Viburnum erosum (Adoxaceae) showed a low level of intra-species variations

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