The complete mitochondrial genome of Arabidopsis thaliana (Brassicaceae) isolated in Korea

Park, Jongsun; Xi, Hong; Kim, Yongsung

doi:10.11110/kjpt.2021.51.2.176

Cited by 9 publications

(1 citation statement)

References 32 publications

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“…The INDEL region was defined as continuous INDELs, as in previous studies. All of these analyses were conducted in the GeIS environment, as used in previous studies (Park et al, 2020d;Park et al, 2021c;Yoo et al, 2021;Park and Xi, 2022).…”

Section: Methodsmentioning

confidence: 99%

The complete chloroplast genome of Erigeron canadensis isolated in Korea (Asteraceae): Insight into the genetic diversity of the invasive species

Park

2023

Korean J. Pl. Taxon

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We have determined the complete chloroplast genome of Erigeron canadensis isolated in Korea. The circular chloroplast genome of E. canadensis is 152,767 bp long and has four subregions: 84,317 bp of large single-copy and 18,446 bp of small single-copy regions are separated by 25,004 bp of inverted repeat regions including 133 genes (88 protein-coding genes, eight rRNAs, and 37 tRNAs). The chloroplast genome isolated in Korea differs from the Chinese isolate by 103 single-nucleotide polymorphisms (SNPs) and 47 insertions and deletion (INDEL) regions, suggesting different invasion sources of E. canadensis in Korea and China. A nucleotide diversity analysis revealed that the trend of the nucleotide diversity of E. canadensis followed that of 11 Erigeron chloroplasts, except for three peaks. The phylogenetic tree showed that our E. canadensis chloroplast is clustered with E. canadensis reported from China. Erigeron canadensis can be a good target when attempting to understand genetic diversity of invasive species.

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Section: Methodsmentioning

confidence: 99%

The complete chloroplast genome of Erigeron canadensis isolated in Korea (Asteraceae): Insight into the genetic diversity of the invasive species

Park

2023

Korean J. Pl. Taxon

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Genome-wide comparative analyses of GATA transcription factors among seven Populus genomes

Kim¹,

Xi²,

Park³

et al. 2021

Sci Rep

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GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17–20CX2C) followed by a basic region. We identified 262 GATA genes (389 GATA TFs) from seven Populus genomes using the pipeline of GATA-TFDB. Alternative splicing forms of Populus GATA genes exhibit dynamics of GATA gene structures including partial or full loss of GATA domain and additional domains. Subfamily III of Populus GATA genes display lack CCT and/or TIFY domains. 21 Populus GATA gene clusters (PCs) were defined in the phylogenetic tree of GATA domains, suggesting the possibility of subfunctionalization and neofunctionalization. Expression analysis of Populus GATA genes identified the five PCs displaying tissue-specific expression, providing the clues of their biological functions. Amino acid patterns of Populus GATA motifs display well conserved manner of Populus GATA genes. The five Populus GATA genes were predicted as membrane-bound GATA TFs. Biased chromosomal distributions of GATA genes of three Populus species. Our comparative analysis approaches of the Populus GATA genes will be a cornerstone to understand various plant TF characteristics including evolutionary insights.

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The complete chloroplast genome of Atriplex gmelinii C. A. Mey. ex Bong. (Amaranthaceae)

Park¹,

Kim

Min³

2022

Mitochondrial DNA Part B

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Atriplex gmelinii C. A. Mey. Ex Bong._1838 is an annual halophytic herb found in East Asia and North America. The chloroplast genome of A. gmelinii was successfully sequenced. The assembled genome (151,852 bp; GC ratio, 37.3%) is composed of four subregions, with the large single copy (LSC; 83,872 bp; 35.4%) and small single copy (SSC; 17,812 bp; 30.9%) regions separated by two regions of inverted repeat regions (25,084 bp; 42.8%). A total of 130 genes were predicted with 85 protein-coding genes, 8 rRNAs, and 37 tRNAs. The phylogenetic analyses inferred from whole chloroplast genomes of 35 species, including 34 species in Amaranthaceae and one outgroup species, suggest a close relationship between A. gmelinii and A. centralasiatica .

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The complete mitochondrial genome of Arabidopsis thaliana (Brassicaceae) isolated in Korea

Cited by 9 publications

References 32 publications

The complete chloroplast genome of <I>Erigeron canadensis</I> isolated in Korea (Asteraceae): Insight into the genetic diversity of the invasive species

The complete chloroplast genome of <I>Erigeron canadensis</I> isolated in Korea (Asteraceae): Insight into the genetic diversity of the invasive species

Genome-wide comparative analyses of GATA transcription factors among seven Populus genomes

The complete chloroplast genome of Atriplex gmelinii C. A. Mey. ex Bong. (Amaranthaceae)

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