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Park J, Kim Y, Min J, Kim ST. The complete chloroplast genome of Atriplex gmelinii C. A. Mey. ex Bong. (Amaranthaceae). Mitochondrial DNA B Resour 2022; 7:541-543. [PMID: 35356788 PMCID: PMC8959532 DOI: 10.1080/23802359.2022.2055501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
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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Affiliation(s)
- Jongsun Park
- InfoBoss Inc, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Yongsung Kim
- Honam National Institute of Biological Resources, Mokpo, Republic of Korea
| | - Juhyeon Min
- InfoBoss Inc, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Sang-Tae Kim
- Department of Medical & Biological Sciences, The Catholic University of Korea, Bucheon, Republic of Korea
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Park J, Xi H, Son J, Shin HT, Kang H, Park S. The complete chloroplast genome of Castanopsis sieboldii (Makino) Hatus (Fagaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2743-2745. [PMID: 34447890 PMCID: PMC8386698 DOI: 10.1080/23802359.2021.1966339] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Castanopsis sieboldii (Makino) Hatus is an evergreen tree that distributes in Eastern Asia including Islands of Korea and Japan. The chloroplast genome of C. sieboldii was successfully sequenced. Its length is 160,705 bp long (GC ratio is 36.8%) and has four subregions: 90,821 bp of large single copy (34.6%) and 19,014 bp of small single copy (30.8%) regions are separated by 25,075 bp of inverted repeat (42.8%) regions including 134 genes (89 protein-coding genes, eight rRNAs, and 37 tRNAs). Interspecific variations of Castanopsis are at a moderate level in comparison to those of the other genera. Phylogenetic trees show that C. sieboldii chloroplast genome was clustered with the other two Castanopsis species.
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Affiliation(s)
- Jongsun Park
- InfoBoss Inc, Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc, Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
| | - Janghyuk Son
- InfoBoss Inc, Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
| | - Hyun Tak Shin
- DMZ Botanic Garden, Korea National Arboretum, Yanggu, South Korea
| | - Hyunmi Kang
- Department of Landscape Architecture, Mokpo National University, Muan, Republic of Korea
| | - Seokgon Park
- Division of Forest Resources and Landscape Architecture, Sunchon National University, Sunchoen, Republic of Korea
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Baek J, Park S, Lee J, Min J, Park J, Lee GW. The complete chloroplast genome of Chrysanthemum zawadskii Herbich (Asteraceae) isolated in Korea. Mitochondrial DNA B Resour 2021; 6:1956-1958. [PMID: 34179479 PMCID: PMC8205035 DOI: 10.1080/23802359.2021.1934148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/19/2021] [Indexed: 11/22/2022] Open
Abstract
We have determined the complete chloroplast genome of Chrysanthemum zawadskii Herbich isolated in Korea. The circular chloroplast genome of C. zawadskii is 151,137 bp long and has four subregions: 83,041 bp of large single copy and 18,350 bp of small single copy regions are separated by 24,873 bp of inverted repeat regions including 133 genes (87 protein-coding genes, eight rRNA genes, 37 tRNAs, and one pseudogene). There are 65 to 152 single nucleotide polymorphisms and 33 to 64 insertion and deletion regions (178 bp to 372 bp in length) identified against three available chloroplast genomes of C. zawadskii. The phylogenetic tree shows that C. zawadskii is clustered as a paraphyletic group with C. zawadskii subsp. coreanum, displaying incongruency between species and clades.
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Affiliation(s)
- Jinwook Baek
- Jeonju AgroBio-Materials Institute, Jeonju-si, Republic of Korea
| | - Suhyeon Park
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Junho Lee
- FromBio Co. Ltd, Suwon-si, Republic of Korea
| | - Juhyeon Min
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Gun Woong Lee
- Jeonju AgroBio-Materials Institute, Jeonju-si, Republic of Korea
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Kim M, Xi H, Park J. Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors. PLoS One 2021; 16:e0252181. [PMID: 34038437 PMCID: PMC8153473 DOI: 10.1371/journal.pone.0252181] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 05/11/2021] [Indexed: 12/30/2022] Open
Abstract
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. Due to the low cost of genome sequencing, multiple strains of specific species have been sequenced: e.g., number of plant genomes in the Plant Genome Database (http://www.plantgenome.info/) is 2,174 originated from 713 plant species. Thus, we investigated GATA TFs of 19 Arabidopsis thaliana genome-widely to understand intraspecific features of Arabidopsis GATA TFs with the pipeline of GATA database (http://gata.genefamily.info/). Numbers of GATA genes and GATA TFs of each A. thaliana genome range from 29 to 30 and from 39 to 42, respectively. Four cases of different pattern of alternative splicing forms of GATA genes among 19 A. thaliana genomes are identified. 22 of 2,195 amino acids (1.002%) from the alignment of GATA domain amino acid sequences display variations across 19 ecotype genomes. In addition, maximally four different amino acid sequences per each GATA domain identified in this study indicate that these position-specific amino acid variations may invoke intraspecific functional variations. Among 15 functionally characterized GATA genes, only five GATA genes display variations of amino acids across ecotypes of A. thaliana, implying variations of their biological roles across natural isolates of A. thaliana. PCA results from 28 characteristics of GATA genes display the four groups, same to those defined by the number of GATA genes. Topologies of bootstrapped phylogenetic trees of Arabidopsis chloroplasts and common GATA genes are mostly incongruent. Moreover, no relationship between geographical distribution and their phylogenetic relationships was found. Our results present that intraspecific variations of GATA TFs in A. thaliana are conserved and evolutionarily neutral along with 19 ecotypes, which is congruent to the fact that GATA TFs are one of the main regulators for controlling essential mechanisms, such as seed germination and hypocotyl elongation.
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Affiliation(s)
- Mangi Kim
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
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Suh HJ, Min J, Park J, Oh SH. The complete chloroplast genome of Aruncus dioicus var. kamtschaticus (Rosaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1256-1258. [PMID: 33829101 PMCID: PMC8009126 DOI: 10.1080/23802359.2021.1906173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Aruncus dioicus var. kamtschaticus is an economically important herb in the cold temperate regions of East Asia, and displays highly variable morphological features. Completed chloroplast genome of A. dioicus var. kamtschaticus isolated in Korea is 157,859 bp long with four subregions: 85,972 bp of large single copy and 19,185 bp of small single-copy regions separated by 26,351 bp of inverted repeat regions. The genome includes 131 genes (86 protein-coding genes, eight rRNAs, and 37 tRNAs). Phylogenetic analyses show that our chloroplast genome was clustered with two partial chloroplast genomes of A. dioicus.
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Affiliation(s)
- Hwa-Jung Suh
- Department of Biology, Daejeon University, Daejeon, Korea
| | - Juhyeon Min
- InfoBoss Inc, Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc, Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
| | - Sang-Hun Oh
- Department of Biology, Daejeon University, Daejeon, Korea
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Lee B, Park J. The complete chloroplast genome of Zoysia matrella (L.) Merr. isolated in Korea (Poaceae): investigation of intraspecific variations on chloroplast genomes. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:572-574. [PMID: 33628934 PMCID: PMC7889194 DOI: 10.1080/23802359.2021.1875907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Completed chloroplast genome of Zoysia matrella (L.) Merr. isolated in Korea is 135,888 bp long (GC ratio is 38.4%) and has four subregions: 81,370 bp of large single copy (36.3%) and 12,594 bp of small single copy (32.7%) regions are separated by 20,962 bp of inverted repeat (44.1%) regions including 130 genes (83 protein-coding genes, eight rRNAs, 38 tRNAs, and one pseudogene). 28 SNPs and 57 INDELs were identified ss intraspecific variations against previously sequenced chloroplast genome. Phylogenetic trees show that Z. matrella and Z. tenuifolia (=Z. pacifica) are clustered in one clade with low level of variations on chloroplast genomes.
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Affiliation(s)
- Bumkyu Lee
- Department of Environmental Science & Biotechnology, Medicical Science, Jeonju University, Jeonju, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
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