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Xu N, Du X, Zhang XX, Yang HL. The complete chloroplast genome of Salix lindleyana (salicaceae), a plateau plant species. Mitochondrial DNA B Resour 2023; 8:877-881. [PMID: 37614527 PMCID: PMC10443960 DOI: 10.1080/23802359.2023.2246675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/04/2023] [Indexed: 08/25/2023] Open
Abstract
Salix lindleyana Wallich ex Andersson 1851 is a species of genus Salix which mainly grows on mountains above 3000 m at sea level in Qinghai-Tibetan Plateau (including the Himalayas and Hengduan Mountains). To determine its phylogenetic position within Salix, we reconstructed S. lindleyana complete chloroplast (cp) genome sequence by de novo assembly using whole-genome sequencing data. The completed chloroplast genome was 155,304 bp, with a total GC content of 36.7%. It had a very typical tetrad structure, including a large single-copy (LSC) region of 84,539 bp, a small single-copy (SSC) region of 16,161 bp, and two inverted repeats (IR) regions of 27,302 bp. A total of 132 functional genes were distributed in the chloroplast genome, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis showed that S. lindleyana was clustered with Salix dasyclados Wimmer 1849 and Salix variegata Franchet 1887. The complete chloroplast genome of S. lindleyana provides potential genetic resources for further phylogenetic studies.
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Affiliation(s)
- Nan Xu
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration; Institute of Tree Development and Genome Editing, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xin Du
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration; Institute of Tree Development and Genome Editing, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xiu-Xing Zhang
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration; Institute of Tree Development and Genome Editing, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Hai-Ling Yang
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration; Institute of Tree Development and Genome Editing, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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Oh SH, Park J. The complete chloroplast genome of Euscaphis japonica (Thunb.) Kanitz (Staphyleaceae) isolated in Korea. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3769-3771. [PMID: 33367094 PMCID: PMC7671708 DOI: 10.1080/23802359.2020.1835571] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The complete chloroplast genome of Euscaphis japonica (Thunb.) Kanitz isolated in Korea is 160,606 bp long and has four subregions: 89,232 bp of large single-copy and 18,734 bp of small single-copy regions are separated by 26,320 bp of inverted repeat regions including 129 genes (84 CDS, 8 rRNAs, and 37 tRNAs) and three pseudogenes. There were 424 SNPs and 809 INDELs compared with the Chinese E. japonica, useful to develop markers for phylogeographic study of the species. Phylogenetic trees show that E. japonica, representing Crossosomatales, is nested within the Malvids clade, confirming previous studies.
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Affiliation(s)
- Sang-Hun Oh
- Department of Biology, Daejeon University, Daejeon, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
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Park J, Xi H, Kim Y. The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana. Int J Genomics 2020; 2020:3236461. [PMID: 32964010 PMCID: PMC7492873 DOI: 10.1155/2020/3236461] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/02/2020] [Accepted: 08/17/2020] [Indexed: 01/18/2023] Open
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.
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Affiliation(s)
- Jongsun Park
- InfoBoss Inc., 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Yongsung Kim
- InfoBoss Inc., 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
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Choi YG, Yun N, Park J, Xi H, Min J, Kim Y, Oh SH. The second complete chloroplast genome sequence of the Viburnum erosum (Adoxaceae) showed a low level of intra-species variations. Mitochondrial DNA B Resour 2019; 5:271-272. [PMID: 33366517 PMCID: PMC7720945 DOI: 10.1080/23802359.2019.1698360] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 11/23/2019] [Indexed: 11/05/2022] Open
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.
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Affiliation(s)
- Yun Gyeong Choi
- Department of Biology, Daejeon University, Daejeon, The Republic of Korea
| | - Narae Yun
- Department of Biology, Daejeon University, Daejeon, The Republic of Korea
- International Biological Material Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, The Republic of Korea
| | - Jongsun Park
- Infoboss Co., Ltd, Seoul, The Republic of Korea
- InfoBoss Research Center, Seoul, The Republic of Korea
| | - Hong Xi
- Infoboss Co., Ltd, Seoul, The Republic of Korea
- InfoBoss Research Center, Seoul, The Republic of Korea
| | - Juhyeon Min
- Infoboss Co., Ltd, Seoul, The Republic of Korea
- InfoBoss Research Center, Seoul, The Republic of Korea
| | - Yongsung Kim
- Infoboss Co., Ltd, Seoul, The Republic of Korea
- InfoBoss Research Center, Seoul, The Republic of Korea
| | - Sang-Hun Oh
- Department of Biology, Daejeon University, Daejeon, The Republic of Korea
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Park J, Choi YG, Yun N, Xi H, Min J, Kim Y, Oh SH. The complete chloroplast genome sequence of Viburnum erosum (Adoxaceae). Mitochondrial DNA B Resour 2019; 4:3278-3279. [PMID: 33365955 PMCID: PMC7707357 DOI: 10.1080/23802359.2019.1667919] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 08/16/2019] [Indexed: 11/08/2022] Open
Abstract
Viburnum erosum is a deciduous shrub distributed in eastern Asia. As part of the systematic study to understand the phylogenetic relationship of V. erosum, we present the complete chloroplast genome of V. erosum. Its length is 158,624 bp and it has four subregions: 87,060 bp of large single-copy and 18,530 bp of small single-copy regions separated by a pair of inverted repeat regions of 26,517 bp each, including 129 genes (84 protein-coding genes, 8 rRNAs, and 37 tRNAs). Phylogenetic analyses show that V. erosum is sister to Viburnum japonicum, supporting morphological affinity of the two species.
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Affiliation(s)
- Jongsun Park
- Infoboss Co., Ltd, Seoul, The Republic of Korea
- InfoBoss Research Center, Seoul, The Republic of Korea
| | - Yun Gyeong Choi
- Department of Biology, Daejeon University, Daejeon, The Republic of Korea
| | - Narae Yun
- Department of Biology, Daejeon University, Daejeon, The Republic of Korea
| | - Hong Xi
- Infoboss Co., Ltd, Seoul, The Republic of Korea
- InfoBoss Research Center, Seoul, The Republic of Korea
| | - Juhyeon Min
- Infoboss Co., Ltd, Seoul, The Republic of Korea
- InfoBoss Research Center, Seoul, The Republic of Korea
| | - Yongsung Kim
- Infoboss Co., Ltd, Seoul, The Republic of Korea
- InfoBoss Research Center, Seoul, The Republic of Korea
| | - Sang-Hun Oh
- Department of Biology, Daejeon University, Daejeon, The Republic of Korea
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