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Park TH. Complete chloroplast genome sequence of Solanum iopetalum, one of the tuber-bearing wild potato relatives. Mitochondrial DNA B Resour 2023; 8:347-351. [PMID: 36876142 PMCID: PMC9980020 DOI: 10.1080/23802359.2023.2183720] [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] [Indexed: 03/06/2023] Open
Abstract
Solanum iopetalum belongs to the Solanaceae family and is one of the tuber-bearing wild Solanum species. In this study, chloroplast genome sequencing of the species, completed with Illumina sequencing technology, is presented. The length of the chloroplast genome is 155,625 bp with a GC content of 37.86%. It comprises a large single copy (LSC) region of 86,057 bp, a small single copy (SSC) region of 18,382 bp, and two inverted repeat regions (IRa and IRb) of 25,593 bp. Additionally, 158 functional genes in the genome are identified, including 105 protein-coding genes, 8 ribosomal RNAs, and 45 transfer RNAs. Phylogenetic analysis revealed that S. iopetalum is grouped into a large clade with other Solanum species, including cultivated potatoes (S. tuberosum) and is closely related to Mexican Solanum species (S. stoloniferum, S. verrucosum, S. hougasii, S. hjertingii, and S. demissum). This study provides useful genomic information for future breeding and evolutionary studies of S. iopetalum and other Solanum species.
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Affiliation(s)
- Tae-Ho Park
- Department of Horticulture, Daegu University, Gyeongsan, South Korea
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Park TH. Complete chloroplast genome sequence of the wild diploid potato relative, Solanum acaule. Mitochondrial DNA B Resour 2021; 6:1189-1191. [PMID: 33829083 PMCID: PMC8008929 DOI: 10.1080/23802359.2021.1902414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Affiliation(s)
- Tae-Ho Park
- Department of Horticulture, Daegu University, Gyeongsan, South Korea
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Park TH. Complete chloroplast genome sequence of the wild diploid potato relative, Solanum brevicaule. Mitochondrial DNA B Resour 2019; 4:4159-4160. [PMID: 33366362 PMCID: PMC7707683 DOI: 10.1080/23802359.2019.1693292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/09/2019] [Indexed: 11/21/2022] Open
Abstract
Solanum brevicaule is a wild tuber-bearing species belonging to Solanaceae family. The complete chloroplast genome of S. brevicaule was constituted by de novo assembly using a small amount of whole genome sequencing data. The chloroplast genome of S. brevicaule was the circular DNA molecule with a length of 155,531 bp and consisted of 85,981 bp of large single copy, 18,352 bp of small single copy, and 25,599 bp of a pair of inverted repeat regions. A total of 158 genes were annotated including 105 protein-coding genes, 45 tRNA genes and eight rRNA genes. Maximum likelihood phylogenetic analysis with 30 Solanaceae species revealed that S. brevicaule is grouped with other Solanum species including S. tuberosum.
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Affiliation(s)
- Tae-Ho Park
- Department of Horticulture, Daegu University, Gyeongsan, South Korea
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Sebastin R, Lee KJ, Cho GT, Lee JR, Shin MJ, Kim SH, Lee GA, Chung JW, Hyun DY. The complete chloroplast genome sequence of Japanese Millet Echinochloa esculenta (A. braun) H. scholz (Poaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2019. [DOI: 10.1080/23802359.2019.1598787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Raveendar Sebastin
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju-Si, Republic of Korea
| | - Kyung Jun Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju-Si, Republic of Korea
| | - Gyu-Taek Cho
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju-Si, Republic of Korea
| | - Jung-Ro Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju-Si, Republic of Korea
| | - Myoung-Jae Shin
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju-Si, Republic of Korea
| | - Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju-Si, Republic of Korea
| | - Gi-An Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju-Si, Republic of Korea
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Do Yoon Hyun
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju-Si, Republic of Korea
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Cho KS, Cho JH, Park YE, Park TH. Chloroplast genome sequence of Solanum demissum, a wild tuber-bearing species was completed. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1612716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Kwang-Soo Cho
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, South Korea
| | - Ji-Hong Cho
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, South Korea
| | - Young-Eun Park
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, South Korea
| | - Tae-Ho Park
- Department of Horticulture, Daegu University, Gyeongsan, South Korea
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Sebastin R, Lee KJ, Cho GT, Shin MJ, Kim SH, Hyun DY, Lee JR. The complete chloroplast genome sequence of a Bolivian wild chili pepper, Capsicum eximium Hunz. (Solanaceae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1601533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Raveendar Sebastin
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Jeonju-Si, Jeollabuk-Do, Republic of Korea
| | - Kyung Jun Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Jeonju-Si, Jeollabuk-Do, Republic of Korea
| | - Gyu-Taek Cho
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Jeonju-Si, Jeollabuk-Do, Republic of Korea
| | - Myoung-Jae Shin
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Jeonju-Si, Jeollabuk-Do, Republic of Korea
| | - Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Jeonju-Si, Jeollabuk-Do, Republic of Korea
| | - Do Yoon Hyun
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Jeonju-Si, Jeollabuk-Do, Republic of Korea
| | - Jung-Ro Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Jeonju-Si, Jeollabuk-Do, Republic of Korea
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Zhang R, Zhang L, Wang W, Zhang Z, Du H, Qu Z, Li XQ, Xiang H. Differences in Codon Usage Bias between Photosynthesis-Related Genes and Genetic System-Related Genes of Chloroplast Genomes in Cultivated and Wild Solanum Species. Int J Mol Sci 2018; 19:E3142. [PMID: 30322061 PMCID: PMC6213243 DOI: 10.3390/ijms19103142] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/30/2018] [Accepted: 10/04/2018] [Indexed: 12/20/2022] Open
Abstract
Solanum is one of the largest genera, including two important crops-potato (Solanum tuberosum) and tomato (Solanum lycopersicum). In this study we compared the chloroplast codon usage bias (CUB) among 12 Solanum species, between photosynthesis-related genes (Photo-genes) and genetic system-related genes (Genet-genes), and between cultivated species and wild relatives. The Photo-genes encode proteins for photosystems, the photosynthetic electron transport chain, and RuBisCO, while the Genet-genes encode proteins for ribosomal subunits, RNA polymerases, and maturases. The following findings about the Solanum chloroplast genome CUB were obtained: (1) the nucleotide composition, gene expression, and selective pressure are identified as the main factors affecting chloroplast CUB; (2) all these 12 chloroplast genomes prefer A/U over G/C and pyrimidines over purines at the third-base of codons; (3) Photo-genes have higher codon adaptation indexes than Genet-genes, indicative of a higher gene expression level and a stronger adaptation of Photo-genes; (4) gene function is the primary factor affecting CUB of Photo-genes but not Genet-genes; (5) Photo-genes prefer pyrimidine over purine, whereas Genet-genes favor purine over pyrimidine, at the third position of codons; (6) Photo-genes are mainly affected by the selective pressure, whereas Genet-genes are under the underlying mutational bias; (7) S. tuberosum is more similar with Solanum commersonii than with Solanum bulbocastanum; (8) S. lycopersicum is greatly different from the analyzed seven wild relatives; (9) the CUB in codons for valine, aspartic acid, and threonine are the same between the two crop species, S. tuberosum and S. lycopersicum. These findings suggest that the chloroplast CUB contributed to the differential requirement of gene expression activity and function between Photo-genes and Genet-genes and to the performance of cultivated potato and tomato.
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Affiliation(s)
- Ruizhi Zhang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China.
| | - Li Zhang
- Department of Math and Information, China West Normal University, Nanchong, Sichuan 637000, China.
| | - Wei Wang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Zhu Zhang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Huihui Du
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Zheng Qu
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Xiu-Qing Li
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, NB E3B 4Z7, Canada.
| | - Heng Xiang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
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Sebastin R, Lee GA, Lee KJ, Shin MJ, Cho GT, Lee JR, Ma KH, Chung JW. The complete chloroplast genome sequences of little millet ( Panicum sumatrense Roth ex Roem. and Schult.) (Poaceae). Mitochondrial DNA B Resour 2018; 3:719-720. [PMID: 33474296 PMCID: PMC7800850 DOI: 10.1080/23802359.2018.1483771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 05/29/2018] [Indexed: 11/28/2022] Open
Abstract
Little millet, Panicum sumatrense Roth ex Roem. & Schult., is an important cultivated species under the tribe Paniceae, sub-family Panicoideae and family Poaceae. In this study, for the first time we sequenced the complete chloroplast (cp) genome of P. sumatrense to investigate their phylogenetic relationship in the family Poaceae. The complete cp genome sequence of P. sumatrense is 139,384 bp in length with 38.6% overall GC content and exhibits a typical quadripartite structure comprising one pair of inverted repeats (22,723 bp) separated by a small single-copy region (12,583 bp) and a large single-copy region (81,355 bp). The P. sumatrense cp genome encodes 125 unique genes, which include 91 protein-coding genes, 4 rRNA genes, 30 tRNA genes, and 20 genes were duplicated in the inverted repeat region. This newly determined cp genome (P. sumatrense) could be valuable information for the breeding programs of this cereal crops in the family Poaceae.
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Affiliation(s)
- Raveendar Sebastin
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Jeonju-Si, Republic of Korea
| | - Gi-An Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Jeonju-Si, Republic of Korea
| | - Kyung Jun Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Jeonju-Si, Republic of Korea
| | - Myoung-Jae Shin
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Jeonju-Si, Republic of Korea
| | - Gyu-Taek Cho
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Jeonju-Si, Republic of Korea
| | - Jung-Ro Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Jeonju-Si, Republic of Korea
| | - Kyung-Ho Ma
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Jeonju-Si, Republic of Korea
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
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Sebastin R, Lee KJ, Shin MJ, Cho GT, Ma KH, Lee JR, Lee GA, Chung JW. The complete chloroplast genome sequence of wild oat, Avena sterilis L. (Poaceae) and its phylogeny. Mitochondrial DNA B Resour 2018; 3:311-312. [PMID: 33474156 PMCID: PMC7799852 DOI: 10.1080/23802359.2018.1444518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 02/13/2018] [Indexed: 11/20/2022] Open
Abstract
Wild oat, Avena sterilis L. is a stout broad-leaved annual grass resembling cultivated oats in general appearance. In this study, we sequenced the complete chloroplast (cp) genome sequence of A. sterilis for the first time to investigate their phylogenetic relationship in the family Poaceae. The complete cp genome sequence is 135,887 bp in length with 38.5% overall GC content and exhibits a typical quadripartite structure comprising one pair of inverted repeats (21,603 bp) separated by a small single-copy region (12,575 bp) and a large single-copy region (80,106). The cp genome encodes 111 unique genes, 76 of which are protein-coding genes, four rRNA genes, 30 tRNA genes, and 18 duplicated genes in the inverted repeat region. The phylogenetic analysis indicated A. sterilis closely clustered with the cultivated oat, A. sativa L.
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Affiliation(s)
- Raveendar Sebastin
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju-Si, Republic of Korea
| | - Kyung Jun Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju-Si, Republic of Korea
| | - Myoung-Jae Shin
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju-Si, Republic of Korea
| | - Gyu-Taek Cho
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju-Si, Republic of Korea
| | - Kyung-Ho Ma
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju-Si, Republic of Korea
| | - Jung-Ro Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju-Si, Republic of Korea
| | - Gi-An Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju-Si, Republic of Korea
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
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