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Zhao M, Wu Y, Ren Y. Complete Chloroplast Genome Sequence Structure and Phylogenetic Analysis of Kohlrabi ( Brassica oleracea var. gongylodes L.). Genes (Basel) 2024; 15:550. [PMID: 38790180 PMCID: PMC11120933 DOI: 10.3390/genes15050550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Kohlrabi is an important swollen-stem cabbage variety belonging to the Brassicaceae family. However, few complete chloroplast genome sequences of this genus have been reported. Here, a complete chloroplast genome with a quadripartite cycle of 153,364 bp was obtained. A total of 132 genes were identified, including 87 protein-coding genes, 37 transfer RNA genes and eight ribosomal RNA genes. The base composition analysis showed that the overall GC content was 36.36% of the complete chloroplast genome sequence. Relative synonymous codon usage frequency (RSCU) analysis showed that most codons with values greater than 1 ended with A or U, while most codons with values less than 1 ended with C or G. Thirty-five scattered repeats were identified and most of them were distributed in the large single-copy (LSC) region. A total of 290 simple sequence repeats (SSRs) were found and 188 of them were distributed in the LSC region. Phylogenetic relationship analysis showed that five Brassica oleracea subspecies were clustered into one group and the kohlrabi chloroplast genome was closely related to that of B. oleracea var. botrytis. Our results provide a basis for understanding chloroplast-dependent metabolic studies and provide new insight for understanding the polyploidization of Brassicaceae species.
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Affiliation(s)
- Mengliang Zhao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
| | - Yanxun Wu
- Qinghai Academy of Agriculture and Forestry Sciences, Xining 810016, China;
| | - Yanjing Ren
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
- Qinghai Academy of Agriculture and Forestry Sciences, Xining 810016, China;
- Laboratory of Research and Utilization of Germplasm Resources in Qinghai-Tibet Plateau, Xining 810016, China
- Qinghai Provincial Key Laboratory of Vegetable Genetics and Physiology, Xining 810016, China
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Jo S, Kim J, Yun NR, Lee C, Choi S, Kim SY. Characterization of the complete plastome sequence of Korean endemic, Cardamine glechomifolia H.Lév. (Brassicaceae, Brassicales). Mitochondrial DNA B Resour 2024; 9:133-137. [PMID: 38274850 PMCID: PMC10810622 DOI: 10.1080/23802359.2024.2305394] [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: 08/02/2023] [Accepted: 01/09/2024] [Indexed: 01/27/2024] Open
Abstract
In this study, we report the complete plastome sequence of Cardamine glechomifolia H.Lév. 1913 (NCBI acc. no. OP894664). This plastome shows typical quadripartite structure. The plastome size is 154,307 bp, which consists of 84,015 bp large single-copy (LSC), 17,690 bp small single-copy (SSC), and 26,301 bp inverted repeat (IR) regions. The plastome contains 112 genes, including 78 protein-coding, 30 tRNA, and four rRNA genes. The infA gene is pseudogenized. Sixteen genes contain one intron and two genes (clpP and ycf3) have two introns. The phylogenomic analysis conducted in our study reveals that the genus Cardamine, which encompasses C. glechomifolia, exhibits three distinct clades. In order to elucidate the interrelationship among the three clades, it is imperative to conduct additional investigations by augmenting the number of Cardamine samples.
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Affiliation(s)
- Sangjin Jo
- International Biological Material Research Center (IBMRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Jinki Kim
- Operation Management Team, National Botanic Garden of Korea Native Plant, Gangwon-do, Republic of Korea
| | - Na-Rae Yun
- Department of Botany, Honam National Institute of Biological Resources, Mokpo, Republic of Korea
| | - Changyoung Lee
- International Biological Material Research Center (IBMRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Sangho Choi
- International Biological Material Research Center (IBMRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Soo-Yong Kim
- International Biological Material Research Center (IBMRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
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Zhou X, Ren H, Zhang J, Xu D, Xiao W, Huang H, Li G, Zhang H, Zheng Y. The complete chloroplast genome of Brassica rapa var. purpuraria (L.H.Bailey) Kitam 1950 and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:143-147. [PMID: 38274856 PMCID: PMC10810650 DOI: 10.1080/23802359.2024.2305403] [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: 06/09/2023] [Accepted: 01/09/2024] [Indexed: 01/27/2024] Open
Abstract
Zicaitai (Brassica rapa var. purpuraria (L.H.Bailey) Kitam 1950) is a vegetable crop that boasts a high nutritional value and unique flavor. It originated from Central China and was formed after long-term cultivation and domestication. In this study, we obtained the complete sequence of the chloroplast genome of zicaitai, a circular molecule of 153,483 bp in length. This chloroplast genome consists of a large single-copy (LSC) region (83,282 bp), a small single-copy (SSC) region (17,775 bp), and a pair of inverted repeats (IRs) (26,213 bp). By sequence annotation, 132 genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes were identified in the zicaitai chloroplast. A total of 315 simple sequence repeats (SSRs) were found located in LSC (197), SSC (72), and IR (46), respectively. Phylogenetic analysis based on chloroplast genomes indicated the relationship of zicaitai and the Brassicaceae family, which supports zicaitai as a variety of B. rapa in taxonomy. The results obtained in this study provide insight into further research on Brassica chloroplasts and their phylogeny.
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Affiliation(s)
- Xianyu Zhou
- Guangzhou Academy of Agricultural Sciences, Guangzhou, PR China
| | - Hailong Ren
- Guangzhou Academy of Agricultural Sciences, Guangzhou, PR China
| | - Jing Zhang
- Guangzhou Academy of Agricultural Sciences, Guangzhou, PR China
| | - Donglin Xu
- Guangzhou Academy of Agricultural Sciences, Guangzhou, PR China
| | - Wanyu Xiao
- Guangzhou Academy of Agricultural Sciences, Guangzhou, PR China
| | - Hongdi Huang
- Guangzhou Academy of Agricultural Sciences, Guangzhou, PR China
| | - Guangguang Li
- Guangzhou Academy of Agricultural Sciences, Guangzhou, PR China
| | - Hua Zhang
- Guangzhou Academy of Agricultural Sciences, Guangzhou, PR China
| | - Yansong Zheng
- Guangzhou Academy of Agricultural Sciences, Guangzhou, PR China
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Xu H, Liu Y, Zhang S, Shui D, Xia Z, Sun J. Genome-wide identification and expression analysis of the AUX/IAA gene family in turnip (Brassica rapa ssp. rapa). BMC PLANT BIOLOGY 2023; 23:342. [PMID: 37370022 DOI: 10.1186/s12870-023-04356-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/20/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND Auxin/indoleacetic acid (AUX/IAA) genes encoding short-lived proteins participate in AUX signaling transduction and play crucial roles in plant growth and development. Although the AUX/IAA gene family has been identified in many plants, a systematic analysis of AUX/IAA genes in Brassica rapa ssp. rapa has not yet been reported. RESULTS We performed a comprehensive genome-wide analysis and found 89 AUX/IAA genes in turnip based on the conserved AUX/IAA domain (pfam02309). Phylogenetic analysis of AUX/IAA genes from turnip, Arabidopsis, and cabbage revealed that these genes cluster into six subgroups (A1, A2, A3, A4, B1, and B2). The motif distribution was also conservative among the internal members of the clade. Enhanced yellow fluorescent protein (EYFP) signals of BrrIAA-EYFPs showed that BrrIAA members functioned as nucleoproteins. Moreover, transcriptional analysis revealed that the expression patterns of AUX/IAA genes in turnip were tissue-dependent. Because orthologs have similar biological functions and interaction networks in plant growth and development, BrrIAA66 in turnip possibly played a role in embryo axis formation, vascular development, lateral root formation, and floral organ development by interacting with BrrARF19 and BrrTIR1. CONCLUSION These results provide a theoretical basis for further investigation of BrrAUX/IAA genes and lay the foundation for functional analysis of BrrIAA66 in turnip.
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Affiliation(s)
- Huanwen Xu
- College of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology (Wenzhou Academy of Agricultural Sciences), Wenzhou, Zhejiang, 325006, China
- Southern Zhejiang Key Laboratory of Crop Breeding, Wenzhou Vocational College of Science and Technology (Wenzhou Academy of Agricultural Sciences), Wenzhou, Zhejiang, 325006, China
| | - Yu Liu
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, Zhejiang, 325005, China
| | - Shengmei Zhang
- College of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology (Wenzhou Academy of Agricultural Sciences), Wenzhou, Zhejiang, 325006, China
- Southern Zhejiang Key Laboratory of Crop Breeding, Wenzhou Vocational College of Science and Technology (Wenzhou Academy of Agricultural Sciences), Wenzhou, Zhejiang, 325006, China
| | - Deju Shui
- College of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology (Wenzhou Academy of Agricultural Sciences), Wenzhou, Zhejiang, 325006, China
- Southern Zhejiang Key Laboratory of Crop Breeding, Wenzhou Vocational College of Science and Technology (Wenzhou Academy of Agricultural Sciences), Wenzhou, Zhejiang, 325006, China
| | - Zhewen Xia
- Wenzhou Lucheng District Agricultural Industry Institute, Wenzhou, Zhejiang, 325000, China
| | - Ji Sun
- College of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology (Wenzhou Academy of Agricultural Sciences), Wenzhou, Zhejiang, 325006, China.
- Southern Zhejiang Key Laboratory of Crop Breeding, Wenzhou Vocational College of Science and Technology (Wenzhou Academy of Agricultural Sciences), Wenzhou, Zhejiang, 325006, China.
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Ren Y, Han R, Ma Y, Li X, Deng C, Zhao M, Li J, Hou Q, Zhong Q, Shao D. Transcriptomics Integrated with Metabolomics Unveil Carotenoids Accumulation and Correlated Gene Regulation in White and Yellow-Fleshed Turnip (Brassica rapa ssp. rapa). Genes (Basel) 2022; 13:genes13060953. [PMID: 35741715 PMCID: PMC9222417 DOI: 10.3390/genes13060953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/17/2022] [Accepted: 05/23/2022] [Indexed: 01/25/2023] Open
Abstract
Turnip (Brassica rapa ssp. rapa) is considered to be a highly nutritious and health-promoting vegetable crop, whose flesh color can be divided into yellow and white. It is widely accepted that yellow-fleshed turnips have higher nutritional value. However, reports about flesh color formation is lacking. Here, the white-fleshed inbred line, W21, and yellow-fleshed inbred line, W25, were profiled from the swollen root of the turnip at three developmental periods to elucidate the yellow color formation. Transcriptomics integrated with metabolomics analysis showed that the PSY gene was the key gene affecting the carotenoids formation in W25. The coding sequence of BrrPSY-W25 was 1278 bp and that of BrrPSY-W21 was 1275 bp, and BrrPSY was more highly expressed in swollen roots in W25 than in W21. Transient transgenic tobacco leaf over-expressing BrrPSY-W and BrrPSY-Y showed higher transcript levels and carotenoids contents. Results revealed that yellow turnip formation is due to high expression of the PSY gene rather than mutations in the PSY gene, indicating that a post-transcriptional regulatory mechanism may affect carotenoids formation. Results obtained in this study will be helpful for explaining the carotenoids accumulation of turnips.
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Affiliation(s)
- Yanjing Ren
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (Y.R.); (R.H.); (Y.M.); (X.L.); (C.D.); (M.Z.); (J.L.); (Q.H.)
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining 810016, China
| | - Rui Han
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (Y.R.); (R.H.); (Y.M.); (X.L.); (C.D.); (M.Z.); (J.L.); (Q.H.)
| | - Yidong Ma
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (Y.R.); (R.H.); (Y.M.); (X.L.); (C.D.); (M.Z.); (J.L.); (Q.H.)
| | - Xiaojuan Li
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (Y.R.); (R.H.); (Y.M.); (X.L.); (C.D.); (M.Z.); (J.L.); (Q.H.)
| | - Changrong Deng
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (Y.R.); (R.H.); (Y.M.); (X.L.); (C.D.); (M.Z.); (J.L.); (Q.H.)
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining 810016, China
| | - Mengliang Zhao
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (Y.R.); (R.H.); (Y.M.); (X.L.); (C.D.); (M.Z.); (J.L.); (Q.H.)
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining 810016, China
| | - Jiang Li
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (Y.R.); (R.H.); (Y.M.); (X.L.); (C.D.); (M.Z.); (J.L.); (Q.H.)
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining 810016, China
| | - Quangang Hou
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (Y.R.); (R.H.); (Y.M.); (X.L.); (C.D.); (M.Z.); (J.L.); (Q.H.)
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining 810016, China
| | - Qiwen Zhong
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (Y.R.); (R.H.); (Y.M.); (X.L.); (C.D.); (M.Z.); (J.L.); (Q.H.)
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining 810016, China
- Correspondence: (Q.Z.); (D.S.); Tel.: +86-0971-531-1167 (Q.Z. & D.S.)
| | - Dengkui Shao
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (Y.R.); (R.H.); (Y.M.); (X.L.); (C.D.); (M.Z.); (J.L.); (Q.H.)
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining 810016, China
- State Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China
- Correspondence: (Q.Z.); (D.S.); Tel.: +86-0971-531-1167 (Q.Z. & D.S.)
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Shao D, Ma Y, Li X, Ga S, Ren Y. The sequence structure and phylogenetic analysis by complete mitochondrial genome of kohlrabi ( Brassica oleracea var. gongylodes L.). Mitochondrial DNA B Resour 2021; 6:2714-2716. [PMID: 34435131 PMCID: PMC8382015 DOI: 10.1080/23802359.2021.1966341] [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: 10/25/2022] Open
Affiliation(s)
- Dengkui Shao
- Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Xining, PR China
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining, PR China
| | - Yidong Ma
- Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Xining, PR China
| | - Xiaojuan Li
- Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Xining, PR China
| | - Sang Ga
- Comprehensive Agriculture and Animal Husbandry Service Center of Yushu Tibetan Autonomous Prefecture, Yushu, PR China
| | - Yanjing Ren
- Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Xining, PR China
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining, PR China
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