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Liu Z, Yang B, Zhang T, Sun H, Mao L, Yang S, Dai X, Suo H, Zhang Z, Chen W, Chen H, Xu W, Dossa K, Zou X, Ou L. Full-length transcriptome sequencing of pepper fruit during development and construction of a transcript variation database. HORTICULTURE RESEARCH 2024; 11:uhae198. [PMID: 39257544 PMCID: PMC11387007 DOI: 10.1093/hr/uhae198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 07/08/2024] [Indexed: 09/12/2024]
Abstract
Chili pepper is an important spice and a model plant for fruit development studies. Large-scale omics information on chili pepper plant development continues to be gathered for understanding development as well as capsaicin biosynthesis. In this study, a full-spectrum transcriptome data of eight chili pepper tissues at five growth stages using the Oxford Nanopore long-read sequencing approach was generated. Of the 485 351 transcripts, 35 336 were recorded as reference transcripts (genes), while 450 015 were novel including coding, lnc, and other non-coding RNAs. These novel transcripts belonged to unknown/intergenic (347703), those retained introns (26336), and had multi-exons with at least one junction match (20333). In terms of alternative splicing, retained intron had the highest proportion (14795). The number of tissue-specific expressed transcripts ranged from 22 925 (stem) to 40 289 (flower). The expression changes during fruit and placenta development are discussed in detail. Integration of gene expression and capsaicin content quantification throughout the placental development clarifies that capsaicin biosynthesis in pepper is mainly derived from valine, leucin, and isoleucine degradation as well as citrate cycle and/or pyrimidine metabolism pathways. Most importantly, a user-friendly Pepper Full-Length Transcriptome Variation Database (PFTVD 1.0) (http://pepper-database.cn/) has been developed. PFTVD 1.0 provides transcriptomics and genomics information and allows users to analyse the data using various tools implemented. This work highlights the potential of long-read sequencing to discover novel genes and transcripts and their diversity in plant developmental biology.
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Affiliation(s)
- Zhoubin Liu
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Bozhi Yang
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | | | - Hao Sun
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Lianzhen Mao
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Sha Yang
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Xiongze Dai
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Huan Suo
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Zhuqing Zhang
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Wenchao Chen
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Hu Chen
- Wuhan Benagen Technology Co., Ltd., Wuhan 430075, China
| | - Wangjie Xu
- Wuhan Benagen Technology Co., Ltd., Wuhan 430075, China
| | - Komivi Dossa
- CIRAD, UMR AGAP Institut, 97170 Petit Bourg, Guadeloupe, France
| | - Xuexiao Zou
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Lijun Ou
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
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Seong GU, Yun DY, Shin DH, Cho JS, Lee G, Choi JH, Park KJ, Ku KH, Lim JH. Comparative 1H NMR-Based Metabolomics of Traditional Landrace and Disease-Resistant Chili Peppers ( Capsicum annuum L.). Foods 2024; 13:1966. [PMID: 38998472 PMCID: PMC11241277 DOI: 10.3390/foods13131966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
Chili peppers (Capsicum annuum L.) are economically valuable crops belonging to the Solanaceae family and are popular worldwide because of their unique spiciness and flavor. In this study, differences in the metabolomes of landrace (Subicho) and disease-resistant pepper cultivars (Bulkala and Kaltanbaksa) widely grown in Korea are investigated using a 1H NMR-based metabolomics approach. Specific metabolites were abundant in the pericarp (GABA, fructose, and glutamine) and placenta (glucose, asparagine, arginine, and capsaicin), highlighting the distinct physiological and functional roles of these components. Both the pericarp and placenta of disease-resistant pepper cultivars contained higher levels of sucrose and hexoses and lower levels of alanine, proline, and threonine than the traditional landrace cultivar. These metabolic differences are linked to enhanced stress tolerance and the activation of defense pathways, imbuing these cultivars with improved resistance characteristics. The present study provides fundamental insights into the metabolic basis of disease resistance in chili peppers, emphasizing the importance of multi-resistant varieties to ensure sustainable agriculture and food security. These resistant varieties ensure a stable supply of high-quality peppers, contributing to safer and more sustainable food production systems.
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Affiliation(s)
- Gi-Un Seong
- Food Safety and Distribution Research Group, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea; (G.-U.S.); (D.-Y.Y.); (D.-H.S.); (J.-S.C.); (J.H.C.); (K.-J.P.); (K.-H.K.)
| | - Dae-Yong Yun
- Food Safety and Distribution Research Group, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea; (G.-U.S.); (D.-Y.Y.); (D.-H.S.); (J.-S.C.); (J.H.C.); (K.-J.P.); (K.-H.K.)
| | - Dong-Hyeok Shin
- Food Safety and Distribution Research Group, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea; (G.-U.S.); (D.-Y.Y.); (D.-H.S.); (J.-S.C.); (J.H.C.); (K.-J.P.); (K.-H.K.)
| | - Jeong-Seok Cho
- Food Safety and Distribution Research Group, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea; (G.-U.S.); (D.-Y.Y.); (D.-H.S.); (J.-S.C.); (J.H.C.); (K.-J.P.); (K.-H.K.)
- Smart Food Manufacturing Project Group, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea;
| | - Gyuseok Lee
- Smart Food Manufacturing Project Group, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea;
| | - Jeong Hee Choi
- Food Safety and Distribution Research Group, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea; (G.-U.S.); (D.-Y.Y.); (D.-H.S.); (J.-S.C.); (J.H.C.); (K.-J.P.); (K.-H.K.)
- Smart Food Manufacturing Project Group, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea;
| | - Kee-Jai Park
- Food Safety and Distribution Research Group, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea; (G.-U.S.); (D.-Y.Y.); (D.-H.S.); (J.-S.C.); (J.H.C.); (K.-J.P.); (K.-H.K.)
- Smart Food Manufacturing Project Group, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea;
| | - Kyung-Hyung Ku
- Food Safety and Distribution Research Group, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea; (G.-U.S.); (D.-Y.Y.); (D.-H.S.); (J.-S.C.); (J.H.C.); (K.-J.P.); (K.-H.K.)
| | - Jeong-Ho Lim
- Food Safety and Distribution Research Group, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea; (G.-U.S.); (D.-Y.Y.); (D.-H.S.); (J.-S.C.); (J.H.C.); (K.-J.P.); (K.-H.K.)
- Smart Food Manufacturing Project Group, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea;
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Del Giúdice LZ, Falquetto-Gomes P, de Almeida Costa PM, Martins AO, Omena-Garcia RP, Araújo WL, Zsögön A, Picoli EADT, Nunes-Nesi A. Dynamic shifts in primary metabolism across fruit development stages in Capsicum chinense (cv. Habanero). JOURNAL OF PLANT PHYSIOLOGY 2023; 291:154121. [PMID: 37924627 DOI: 10.1016/j.jplph.2023.154121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 11/06/2023]
Abstract
The development of fleshy fruits involves changes in size and mass, followed by cell differentiation, which is associated with anatomical and histological changes. Parallel to these changes, metabolic alterations lead to the production of osmolytes and energy that modify cell turgor pressure, thereby promoting cell expansion and fruit growth. Detailed information is known about these processes in climacteric fruits (e.g. tomato); however, the regulation of metabolism and its association with anatomical changes in non-climacteric fruit development are poorly understood. In this study, we used detailed anatomical and histological analyses to define three developmental phases of chili pepper (Capsicum chinense cv. Habanero): cell division, cell expansion, and ripening. We showed that each was marked by distinct metabolic profiles, underpinning the switches in energy metabolism to support cellular processes. Interestingly, mitochondrial activity was high in the early stages of development and declined over time, with a modest increase in O2 consumption by pericarp tissues at the beginning of the ripening stage. This respiratory-like burst was associated with the degradation of starch and malate, which are the sources of energy and carbon required for other processes associated with fruit maturation.
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Affiliation(s)
- Luciana Zacour Del Giúdice
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Priscilla Falquetto-Gomes
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | | | - Auxiliadora O Martins
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Rebeca Patrícia Omena-Garcia
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Wagner L Araújo
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Agustín Zsögön
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | | | - Adriano Nunes-Nesi
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
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Zhao Y, Sun C, Wang S, Zhang M, Li Y, Xue Q, Guo Q, Lai H. Widely targeted metabolomic, transcriptomic, and metagenomic profiling reveal microbe-plant-metabolic reprogramming patterns mediated by Streptomyces pactum Act12 enhance the fruit quality of Capsicum annuum L. Food Res Int 2023; 166:112587. [PMID: 36914318 DOI: 10.1016/j.foodres.2023.112587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/02/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023]
Abstract
Plant growth-promoting rhizobacteria, such as Streptomyces pactum Act12, promote crop growth and stress resistance, but their contribution to fruit quality is still poorly understood. Herein we conducted a field experiment to ascertain the effects of S. pactum Act12-mediated metabolic reprogramming and underlying mechanisms in pepper (Capsicum annuum L.) fruit based on widely targeted metabolomic and transcriptomic profiling. We additionally performed metagenomic analysis to elucidate the potential relationship between S. pactum Act12-mediated reshaping of rhizosphere microbial communities and pepper fruit quality. Soil inoculation with S. pactum Act12 considerably increased the accumulation of capsaicinoids, carbohydrates, organic acids, flavonoids, anthraquinones, unsaturated fatty acids, vitamins, and phenolic acids in pepper fruit samples. Consequently, fruit flavor, taste, and color were modified, accompanied by elevated contents of nutrients and bioactive compounds. Increased microbial diversity and recruitment of potentially beneficial taxa were observed in inoculated soil samples, with crosstalk between microbial gene functions and pepper fruit metabolism. The reformed structure and function of rhizosphere microbial communities were closely associated with pepper fruit quality. Our findings indicate that S. pactum Act12-mediated interactions between rhizosphere microbial communities and pepper plants are responsible for intricate fruit metabolic reprogramming patterns, which enhance not only overall fruit quality but also consumer acceptability.
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Affiliation(s)
- Yisen Zhao
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Chenyu Sun
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Suzhen Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Meilin Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Yulong Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Quanhong Xue
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Qiao Guo
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Hangxian Lai
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China.
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Heterosis for capsacinoids accumulation in chili pepper hybrids is dependent on parent-of-origin effect. Sci Rep 2022; 12:14450. [PMID: 36002476 PMCID: PMC9402712 DOI: 10.1038/s41598-022-18711-w] [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] [Received: 12/29/2021] [Accepted: 08/18/2022] [Indexed: 11/09/2022] Open
Abstract
Heterosis for agronomic traits is a widespread phenomenon that underpins hybrid crop breeding. However, heterosis at the level of cellular metabolites has not yet been fully explored. Some metabolites are highly sought after, like capsaicinoids found in peppers of the Capsicum genus, which confer the characteristic pungent ('hot') flavour of the fruits. We analysed the metabolic profile of the fruit placenta and pericarp of inter- and intra-specific hybrids of two species of Capsicum peppers, C. chinense (cv. Habanero and cv. Biquinho) and C. annuum var. annuum (cv. Jalapeño and cv. Cascadura Ikeda) in complete diallel crosses with reciprocals. The parents and hybrids were grown in a glasshouse and the profile of primary metabolites (sugars, amino acids and organic acids) and capsaicinoids was generated via gas chromatography-time of flight-mass spectrometry (GC-TOF-MS) and ultra-performance liquid chromatography coupled to a mass spectrometer (UPLC-MS), respectively. We found considerable heterotic effects specifically for capsaicinoids accumulation in the fruit placenta of the hybrids, including those derived from non-pungent parents. Furthermore, a large fraction of fruit primary metabolism was influenced by the specific cross combination, with marked parent-of-origin effects, i.e. whether a specific genotype was used as the pistillate or pollen parent. The differences in metabolite levels between the hybrids and their parents provide a snapshot of heterosis for primary and secondary metabolites and may contribute to explain the manifestation of whole-plant heterotic phenotypes.
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