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Villalba-Bermell P, Marquez-Molins J, Gomez G. A multispecies study reveals the diversity and potential regulatory role of long noncoding RNAs in cucurbits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39254680 DOI: 10.1111/tpj.17013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/31/2024] [Accepted: 08/23/2024] [Indexed: 09/11/2024]
Abstract
Plant long noncoding RNAs (lncRNAs) exhibit features such as tissue-specific expression, spatiotemporal regulation, and stress responsiveness. Although diverse studies support the regulatory role of lncRNAs in model plants, our knowledge about lncRNAs in crops is limited. We employ a custom pipeline on a dataset of over 1000 RNA-seq samples across nine representative species of the family Cucurbitaceae to predict 91 209 nonredundant lncRNAs. The lncRNAs were characterized according to three confidence levels and classified by their genomic context into intergenic, natural antisense, intronic, and sense-overlapping. Compared with protein-coding genes, lncRNAs were, on average, expressed at low levels and displayed significantly higher specificity when considering tissue, developmental stages, and stress responsiveness. The evolutionary analysis indicates higher positional conservation than sequence conservation, probably linked to the conserved modular motifs within syntenic lncRNAs. Moreover, a positive correlation between the expression of intergenic/natural antisense lncRNAs and their closest/parental gene was observed. For those intergenic, the correlation decreases with the distance to the neighboring gene, supporting that their potential cis-regulatory effect is within a short-range. Furthermore, the analysis of developmental studies showed that a conserved NAT-lncRNA family is differentially expressed in a coordinated way with their cognate sense protein-coding genes. These genes code for proteins associated with phloem development, thus providing insights about the potential involvement of some of the identified lncRNAs in a developmental process. We expect that this extensive inventory will constitute a valuable resource for further research lines focused on elucidating the regulatory mechanisms mediated by lncRNAs in cucurbits.
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Affiliation(s)
- Pascual Villalba-Bermell
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Cat. Agustín Escardino 9, 46980, Paterna, Spain
| | - Joan Marquez-Molins
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Cat. Agustín Escardino 9, 46980, Paterna, Spain
| | - Gustavo Gomez
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Cat. Agustín Escardino 9, 46980, Paterna, Spain
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2
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Polyzos N, Fernandes Â, Calhelha RC, Petrović J, Soković M, Ferreira ICFR, Barros L, Petropoulos SA. Biochemical Composition of Pumpkin Seeds and Seed By-Products. PLANTS (BASEL, SWITZERLAND) 2024; 13:2395. [PMID: 39273879 DOI: 10.3390/plants13172395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 08/17/2024] [Accepted: 08/26/2024] [Indexed: 09/15/2024]
Abstract
The goal of the current work was to assess the nutritional profile and phytochemical properties of cucurbit (Cucurbita maxima L.) seeds, seed oils and oil extraction by-products (e.g., seed-cakes). Our results suggest a high nutritional value for both cucurbit seeds and cucurbit cake, while γ-tocopherol was the richest compound, with traces of α, β and δ-tocopherol compounds also detected. Regarding the free sugars composition, there were recorded significant statistical differences between seeds and cucurbit seed-cake, although sucrose content was the highest for both matrices (1.97 and 2.9 g/100 g dw, respectively) followed by trehalose (0.26 and 0.25 g/100 g dw, respectively), fructose (0.20 and 0.34 g/100 g dw, respectively) and glucose (0.21 and 0.19 g/100 g dw, respectively). In terms of organic acids, oxalic was the only compound detected in seed cake (0.006 g/100 g dw), while in seeds only traces of oxalic and malic acid were detected. In relation to fatty acid composition, linolenic acid was the most abundant compound in both seeds and seed-cake (43.9% and 41.5%, respectively), while oleic acid (37.0% and 36.3%, respectively), palmitic acid (12.2% and 14.0%, respectively) and stearic acid (4.83% and 5.46%, respectively) were detected in lesser amounts. Moreover, polyunsaturated fatty acids (PUFA) were the major fatty acids class (44.5% and 42.3% in seeds and seed cake, respectively) compared to monounsaturated fatty acids (MUFA; 37.4% and 36.7% in seeds and seed cake, respectively) and saturated fatty acids (SFA; 18.1% and 21.0% in seeds and seed cake, respectively) which were detected in lower amounts. Furthermore, the tested extracts did not present any cytotoxic or hepatoxic activity at the maximum tested concentration (GI50 > 400 μg/mL), while seed oils presented satisfactory antimicrobial properties with inhibitory activity against the studied bacterial strains and fungi. Our findings provide valuable knowledge regarding the exploitation of pumpkin seeds and seed by-products as valuable natural sources of nutrients and phytochemicals in the food industry sector within the context of a circular economy.
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Affiliation(s)
- Nikolaos Polyzos
- Laboratory of Vegetable Production, Department of Agriculture, Crop Production and Rural Environment, University of Thessaly, Fytokou Street, 384 46 Volos, Greece
| | - Ângela Fernandes
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Ricardo C Calhelha
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Jovana Petrović
- Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, 11108 Belgrade, Serbia
| | - Marina Soković
- Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, 11108 Belgrade, Serbia
| | - Isabel C F R Ferreira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Lillian Barros
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Spyridon A Petropoulos
- Laboratory of Vegetable Production, Department of Agriculture, Crop Production and Rural Environment, University of Thessaly, Fytokou Street, 384 46 Volos, Greece
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Magalhães ICS, Souza-Neto CSD, Souza GTD, Baronio GJ, Castro CCD. Bee pollination effects on yield and chemical composition of West Indian gherkin fruits (Cucumis anguria L., Cucurbitaceae) in the Brazilian semi-arid region. BRAZ J BIOL 2024; 84:e284217. [PMID: 39194022 DOI: 10.1590/1519-6984.284217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 07/04/2024] [Indexed: 08/29/2024] Open
Abstract
Animal pollination plays a key role in global agricultural production and especially of monoecious crops, which are essentially dependent on pollinators. The West Indian gherkin fruit (Cucumis anguria L., Cucurbitaceae) is a monoecious vegetable adaptable to adverse abiotic conditions, resistant to diseases, and rich in minerals and vitamins, thus being a relevant alternative for improving nutritional security of socioeconomically vulnerable populations. The knowledge on the influence of pollination and of specific pollinators on chemical characteristics of fruits would help pollinators' management, but it is still poorly understood. In this study we investigated the influence of pollination on quantitative and qualitative aspects of fruits fruits of West Indian gherkin fruits (Cucumis anguria L., Cucurbitaceae) in the Brazilian semi-arid region. Data on pollination biology and on fruits resulted from controlled crosses (open-OP, cross-CP and Apis mellifera Linnaeus, 1758 pollinations) were compared among crosses: number, length, weight, number of seeds, firmness and chemical traits related to flavor and shelf life. Flowers were pollinated by four bee species, and Apis mellifera was the most frequent. followed by two native bee species. OP and A. mellifera resulted in more fruits than CP. Fruits resulting from OP were heavier than CP and had similar weight when compared to A. mellifera. The other variables did not differ between treatments. The better performance of OP and A. mellifera when compared to CP is probably related to the xenia, i.e., the influence of tissues bearing paternal genes (pollen and pollen tube) in maternal tissues. OP and A. mellifera experiments apparently resulted in the deposition of a greater genotypic diversity of the pollen loads when compared to CP. This result is also explained by the higher functional diversity of pollinators related to OP when compared to CP. This study not only elucidates immediate impacts on yield but also emphasizes the deeper connections between floral biology, pollinator diversity, and sustainable crop production, once West Indian gherkin profit was enhanced by bee pollination.
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Affiliation(s)
- I C S Magalhães
- Universidade Federal Rural de Pernambuco, Programa de Pós-Graduação em Biodiversidade, Recife, PE, Brasil
| | - C S de Souza-Neto
- Universidade Federal do Agreste de Pernambuco, Garanhuns, PE, Brasil
| | - G T de Souza
- Universidade Federal Rural de Pernambuco, Programa de Pós-Graduação em Biodiversidade, Recife, PE, Brasil
| | - G J Baronio
- Universidade de São Paulo, Departamento de Ecologia, São Paulo, SP, Brasil
- Centro de Investigaciones sobre Desertificación (CIDE-CSIC), Valencia, Spain
| | - C C de Castro
- Universidade Federal Rural de Pernambuco, Programa de Pós-Graduação em Biodiversidade, Recife, PE, Brasil
- Universidade Federal do Agreste de Pernambuco, Garanhuns, PE, Brasil
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Zhu X, Chen F, Qiao C, Zhang Y, Zhang L, Gao W, Wang Y. Cucumber pathogenic spores' detection using the GCS-YOLOv8 network with microscopic images in natural scenes. PLANT METHODS 2024; 20:131. [PMID: 39169365 PMCID: PMC11337645 DOI: 10.1186/s13007-024-01243-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 07/22/2024] [Indexed: 08/23/2024]
Abstract
Fungal diseases are the main factors affecting the quality and production of vegetables. Rapid and accurate detection of pathogenic spores is of great practical significance for early prediction and prevention of diseases. However, there are some problems with microscopic images collected in the natural environment, such as complex backgrounds, more disturbing materials, small size of spores, and various forms. Therefore, this study proposed an improved detection method of GCS-YOLOv8 (Global context and CARFAE and Small detector-optimized YOLOv8), effectively improving the detection accuracy of small-target pathogen spores in natural scenes. Firstly, by adding a small target detection layer in the network, the network's sensitivity to small targets is enhanced, and the problem of low detection accuracy of the small target is effectively improved. Secondly, Global Context attention is introduced in Backbone to optimize the CSPDarknet53 to 2-Stage FPN (C2F) module and model global context information. At the same time, the feature up-sampling module Content-Aware Reassembly of Features (CARAFE) was introduced into Neck to enhance the ability of the network to extract spore features in natural scenes further. Finally, we used an Explainable Artificial Intelligence (XAI) approach to interpret the model's predictions. The experimental results showed that the improved GCS-YOLOv8 model could detect the spores of the three fungi with an accuracy of 0.926 and a model size of 22.8 MB, which was significantly superior to the existing model and showed good robustness under different brightness conditions. The test on the microscopic images of the infection structure of cucumber down mildew also proved that the model had good generalization. Therefore, this study realized the accurate detection of pathogen spores in natural scenes and provided feasible technical support for early predicting and preventing fungal diseases.
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Affiliation(s)
- Xinyi Zhu
- College of Information and Electrical Engineering, China Agricultural University, Beijing, 100083, China
| | - Feifei Chen
- College of Information and Electrical Engineering, China Agricultural University, Beijing, 100083, China
| | - Chen Qiao
- College of Information and Electrical Engineering, China Agricultural University, Beijing, 100083, China
| | - Yiding Zhang
- College of Engineering, China Agricultural University, No.17 Qinghua East Road, Haidian District, Beijing, 100083, China.
| | - Lingxian Zhang
- College of Information and Electrical Engineering, China Agricultural University, Beijing, 100083, China.
- Key Laboratory of Agricultural Informationization Standardization, Ministry of Agriculture and Rural Affairs, Beijing, 100083, China.
| | - Wei Gao
- Tianjin Academy of Agricultural Sciences, Tianjin, 300384, China
| | - Yong Wang
- Tianjin Academy of Agricultural Sciences, Tianjin, 300384, China
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Hernández-Pérez T, Paredes-López O. Selected Mesoamerican Crops - Anti-Obesity Potential and Health Promotion. A Review. PLANT FOODS FOR HUMAN NUTRITION (DORDRECHT, NETHERLANDS) 2024:10.1007/s11130-024-01211-9. [PMID: 39105985 DOI: 10.1007/s11130-024-01211-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/28/2024] [Indexed: 08/07/2024]
Abstract
Mesoamerica is the center of origin of a great number of food crops that nowadays are part of a healthy diet. Pre-Columbian civilizations utilized more than 90% of these foods as ingredient or in main dishes, as well as for remedies and religious ceremonies. Since several years ago, Mesoamerican foods have been recognized by their outstanding concentration of bioactive compounds, including, phenolic compounds, pigments, essential fatty acids, amino acids, peptides, carbohydrates and vitamins, which provide a great number of health benefits. As a result of their unique composition, these ancient crops have several positive effects, such as hypoglycemic, antioxidant, anti-obesity, anti-inflammatory, anti-ageing, neuroprotective, anti-diarrheal, and anti-hypercholesterolemic capacity. Hence, this review is focused mainly in the anti-obesity and antioxidant potential of some of the most cultivated, harvested, as well as commercialized and consumed, food crops native of Mesoamerica, like, nopal and its fruit (Opuntia ficus indica spp.), chia (Salvia hispanica L.), pumpkin (Cucurbita spp.) and cacao (Theobroma cacao).
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Affiliation(s)
- Talía Hernández-Pérez
- Centro de Investigación y de Estudios Avanzados del IPN (Instituto Politécnico Nacional), Irapuato, Guanajuato, 36824, México
| | - Octavio Paredes-López
- Centro de Investigación y de Estudios Avanzados del IPN (Instituto Politécnico Nacional), Irapuato, Guanajuato, 36824, México.
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6
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Zhang Y, Zhao M, Tan J, Huang M, Chu X, Li Y, Han X, Fang T, Tian Y, Jarret R, Lu D, Chen Y, Xue L, Li X, Qin G, Li B, Sun Y, Deng XW, Deng Y, Zhang X, He H. Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding. Nat Genet 2024; 56:1750-1761. [PMID: 38977857 PMCID: PMC11319210 DOI: 10.1038/s41588-024-01823-6] [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: 08/26/2023] [Accepted: 06/04/2024] [Indexed: 07/10/2024]
Abstract
To decipher the genetic diversity within the cucurbit genus Citrullus, we generated telomere-to-telomere (T2T) assemblies of 27 distinct genotypes, encompassing all seven Citrullus species. This T2T super-pangenome has expanded the previously published reference genome, T2T-G42, by adding 399.2 Mb and 11,225 genes. Comparative analysis has unveiled gene variants and structural variations (SVs), shedding light on watermelon evolution and domestication processes that enhanced attributes such as bitterness and sugar content while compromising disease resistance. Multidisease-resistant loci from Citrullus amarus and Citrullus mucosospermus were successfully introduced into cultivated Citrullus lanatus. The SVs identified in C. lanatus have not only been inherited from cordophanus but also from C. mucosospermus, suggesting additional ancestors beyond cordophanus in the lineage of cultivated watermelon. Our investigation substantially improves the comprehension of watermelon genome diversity, furnishing comprehensive reference genomes for all Citrullus species. This advancement aids in the exploration and genetic enhancement of watermelon using its wild relatives.
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Affiliation(s)
- Yilin Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Mingxia Zhao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Jingsheng Tan
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Minghan Huang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Xiao Chu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yan Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Xue Han
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Taohong Fang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yao Tian
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | | | - Dongdong Lu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yijun Chen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Lifang Xue
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Xiaoni Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Guochen Qin
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Bosheng Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yudong Sun
- Vegetable Research and Development Center, Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huai'an, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Yun Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China.
| | - Xingping Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China.
| | - Hang He
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China.
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China.
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Jiang Z, Chen Y, Zhang X, Meng F, Chen J, Cheng X. Assembly and evolutionary analysis of the complete mitochondrial genome of Trichosanthes kirilowii, a traditional Chinese medicinal plant. PeerJ 2024; 12:e17747. [PMID: 39035164 PMCID: PMC11260417 DOI: 10.7717/peerj.17747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024] Open
Abstract
Trichosanthes kirilowii (T. kirilowii) is a valuable plant used for both medicinal and edible purposes. It belongs to the Cucurbitaceae family. However, its phylogenetic position and relatives have been difficult to accurately determine due to the lack of mitochondrial genomic information. This limitation has been an obstacle to the potential applications of T. kirilowii in various fields. To address this issue, Illumina and Nanopore HiFi sequencing were used to assemble the mitogenome of T. kirilowii into two circular molecules with sizes of 245,700 bp and 107,049 bp, forming a unique multi-branched structure. The mitogenome contains 61 genes, including 38 protein-coding genes (PCGs), 20 tRNAs, and three rRNAs. Within the 38 PCGs of the T. kirilowii mitochondrial genome, 518 potential RNA editing sites were identified. The study also revealed the presence of 15 homologous fragments that span both the chloroplast and mitochondrial genomes. The phylogenetic analysis strongly supports that T. kirilowii belongs to the Cucurbitaceae family and is closely related to Luffa. Collinearity analysis of five Cucurbitaceae mitogenomes shows a high degree of structural variability. Interestingly, four genes, namely atp1, ccmFC, ccmFN, and matR, played significant roles in the evolution of T. kirilowii through selection pressure analysis. The comparative analysis of the T. kirilowii mitogenome not only sheds light on its functional and structural features but also provides essential information for genetic studies of the genus of Cucurbitaceae.
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Affiliation(s)
- Zhuanzhuan Jiang
- Anqing Normal University, Anqing, Anhui, China
- Provincial Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui, Anqing, Anhui, China
| | - Yuhan Chen
- Anqing Normal University, Anqing, Anhui, China
- Provincial Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui, Anqing, Anhui, China
| | - Xingyu Zhang
- Anqing Normal University, Anqing, Anhui, China
- Provincial Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui, Anqing, Anhui, China
| | - Fansong Meng
- Anqing Normal University, Anqing, Anhui, China
- Provincial Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui, Anqing, Anhui, China
| | - Jinli Chen
- Anqing Normal University, Anqing, Anhui, China
- Provincial Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui, Anqing, Anhui, China
| | - Xu Cheng
- Anqing Normal University, Anqing, Anhui, China
- Provincial Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui, Anqing, Anhui, China
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8
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Huang A, Feng S, Ye Z, Zhang T, Chen S, Chen C, Chen S. Genome Assembly and Structural Variation Analysis of Luffa acutangula Provide Insights on Flowering Time and Ridge Development. PLANTS (BASEL, SWITZERLAND) 2024; 13:1828. [PMID: 38999668 PMCID: PMC11243878 DOI: 10.3390/plants13131828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/21/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024]
Abstract
Luffa spp. is an important worldwide cultivated vegetable and medicinal plant from the Cucurbitaceae family. In this study, we report a high-quality chromosome-level genome of the high-generation inbred line SG261 of Luffa acutangula. The genomic sequence was determined by PacBio long reads, Hi-C sequencing reads, and 10× Genomics sequencing, with an assembly size of 739.82 Mb, contig N50 of 18.38 Mb, and scaffold N50 of 56.08 Mb. The genome of L. acutangula SG261 was predicted to contain 27,312 protein-coding genes and 72.56% repetitive sequences, of which long terminal repeats (LTRs) were an important form of repetitive sequences, accounting for 67.84% of the genome. Phylogenetic analysis reveals that L. acutangula evolved later than Luffa cylindrica, and Luffa is closely related to Momodica charantia. Comparing the genome of L. acutangula SG261 and L. cylindrica with PacBio data, 67,128 high-quality structural variations (SVs) and 55,978 presence-absence variations (PAVs) were identified in SG261, resulting in 2424 and 1094 genes with variation in the CDS region, respectively, and there are 287 identical genes affected by two different structural variation analyses. In addition, we found that the transcription factor FY (FLOWERING LOCUS Y) families had a large expansion in L. acutangula SG261 (flowering in the morning) compared to L. cylindrica (flowering in the afternoon), which may result in the early flowering time in L. acutangula SG261. This study provides valuable reference for the breeding of and pan-genome research into Luffa species.
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Affiliation(s)
- Aizheng Huang
- Institute of Agricultural Science Research of Jiangmen, Jiangmen 529060, China;
| | - Shuo Feng
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.F.)
| | - Zhuole Ye
- Dongguan Agricultural Scientific Research Center, Dongguan 523086, China
| | - Ting Zhang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.F.)
| | - Shenglong Chen
- Dongguan Agricultural Scientific Research Center, Dongguan 523086, China
| | - Changming Chen
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.F.)
| | - Shijun Chen
- Institute of Agricultural Science Research of Jiangmen, Jiangmen 529060, China;
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9
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Shigita G, Shimomura K, Dung TP, Haque NP, Duong TT, Imoh ON, Monden Y, Nishida H, Tanaka K, Sugiyama M, Kawazu Y, Tomooka N, Kato K. Genetic characterization of cucumber genetic resources in the NARO Genebank indicates their multiple dispersal trajectories to the East. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:174. [PMID: 38954043 PMCID: PMC11219412 DOI: 10.1007/s00122-024-04683-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/22/2024] [Indexed: 07/04/2024]
Abstract
KEY MESSAGE Genotyping-by-sequencing of 723 worldwide cucumber genetic resources revealed that cucumbers were dispersed eastward via at least three distinct routes, one to Southeast Asia and two from different directions to East Asia. The cucumber (Cucumis sativus) is an economically important vegetable crop cultivated and consumed worldwide. Despite its popularity, the manner in which cucumbers were dispersed from their origin in South Asia to the rest of the world, particularly to the east, remains a mystery due to the lack of written records. In this study, we performed genotyping-by-sequencing (GBS) on 723 worldwide cucumber accessions, mainly deposited in the Japanese National Agriculture and Food Research Organization (NARO) Genebank, to characterize their genetic diversity, relationships, and population structure. Analyses based on over 60,000 genome-wide single-nucleotide polymorphisms identified by GBS revealed clear genetic differentiation between Southeast and East Asian populations, suggesting that they reached their respective region independently, not progressively. A deeper investigation of the East Asian population identified two subpopulations with different fruit characteristics, supporting the traditional classification of East Asian cucumbers into two types thought to have been introduced by independent routes. Finally, we developed a core collection of 100 accessions representing at least 93.2% of the genetic diversity present in the entire collection. The genetic relationships and population structure, their associations with geographic distribution and phenotypic traits, and the core collection presented in this study are valuable resources for elucidating the dispersal history and promoting the efficient use and management of genetic resources for research and breeding in cucumber.
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Affiliation(s)
- Gentaro Shigita
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
- Department of Life Science Systems, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Strasse 2, 85354, Freising, Germany
| | - Koichiro Shimomura
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Tran Phuong Dung
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Naznin Pervin Haque
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Thuy Thanh Duong
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
- Faculty of Agronomy, University of Agriculture and Forestry, Hue University, 102 Phung Hung Street, Hue, Vietnam
| | - Odirich Nnennaya Imoh
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Yuki Monden
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Hidetaka Nishida
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Katsunori Tanaka
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| | - Mitsuhiro Sugiyama
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Yoichi Kawazu
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Norihiko Tomooka
- Genetic Resources Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Kenji Kato
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan.
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10
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Ye W, Di Caprio L, Bruno P, Jaccard C, Bustos-Segura C, Arce CCM, Benrey B. Cultivar-Specific Defense Responses in Wild and Cultivated Squash Induced by Belowground and Aboveground Herbivory. J Chem Ecol 2024:10.1007/s10886-024-01523-9. [PMID: 38914799 DOI: 10.1007/s10886-024-01523-9] [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: 03/24/2024] [Revised: 06/08/2024] [Accepted: 06/14/2024] [Indexed: 06/26/2024]
Abstract
Plant domestication often alters plant traits, including chemical and physical defenses against herbivores. In squash, domestication leads to reduced levels of cucurbitacins and leaf trichomes, influencing interactions with insects. However, the impact of domestication on inducible defenses in squash remains poorly understood. Here, we investigated the chemical and physical defensive traits of wild and domesticated squash (Cucurbita argyrosperma), and compared their responses to belowground and aboveground infestation by the root-feeding larvae and the leaf-chewing adults of the banded cucumber beetle Diabrotica balteata (Coleoptera: Chrysomelidae). Wild populations contained cucurbitacins in roots and cotyledons but not in leaves, whereas domesticated varieties lacked cucurbitacins in all tissues. Belowground infestation by D. balteata larvae did not increase cucurbitacin levels in the roots but triggered the expression of cucurbitacin biosynthetic genes, irrespective of domestication status, although the response varied among different varieties. Conversely, whereas wild squash had more leaf trichomes than domesticated varieties, the induction of leaf trichomes in response to herbivory was greater in domesticated plants. Leaf herbivory varied among varieties but there was a trend of higher leaf damage on wild squash than domesticated varieties. Overall, squash plants responded to both belowground and aboveground herbivory by activating chemical defense-associated gene expression in roots and upregulating their physical defense in leaves, respectively. While domestication suppressed both chemical and physical defenses, our findings suggest that it may enhance inducible defense mechanisms by increasing trichome induction in response to herbivory.
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Affiliation(s)
- Wenfeng Ye
- Laboratory of Fundamental and Applied Research in Chemical Ecology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Leandro Di Caprio
- Laboratory of Evolutionary Entomology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Pamela Bruno
- Laboratory of Fundamental and Applied Research in Chemical Ecology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Plant Production Systems, Route Des Eterpys 18, 1964, Agroscope, Conthey, Switzerland
| | - Charlyne Jaccard
- Laboratory of Evolutionary Entomology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Carlos Bustos-Segura
- Laboratory of Evolutionary Entomology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Sensory Ecology, Institute of Ecology and Environmental Sciences of Paris, INRAE, Versailles, France
| | - Carla C M Arce
- Laboratory of Fundamental and Applied Research in Chemical Ecology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Betty Benrey
- Laboratory of Evolutionary Entomology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
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11
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Ding W, Luo Y, Li W, Chen F, Wang C, Xu W, Wang Y, Qu S. Fine mapping and transcriptome profiling reveal CpAPRR2 to modulate immature fruit rind color formation in zucchini (Cucurbita pepo). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:167. [PMID: 38909110 DOI: 10.1007/s00122-024-04676-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/11/2024] [Indexed: 06/24/2024]
Abstract
KEY MESSAGE A large fragment deletion of CpAPRR2, encoding a two-component response regulator-like protein, which influences immature white rind color formation in zucchini (Cucurbita pepo). Fruit rind color is an important agronomic trait that affects commodity quality and consumer choice in zucchini (Cucurbita pepo). However, the molecular mechanism controlling rind color is unclear. We characterized two zucchini inbred lines: '19' (dark green rind) and '113' (white rind). Genetic analysis revealed white immature fruit rind color to be controlled by a dominant locus (CpW). Combining bulked segregant analysis sequencing (BSA-seq) and Kompetitive Allele-Specific PCR (KASP) markers, we mapped the CpW locus to a 100.4 kb region on chromosome 5 and then narrow down the candidate region to 37.5 kb using linkage analysis of 532 BC1 and 1613 F2 individuals, including 6 coding genes. Among them, Cp4.1LG05g02070 (CpAPRR2), encoding a two-component response regulator-like protein, was regarded to be a promising candidate gene. The expression level of CpAPRR2 in dark green rind was significantly higher than that in white rind and was induced by light. A deletion of 2227 bp at the 5' end of CpAPRR2 in '113' might explain the white phenotype. Further analysis of allelic diversity in zucchini germplasm resources revealed rind color to be associated with the deletion of CpAPRR2. Subcellular localization analysis indicated that CpAPRR2 was a nuclear protein. Transcriptome analysis using near-isogenic lines with dark green (DG) and white (W) rind indicated that genes involved in photosynthesis and porphyrin metabolism pathways were enriched in DG compared with W. Additionally, chlorophyll synthesis-related genes were upregulated in DG. These results identify mechanisms of zucchini rind color and provide genetic resources for breeding.
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Affiliation(s)
- Wenqi Ding
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Yusong Luo
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Wenling Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Fangyuan Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Chaojie Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Wenlong Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, 150030, China.
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
| | - Yunli Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, 150030, China.
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
| | - Shuping Qu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, 150030, China.
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
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12
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Li X, Wang X, Zhang D, Huang J, Shi W, Wang J. Historical spread routes of wild walnuts in Central Asia shaped by man-made and nature. FRONTIERS IN PLANT SCIENCE 2024; 15:1394409. [PMID: 38903444 PMCID: PMC11187337 DOI: 10.3389/fpls.2024.1394409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/17/2024] [Indexed: 06/22/2024]
Abstract
Walnuts have substantial economic value and are of significant interest being a wild-cultivated species. The study has re-sequenced the entire genome of the wild walnut, aligning it with the walnut reference genome, to identify 2,021,717 single nucleotide polymorphisms (SNPs). These were used to examine the genetics of 130 wild walnut samples collected from three countries. Utilizing structural and principal component analysis, the walnut samples from Central Asia were classified into four populations: Ili ah in Xinjiang (I), Dushanbe region in Tajikistan (II), Sary-Chelek, Arslanbob in Kara-Alma regions of Kyrgyzstan (III), and Kok-Tundy region of Kyrgyzstan (IV). The 4 groups showed large differences in nucleotide diversity, population differentiation, and linkage disequilibrium decay, as well as gene flow among them. The present geographic distribution of these populations does not align with the genetic distribution pattern as the populations of Central Asian wild walnuts have experienced similar population dynamics in the past, i.e., the highest effective population size at ca. 6 Ma, two sharp population declines at 6 and 0.2 Ma, and convergence at ca. 0.2 Ma. The genetic distribution patterns are better explained by human activity, notably through archaeological findings of walnut use and the influence of the Silk Road, rather than by current geographic distributions.
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Affiliation(s)
- Xuerong Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi, China
| | - Xiyong Wang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Turpan Eremophytes Botanic Garden, Chinese Academy of Sciences, Turpan, China
| | - Daoyuan Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi, China
- Turpan Eremophytes Botanic Garden, Chinese Academy of Sciences, Turpan, China
| | - Junhua Huang
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi, China
| | - Wei Shi
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi, China
| | - Jiancheng Wang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Turpan Eremophytes Botanic Garden, Chinese Academy of Sciences, Turpan, China
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13
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Katuuramu DN, Levi A, Wechter WP. Mapping the genetic architecture of low-temperature stress tolerance in citron watermelon. THE PLANT GENOME 2024; 17:e20443. [PMID: 38462711 DOI: 10.1002/tpg2.20443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 12/02/2023] [Accepted: 02/07/2024] [Indexed: 03/12/2024]
Abstract
Sweet-fleshed watermelon (Citrullus lanatus) is an important vegetable crop of the tropical origin. It is widely grown and consumed around the world for its hydration and nutritional quality values. Low-temperature stress can affect early planting, seedling establishment, and expansion of crop production to new areas. A collection of 122 citron watermelon (Citrullus amarus) accessions were obtained from the USDA's National Plant Germplasm Repository System gene bank in Griffin, GA. The accessions were genotyped using whole genome resequencing to generate single nucleotide polymorphisms (SNPs) molecular markers and screened under cold-stressed and non-stressed control conditions. Four low-temperature stress tolerance related traits including shoot biomass, vine length, maximum quantum efficiency of photosystem II, and chlorophyll content were measured under cold-stressed and non-stressed control treatment conditions. Correlation analysis revealed the presence of positive relationships among traits. Broad-sense heritability for all traits ranged from 0.35 to 0.73, implying the presence of genetic contributions to the observed phenotypic variation. Genomic regions underlying these traits across several citron watermelon chromosomes were identified. Four low-temperature stress tolerance related putative candidate genes co-located with the peak SNPs from genome-wide association study. These genomic regions and marker information could potentially be used in molecular breeding to accelerate genetic improvements for low-temperature stress tolerance in watermelon.
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Affiliation(s)
| | - Amnon Levi
- USDS-ARS, U.S. Vegetable Laboratory, Charleston, South Carolina, USA
| | - William P Wechter
- USDS-ARS, U.S. Vegetable Laboratory, Charleston, South Carolina, USA
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14
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Segura M, García A, Gamarra G, Benítez Á, Iglesias-Moya J, Martínez C, Jamilena M. The transcription factor CpMYB62 controls the genetic network that leads to the determination of female flowers in Cucurbita pepo. HORTICULTURE RESEARCH 2024; 11:uhae115. [PMID: 38919554 PMCID: PMC11197297 DOI: 10.1093/hr/uhae115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/09/2024] [Indexed: 06/27/2024]
Abstract
In monoecious species, female flowering constitutes the developmental process that determines the onset and production of fruit and is therefore closely related to crop yield. This article presents the identification and phenotypic and molecular characterization of myb62, an ethylmethane sulfonate loss-of-function mutation that completely blocks the female floral transition, converting all female flowers into male flowers. BSA-seq analysis coupled with WGS showed that myb62 corresponds to a C>T transition in the coding region of the gene CpMYB62, generating a premature stop codon and a truncated transcription factor without its N-terminal effector domain. The myb62 phenotype was partially rescued by exogenous ethylene application, indicating that the function of CpMYB62 is mediated by ethylene. Different evidence supports this conclusion: first, the reduced ethylene production of the mutant, and second, the male flower productive phenotype of the double mutant between myb62 and the ethylene-insensitive mutant etr2b, which demonstrated that myb62 is epistatic over etr2b. Furthermore, transcriptomic analysis of WT and myb62 apical shoots confirmed that CpMYB62 regulates master sex-determining genes, upregulating those encoding the ethylene biosynthesis enzymes CpACO2B and CpACS27A and those encoding for transcription factors that promote the development of carpels(CpCRC), but downregulating those involved in the arrest of carpels (CpWIP1), In the gene network controlling sex determination in cucurbits, CpMYB62 occupies the most upstream position, activating ethylene and other sex determining genes involved in female flower determination in Cucurbita pepo.
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Affiliation(s)
- María Segura
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Alicia García
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - German Gamarra
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Álvaro Benítez
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Jessica Iglesias-Moya
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Cecilia Martínez
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Manuel Jamilena
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
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15
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Domic AI, VanDerwarker AM, Thakar HB, Hirth K, Capriles JM, Harper TK, Scheffler TE, Kistler L, Kennett DJ. Archaeobotanical evidence supports indigenous cucurbit long-term use in the Mesoamerican Neotropics. Sci Rep 2024; 14:10885. [PMID: 38740801 DOI: 10.1038/s41598-024-60723-1] [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: 11/29/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
The squash family (Cucurbitaceae) contains some of the most important crops cultivated worldwide and has played an important ecological, economic, and cultural role for millennia. In the American tropics, squashes were among the first cultivated crop species, but little is known about how their domestication unfolded. Here, we employ direct radiocarbon dating and morphological analyses of desiccated cucurbit seeds, rinds, and stems from El Gigante Rockshelter in Honduras to reconstruct human practices of selection and cultivation of Lagenaria siceraria, Cucurbita pepo, and Cucurbita moschata. Direct radiocarbon dating indicates that humans started using Lagenaria and wild Cucurbita starting ~ 10,950 calendar years before present (cal B.P.), primarily as watertight vessels and possibly as cooking and drinking containers. A rind directly dated to 11,150-10,765 cal B.P. represents the oldest known bottle gourd in the Americas. Domesticated C. moschata subsequently appeared ~ 4035 cal B.P., followed by domesticated C. pepo ~ 2190 cal B.P. associated with increasing evidence for their use as food crops. Multivariate statistical analysis of seed size and shape show that the archaeological C. pepo assemblage exhibits significant variability, representing at least three varieties: one similar to present-day zucchini, another like present-day vegetable marrow, and a native cultivar without modern analogs. Our archaeobotanical data supports the hypothesis that Indigenous cucurbit use started in the Early Holocene, and that agricultural complexity during the Late Holocene involved selective breeding that encouraged crop diversification.
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Affiliation(s)
- Alejandra I Domic
- Department of Anthropology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Department of Geosciences, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Amber M VanDerwarker
- Department of Anthropology, University of California, Santa Barbara, CA, 93106, USA
| | - Heather B Thakar
- Department of Anthropology, Texas A&M University, College Station, TX, 77843, USA
| | - Kenneth Hirth
- Department of Anthropology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - José M Capriles
- Department of Anthropology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Thomas K Harper
- Department of Anthropology, The Pennsylvania State University, University Park, PA, 16802, USA
| | | | - Logan Kistler
- Department of Anthropology, Smithsonian National Museum of Natural History, Washington, DC, USA
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA, 93106, USA
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16
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Xia W, Chen C, Jin S, Chang H, Ding X, Fan Q, Zhang Z, Hua B, Miao M, Liu J. Multi-Omics Analysis Reveals the Distinct Features of Metabolism Pathways Supporting the Fruit Size and Color Variation of Giant Pumpkin. Int J Mol Sci 2024; 25:3864. [PMID: 38612673 PMCID: PMC11012166 DOI: 10.3390/ijms25073864] [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: 02/29/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Pumpkin (Cucurbita maxima) is an important vegetable crop of the Cucurbitaceae plant family. The fruits of pumpkin are often used as directly edible food or raw material for a number of processed foods. In nature, mature pumpkin fruits differ in size, shape, and color. The Atlantic Giant (AG) cultivar has the world's largest fruits and is described as the giant pumpkin. AG is well-known for its large and bright-colored fruits with high ornamental and economic value. At present, there are insufficient studies that have focused on the formation factors of the AG cultivar. To address these knowledge gaps, we performed comparative transcriptome, proteome, and metabolome analysis of fruits from the AG cultivar and a pumpkin with relatively small fruit (Hubbard). The results indicate that up-regulation of gene-encoded expansins contributed to fruit cell expansion, and the increased presence of photoassimilates (stachyose and D-glucose) and jasmonic acid (JA) accumulation worked together in terms of the formation of large fruit in the AG cultivar. Notably, perhaps due to the rapid transport of photoassimilates, abundant stachyose that was not converted into glucose in time was detected in giant pumpkin fruits, implying that a unique mode of assimilate unloading is in existence in the AG cultivar. The potential molecular regulatory network of photoassimilate metabolism closely related to pumpkin fruit expansion was also investigated, finding that three MYB transcription factors, namely CmaCh02G015900, CmaCh01G018100, and CmaCh06G011110, may be involved in metabolic regulation. In addition, neoxanthin (a type of carotenoid) exhibited decreased accumulation that was attributed to the down-regulation of carotenoid biosynthesis genes in AG fruits, which may lead to pigmentation differences between the two pumpkin cultivars. Our current work will provide new insights into the potential formation factors of giant pumpkins for further systematic elucidation.
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Affiliation(s)
- Wenhao Xia
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
| | - Chen Chen
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
| | - Siying Jin
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
| | - Huimin Chang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
| | - Xianjun Ding
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
| | - Qinyi Fan
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
| | - Zhiping Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
| | - Bing Hua
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
| | - Minmin Miao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Jiexia Liu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China (S.J.); (H.C.); (Q.F.); (B.H.); (M.M.)
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17
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He K, Hui C, Yao W, Wang J, Wang L, Li Q, Shi P. Evidence That Field Muskmelon ( Cucumis melo L. var. agrestis Naud.) Fruits Are Solids of Revolution. PLANTS (BASEL, SWITZERLAND) 2023; 12:4186. [PMID: 38140513 PMCID: PMC10747953 DOI: 10.3390/plants12244186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/02/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Abstract
In nature, the fruit shapes of many plants resemble avian eggs, a form extensively studied as solids of revolution. Despite this, the hypothesis that egg-shaped fruits are themselves solids of revolution remains unvalidated. To address this, 751 Cucumis melo L. var. agrestis Naud. fruits were photographed, and the two-dimensional (2D) boundary coordinates of each fruit profile were digitized. Then, the explicit Preston equation (EPE), a universal egg-shape model, was used to fit the 2D boundary coordinates to obtain the estimates of the EPE's parameters of each fruit. Under the hypothesis that egg-shaped fruits are solids of revolution, the fruit volumes were estimated using the solid of revolution formula based on the estimated EPE's parameters. To test whether the fruits are solids of revolution, the fruit volumes were measured by using a graduated cylinder and compared with the estimated volumes using the solid of revolution formula. The EPE was demonstrated to be valid in describing the 2D profiles of C. melo var. agrestis fruits. There was a significant correlation between the measured fruit volumes using the graduated cylinder and the estimated fruit volumes using the solid of revolution formula based on the estimated EPE's parameters. Acknowledging potential measurement errors, particularly fruit fuzz causing air bubbles during volume measurements, we recognize slight deviations between measured volumes and estimated values. Despite this, our findings strongly suggest that C. melo var. agrestis fruits are solids of revolution. This study contributes insights into the evolutionary aspects of fruit geometries in plants with egg-shaped fruits and introduces a practical tool for non-destructively calculating fruit volume and surface area based on photographed 2D fruit profiles.
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Affiliation(s)
- Ke He
- Architectural Design and Research Institute, Shenzhen University, #3688 Nanhai Avenue, Shenzhen 518000, China;
- Bamboo Research Institute, College of Ecology and Environment, Nanjing Forestry University, #159 Longpan Road, Nanjing 210037, China; (W.Y.); (J.W.); (L.W.); (Q.L.)
| | - Cang Hui
- Centre for Invasion Biology, Department of Mathematical Sciences, Stellenbosch University, Stellenbosch 7602, South Africa;
- Mathematical and Physical Biosciences, African Institute for Mathematical Sciences, Cape Town 7945, South Africa
| | - Weihao Yao
- Bamboo Research Institute, College of Ecology and Environment, Nanjing Forestry University, #159 Longpan Road, Nanjing 210037, China; (W.Y.); (J.W.); (L.W.); (Q.L.)
| | - Jinfeng Wang
- Bamboo Research Institute, College of Ecology and Environment, Nanjing Forestry University, #159 Longpan Road, Nanjing 210037, China; (W.Y.); (J.W.); (L.W.); (Q.L.)
| | - Lin Wang
- Bamboo Research Institute, College of Ecology and Environment, Nanjing Forestry University, #159 Longpan Road, Nanjing 210037, China; (W.Y.); (J.W.); (L.W.); (Q.L.)
| | - Qiying Li
- Bamboo Research Institute, College of Ecology and Environment, Nanjing Forestry University, #159 Longpan Road, Nanjing 210037, China; (W.Y.); (J.W.); (L.W.); (Q.L.)
| | - Peijian Shi
- Bamboo Research Institute, College of Ecology and Environment, Nanjing Forestry University, #159 Longpan Road, Nanjing 210037, China; (W.Y.); (J.W.); (L.W.); (Q.L.)
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18
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Lee CY, Wang JF, Chang CH, Tung CW. Analyzing genomic variation in cultivated pumpkins and identification of candidate genes controlling seed traits. THE PLANT GENOME 2023; 16:e20393. [PMID: 37776006 DOI: 10.1002/tpg2.20393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/02/2023] [Accepted: 09/08/2023] [Indexed: 10/01/2023]
Abstract
Pumpkins are important vegetable crops widely grown worldwide, and seeds are considered a popular nutraceutical food and an excellent source of protein, oil, and vitamins. Seed size is one of the most important targets for commercial breeding in Cucurbita species; studies have shown that pumpkin seed size variation has a similar trend with fruit size, shape, and seed yield. However, few studies have been conducted to identify genetic loci controlling seed-related traits in cultivated pumpkins. This study analyzed the genomic characteristics of pumpkin breeding materials of 321 Cucurbita accessions collected worldwide, including Cucurbita moschata, Cucurbita maxima, and Cucurbita pepo, using extensive single nucleotide polymorphisms obtained from the genotyping-by-sequencing method, significant genetic variations were identified within and between Cucurbita species. Four major cultivar fruit types were further revealed in C. moschata species, and significant differentiation patterns were detected in several chromosomal regions. A total of 15 significant loci associated with pumpkin seed traits were mapped through a genome-wide association approach; 32 genes previously reported to be associated with seed size regulation in Arabidopsis and Oryza sativa were located in the intervals defined by linkage disequilibrium. Through this study, we gained a deep understanding of the genomic variation distribution across Cucurbita species. The available genetic resources and the associated genetic contents could be used in commercial pumpkin breeding and will facilitate molecular marker-assisted selection in pumpkin seed trait improvement.
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Affiliation(s)
- Chieh-Ying Lee
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
- Breeding Technology Group, Known-you Seed Co., Ltd, Kaohsiung, Taiwan
| | - Jaw-Fen Wang
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Chia-Hui Chang
- Breeding Technology Group, Known-you Seed Co., Ltd, Kaohsiung, Taiwan
| | - Chih-Wei Tung
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
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19
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Tian S, Yang J, Fu Y, Zhang X, Zhang J, Zhao H, Hu Q, Liu P, He W, Han X, Wen C. McAPRR2: The Key Regulator of Domesticated Pericarp Color in Bitter Gourd. PLANTS (BASEL, SWITZERLAND) 2023; 12:3585. [PMID: 37896048 PMCID: PMC10610206 DOI: 10.3390/plants12203585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023]
Abstract
Pericarp color is a crucial commercial trait influencing consumer preferences for bitter gourds. However, until now, the gene responsible for this trait has remained unidentified. In this study, we identified a gene (McAPRR2) controlling pericarp color via a genome-wide association study (GWAS) utilizing the resequencing data of 106 bitter gourd accessions. McAPRR2 exhibits three primary haplotypes: Hap1 is a wild type with a green pericarp, Hap2 is a SA (South Asian) and SEA (Southeast Asia) type with a green pericarp, and Hap3 is primarily a SEA type with a light green pericarp. The McAPRR2 haplotype is significantly correlated with both pericarp color and ecological type. Importantly, McAPRR2 with the light green pericarp demonstrated premature termination due to a 15 bp sequence insertion. The phylogenetic tree clustered according to pericarp color and ecological type, using SNPs located in the McAPRR2 gene and its promoter. High πwild/SEA and πSA/SEA values indicate high nucleotide diversity between wild and SEA types and between SA and SEA types in the McAPRR2 gene. The haplotypes, phylogenetic tree, and nucleotide diversity of McAPRR2 suggest that McAPRR2 has undergone domestication selection. This study identifies McAPRR2 as the key gene determining pericarp color in bitter gourds and introduces a novel insight that McAPRR2 is subject to domestication selection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Changlong Wen
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China (J.Y.); (J.Z.); (H.Z.)
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20
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Tian S, Zhang Z, Qin G, Xu Y. Parthenocarpy in Cucurbitaceae: Advances for Economic and Environmental Sustainability. PLANTS (BASEL, SWITZERLAND) 2023; 12:3462. [PMID: 37836203 PMCID: PMC10574560 DOI: 10.3390/plants12193462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
Parthenocarpy is an important agricultural trait that not only produces seedless fruits, but also increases the rate of the fruit set under adverse environmental conditions. The study of parthenocarpy in Cucurbitaceae crops has considerable implications for cultivar improvement. This article provides a comprehensive review of relevant studies on the parthenocarpic traits of several major Cucurbitaceae crops and offers a perspective on future developments and research directions.
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Affiliation(s)
- Shouwei Tian
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Zeliang Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Genji Qin
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yong Xu
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
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21
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Flores-Iga G, Lopez-Ortiz C, Gracia-Rodriguez C, Almeida A, Nimmakayala P, Reddy UK, Balagurusamy N. A Genome-Wide Identification and Comparative Analysis of the Heavy-Metal-Associated Gene Family in Cucurbitaceae Species and Their Role in Cucurbita pepo under Arsenic Stress. Genes (Basel) 2023; 14:1877. [PMID: 37895226 PMCID: PMC10606463 DOI: 10.3390/genes14101877] [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: 09/05/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
The heavy-metal-associated (HMA) proteins are a class of PB1-type ATPases related to the intracellular transport and detoxification of metals. However, due to a lack of information regarding the HMA gene family in the Cucurbitaceae family, a comprehensive genome-wide analysis of the HMA family was performed in ten Cucurbitaceae species: Citrullus amarus, Citrullus colocynthis, Citrullus lanatus, Citrullus mucosospermus, Cucumis melo, Cucumis sativus, Cucurbita maxima, Cucurbita moschata, Cucurbita pepo, and Legenaria siceraria. We identified 103 Cucurbit HMA proteins with various members, ranging from 8 (Legenaria siceraria) to 14 (Cucurbita pepo) across species. The phylogenetic and structural analysis confirmed that the Cucurbitaceae HMA protein family could be further classified into two major clades: Zn/Co/Cd/Pb and Cu/Ag. The GO-annotation-based subcellular localization analysis predicted that all HMA gene family members were localized on membranes. Moreover, the analysis of conserved motifs and gene structure (intron/exon) revealed the functional divergence between clades. The interspecies microsynteny analysis demonstrated that maximum orthologous genes were found between species of the Citrullus genera. Finally, nine candidate HMA genes were selected, and their expression analysis was carried out via qRT-PCR in root, leaf, flower, and fruit tissues of C. pepo under arsenic stress. The expression pattern of the CpeHMA genes showed a distinct pattern of expression in root and shoot tissues, with a remarkable expression of CpeHMA6 and CpeHMA3 genes from the Cu/Ag clade. Overall, this study provides insights into the functional analysis of the HMA gene family in Cucurbitaceae species and lays down the basic knowledge to explore the role and mechanism of the HMA gene family to cope with arsenic stress conditions.
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Affiliation(s)
- Gerardo Flores-Iga
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón 27275, Coahuila, México; (G.F.-I.); (C.G.-R.)
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Carlos Lopez-Ortiz
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Celeste Gracia-Rodriguez
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón 27275, Coahuila, México; (G.F.-I.); (C.G.-R.)
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Aldo Almeida
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark;
| | - Padma Nimmakayala
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Umesh K. Reddy
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Nagamani Balagurusamy
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón 27275, Coahuila, México; (G.F.-I.); (C.G.-R.)
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22
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Nayaka SN, Singh OW, Kumar P, Roy A, Mandal B. Geographical distribution of tomato-infecting begomoviruses in major cucurbits in India: a diagnostic analysis using begomovirus species specific PCR. Virusdisease 2023; 34:421-430. [PMID: 37780909 PMCID: PMC10533461 DOI: 10.1007/s13337-023-00837-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/21/2023] [Indexed: 10/03/2023] Open
Abstract
Cucurbits are an essential summer-season vegetable crops, but they are highly vulnerable from a range of abiotic and biotic factors. One of the significant biotic factors posing a growing menace to the production of major cucurbits in India is the emergence of tomato-infecting begomoviruses. In this study, we utilized PCR-based species-specific primers, developed earlier in our laboratory for the detection of begomoviruses infecting tomato and chilli plants, to identify begomoviruses in cucurbits across various regions of India. Leaf samples from major cucurbits were collected from different regions of Haryana, Delhi, Uttar Pradesh, Chhattisgarh, Maharashtra, Telangana and Karnataka, during the year 2020-2021. Total nucleic acid (TNA) was extracted from the samples and subjected to PCR using a generic primer specific to begomoviruses. The samples that exhibited positive amplification were further tested using six different species-specific primers targeting specific begomovirus species, namely Tomato leaf curl New Delhi virus (ToLCNDV), Tomato leaf curl Palampur virus (ToLCPalV), Tomato leaf curl Bangalore virus (ToLCBV), Tomato leaf curl Joydebpur virus (ToLCJoV), Tomato leaf curl Gujarat virus (ToLCGuV), and Chilli leaf curl virus (ChiLCV). The PCR analysis revealed that among the 551 plant samples tested, a total of 124 samples exhibited positive amplification using the universal begomovirus PCR. Specifically, 47 samples tested positive for ToLCNDV, 73 samples were positive for ToLCPalV and only one sample showed positive amplification for ChiLCV. However, none of the samples tested positive for ToLCJoV, ToLCGuV and ToLCBV. These findings from our study indicate the prevalence of ToLCNDV and ToLCPalV in major cucurbits across India. Furthermore, the study highlights the varied distribution of begomoviruses in major cucurbits between northern and southern regions of India.
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Affiliation(s)
- S. Naveen Nayaka
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Oinam Washington Singh
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pradeep Kumar
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anirban Roy
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Bikash Mandal
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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23
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Gonçalves-Dias J, Singh A, Graf C, Stetter MG. Genetic Incompatibilities and Evolutionary Rescue by Wild Relatives Shaped Grain Amaranth Domestication. Mol Biol Evol 2023; 40:msad177. [PMID: 37552934 PMCID: PMC10439364 DOI: 10.1093/molbev/msad177] [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: 04/25/2023] [Revised: 07/20/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023] Open
Abstract
Crop domestication and the subsequent expansion of crops have long been thought of as a linear process from a wild ancestor to a domesticate. However, evidence of gene flow from locally adapted wild relatives that provided adaptive alleles into crops has been identified in multiple species. Yet, little is known about the evolutionary consequences of gene flow during domestication and the interaction of gene flow and genetic load in crop populations. We study the pseudo-cereal grain amaranth that has been domesticated three times in different geographic regions of the Americas. We quantify the amount and distribution of gene flow and genetic load along the genome of the three grain amaranth species and their two wild relatives. Our results show ample gene flow between crop species and between crops and their wild relatives. Gene flow from wild relatives decreased genetic load in the three crop species. This suggests that wild relatives could provide evolutionary rescue by replacing deleterious alleles in crops. We assess experimental hybrids between the three crop species and found genetic incompatibilities between one Central American grain amaranth and the other two crop species. These incompatibilities might have created recent reproductive barriers and maintained species integrity today. Together, our results show that gene flow played an important role in the domestication and expansion of grain amaranth, despite genetic species barriers. The domestication of plants was likely not linear and created a genomic mosaic by multiple contributors with varying fitness effects for today's crops.
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Affiliation(s)
| | - Akanksha Singh
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Corbinian Graf
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Markus G Stetter
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
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24
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Shirazi Parsa H, Sabet MS, Moieni A, Shojaeiyan A, Dogimont C, Boualem A, Bendahmane A. CRISPR/Cas9-Mediated Cytosine Base Editing Using an Improved Transformation Procedure in Melon ( Cucumis melo L.). Int J Mol Sci 2023; 24:11189. [PMID: 37446368 DOI: 10.3390/ijms241311189] [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: 04/24/2023] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Melon is a recalcitrant plant for stable genetic transformation. Various protocols have been tried to improve melon transformation efficiency; however, it remains significantly low compared to other plants such as tomato. In this study, the primary focus was on the optimization of key parameters during the inoculation and co-culture steps of the genetic transformation protocol. Our results showed that immersing the explants in the inoculation medium for 20 min significantly enhanced transformation efficiency. During the co-culture step, the use of filer paper, 10 mM 2-(N-morpholino)-ethanesulfonic acid (MES), and a temperature of 24 °C significantly enhanced the melon transformation efficiency. Furthermore, the impact of different ethylene inhibitors and absorbers on the transformation efficiency of various melon varieties was explored. Our findings revealed that the use of these compounds led to a significant improvement in the transformation efficiency of the tested melon varieties. Subsequently, using our improved protocol and reporter-gene construct, diploid transgenic melons successfully generated. The efficiency of plant genetic transformation ranged from 3.73 to 4.83%. Expanding the scope of our investigation, the optimized protocol was applied to generate stable gene-edited melon lines using the Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated cytosine base editor and obtained melon lines with editions (C-to-T and C-to-G) in the eukaryotic translation initiation factor 4E, CmeIF4E gene. In conclusion, the optimized melon transformation protocol, along with the utilization of the CRISPR/Cas9-mediated cytosine base editor, provides a reliable framework for functional gene engineering in melon. These advancements hold significant promise for furthering genetic research and facilitating crop improvement in this economically important plant species.
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Affiliation(s)
- Hadi Shirazi Parsa
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Department of Plant Genetics and Breeding, Faculty of Agriculture, Tarbiat Modares University, Tehran 14115-336, Iran
| | - Mohammad Sadegh Sabet
- Department of Plant Genetics and Breeding, Faculty of Agriculture, Tarbiat Modares University, Tehran 14115-336, Iran
| | - Ahmad Moieni
- Department of Plant Genetics and Breeding, Faculty of Agriculture, Tarbiat Modares University, Tehran 14115-336, Iran
| | - Abdolali Shojaeiyan
- Department of Horticulture, Faculty of Agriculture, Tarbiat Modares University, Tehran 14115-336, Iran
| | - Catherine Dogimont
- INRAE, Génétique et Amélioration des Fruits et Légumes (GAFL), 84143 Montfavet, France
| | - Adnane Boualem
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Abdelhafid Bendahmane
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
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25
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Jaccard C, Ye W, Bustos-Segura C, Glauser G, Kaplan I, Benrey B. Consequences of squash (Cucurbita argyrosperma) domestication for plant defence and herbivore interactions. PLANTA 2023; 257:106. [PMID: 37127808 PMCID: PMC10151309 DOI: 10.1007/s00425-023-04139-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/19/2023] [Indexed: 05/03/2023]
Abstract
MAIN CONCLUSION Cucurbita argyrosperma domestication affected plant defence by downregulating the cucurbitacin synthesis-associated genes. However, tissue-specific suppression of defences made the cultivars less attractive to co-evolved herbivores Diabrotica balteata and Acalymma spp. Plant domestication reduces the levels of defensive compounds, increasing susceptibility to insects. In squash, the reduction of cucurbitacins has independently occurred several times during domestication. The mechanisms underlying these changes and their consequences for insect herbivores remain unknown. We investigated how Cucurbita argyrosperma domestication has affected plant chemical defence and the interactions with two herbivores, the generalist Diabrotica balteata and the specialist Acalymma spp. Cucurbitacin levels and associated genes in roots and cotyledons in three wild and four domesticated varieties were analysed. Domesticated varieties contained virtually no cucurbitacins in roots and very low amounts in cotyledons. Contrastingly, cucurbitacin synthesis-associated genes were highly expressed in the roots of wild populations. Larvae of both insects strongly preferred to feed on the roots of wild squash, negatively affecting the generalist's performance but not that of the specialist. Our findings illustrate that domestication results in tissue-specific suppression of chemical defence, making cultivars less attractive to co-evolved herbivores. In the case of squash, this may be driven by the unique role of cucurbitacins in stimulating feeding in chrysomelid beetles.
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Affiliation(s)
- Charlyne Jaccard
- Laboratory of Evolutionary Entomology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Wenfeng Ye
- Laboratory for Fundamental and Applied Research in Chemical Ecology (FARCE), Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Carlos Bustos-Segura
- Laboratory of Evolutionary Entomology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Gaetan Glauser
- Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, Avenue de Bellevaux 51, 2000, Neuchâtel, Switzerland
| | - Ian Kaplan
- Department of Entomology, Purdue University, West Lafayette, IN, 47907, USA
| | - Betty Benrey
- Laboratory of Evolutionary Entomology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland.
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26
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Sánchez-Hernández E, Martín-Ramos P, Navas-Gracia LM, Martín-Gil J, Garcés-Claver A, Flores-León A, González-García V. Armeria maritima (Mill.) Willd. Flower Hydromethanolic Extract for Cucurbitaceae Fungal Diseases Control. Molecules 2023; 28:molecules28093730. [PMID: 37175142 PMCID: PMC10180270 DOI: 10.3390/molecules28093730] [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: 03/22/2023] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
The cliff rose (Armeria maritima), like other halophytes, has a phenolics-based antioxidant system that allows it to grow in saline habitats. Provided that antioxidant properties are usually accompanied by antimicrobial activity, in this study we investigated the phytochemicals present in a hydromethanolic extract of A. maritima flowers and explored its antifungal potential. The main phytocompounds, identified by gas chromatography-mass spectrometry, were: hexadecanoic acid, octadecanoic acid, 9-octadecenoic acid, 3-(3,4-dihydroxy-phenyl)-acrylic acid ethyl ester, and benzeneacetaldehyde. The antifungal activity of the extract and its main constituents-alone and in combination with chitosan oligomers-was tested against six pathogenic taxa associated with soil-borne diseases of plant hosts in the family Cucurbitaceae: Fusarium equiseti, F. oxysporum f. sp. niveum, Macrophomina phaseolina, Neocosmospora falciformis, N. keratoplastica, and Sclerotinia sclerotiorum. In in vitro tests, EC90 effective concentrations in the 166-865 μg·mL-1 range were obtained for the chitosan oligomers-A. maritima extract conjugate complexes, lower than those obtained for fosetyl-Al and azoxystrobin synthetic fungicides tested for comparison purposes, and even outperforming mancozeb against F. equiseti. In ex situ tests against S. sclerotiorum conducted on artificially inoculated cucumber slices, full protection was achieved at a dose of 250 μg·mL-1. Thus, the reported results support the valorization of A. maritima as a source of biorationals for Cucurbitaceae pathogens protection, suitable for both organic and conventional agriculture.
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Affiliation(s)
- Eva Sánchez-Hernández
- Department of Agricultural and Forestry Engineering, ETSIIAA, Universidad de Valladolid, Avda. Madrid 44, 34004 Palencia, Spain
| | - Pablo Martín-Ramos
- Department of Agricultural and Forestry Engineering, ETSIIAA, Universidad de Valladolid, Avda. Madrid 44, 34004 Palencia, Spain
| | - Luis Manuel Navas-Gracia
- Department of Agricultural and Forestry Engineering, ETSIIAA, Universidad de Valladolid, Avda. Madrid 44, 34004 Palencia, Spain
| | - Jesús Martín-Gil
- Department of Agricultural and Forestry Engineering, ETSIIAA, Universidad de Valladolid, Avda. Madrid 44, 34004 Palencia, Spain
| | - Ana Garcés-Claver
- Department of Plant Science, Agrifood Research and Technology Centre of Aragón, Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), Avda. Montañana 930, 50059 Zaragoza, Spain
| | - Alejandro Flores-León
- Institute for the Preservation and Improvement of Valencian Agrodiversity, Universitat Politècnica de València, Camí de Vera, s/n, 46022 Valencia, Spain
| | - Vicente González-García
- Department of Agricultural, Forestry, and Environmental Systems, Agrifood Research and Technology Centre of Aragón, Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), Avda. Montañana 930, 50059 Zaragoza, Spain
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Zhou C, Wang P, Zeng Q, Zeng R, Hu W, Sun L, Liu S, Luan F, Zhu Q. Comparative chloroplast genome analysis of seven extant Citrullus species insight into genetic variation, phylogenetic relationships, and selective pressure. Sci Rep 2023; 13:6779. [PMID: 37185306 PMCID: PMC10130142 DOI: 10.1038/s41598-023-34046-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 04/23/2023] [Indexed: 05/17/2023] Open
Abstract
Citrullus ecirrhosus, Citrullus rehmii, and Citrullus naudinianus are three important related wild species of watermelon in the genus Citrullus, and their morphological differences are clear, however, their chloroplast genome differences remain unknown. This study is the first to assemble, analyze, and publish the complete chloroplast genomes of C. ecirrhosus, C. rehmii, and C. naudinianus. A comparative analysis was then conducted among the complete chloroplast genomes of seven extant Citrullus species, and the results demonstrated that the average genome sizes of Citrullus is 157,005 bp, a total of 130-133 annotated genes were identified, including 8 rRNA, 37 tRNA and 85-88 protein-encoding genes. Their gene content, order, and genome structure were similar. However, noncoding regions were more divergent than coding regions, and rps16-trnQ was a hypervariable fragment. Thirty-four polymorphic SSRs, 1,271 SNPs and 234 INDELs were identified. Phylogenetic trees revealed a clear phylogenetic relationship of Citrullus species, and the developed molecular markers (SNPs and rps16-trnQ) could be used for taxonomy in Citrullus. Three genes (atpB, clpP1, and rpoC2) were identified to undergo selection and would promote the environmental adaptation of Citrullus.
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Affiliation(s)
- Cong Zhou
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, NO. 1101 Zhimin Street, Qingshanhu District, Nanchang, 330045, People's Republic of China
| | - Putao Wang
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, NO. 1101 Zhimin Street, Qingshanhu District, Nanchang, 330045, People's Republic of China
| | - Qun Zeng
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, NO. 1101 Zhimin Street, Qingshanhu District, Nanchang, 330045, People's Republic of China
| | - Rongbin Zeng
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, NO. 1101 Zhimin Street, Qingshanhu District, Nanchang, 330045, People's Republic of China
| | - Wei Hu
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, NO. 1101 Zhimin Street, Qingshanhu District, Nanchang, 330045, People's Republic of China
| | - Lei Sun
- Department of Agronomy and Horticulture, Liaoning Agricultural Technical College, Yingkou, 115009, People's Republic of China
| | - Shi Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Qianglong Zhu
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, NO. 1101 Zhimin Street, Qingshanhu District, Nanchang, 330045, People's Republic of China.
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Hernandez CO, Labate J, Reitsma K, Fabrizio J, Bao K, Fei Z, Grumet R, Mazourek M. Characterization of the USDA Cucurbita pepo, C. moschata, and C. maxima germplasm collections. FRONTIERS IN PLANT SCIENCE 2023; 14:1130814. [PMID: 36993863 PMCID: PMC10040574 DOI: 10.3389/fpls.2023.1130814] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/22/2023] [Indexed: 06/19/2023]
Abstract
The Cucurbita genus is home to a number of economically and culturally important species. We present the analysis of genotype data generated through genotyping-by-sequencing of the USDA germplasm collections of Cucurbita pepo, C. moschata, and C. maxima. These collections include a mixture of wild, landrace, and cultivated specimens from all over the world. Roughly 1,500 - 32,000 high-quality single nucleotide polymorphisms (SNPs) were called in each of the collections, which ranged in size from 314 to 829 accessions. Genomic analyses were conducted to characterize the diversity in each of the species. Analysis revealed extensive structure corresponding to a combination of geographical origin and morphotype/market class. Genome-wide associate studies (GWAS) were conducted using both historical and contemporary data. Signals were observed for several traits, but the strongest was for the bush (Bu) gene in C. pepo. Analysis of genomic heritability, together with population structure and GWAS results, was used to demonstrate a close alignment of seed size in C. pepo, maturity in C. moschata, and plant habit in C. maxima with genetic subgroups. These data represent a large, valuable collection of sequenced Cucurbita that can be used to direct the maintenance of genetic diversity, for developing breeding resources, and to help prioritize whole-genome re-sequencing.
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Affiliation(s)
- Christopher O. Hernandez
- Department of Agriculture Nutrition and Food Systems, University of New Hampshire, Durham, NH, United States
| | - Joanne Labate
- Plant Genetic Resource Conservation Unit, United States Department of Agricultural Research Service, Geneva, NY, United States
| | - Kathleen Reitsma
- North Central Regional Plant Introduction Station, Iowa State University, Ames, IA, United States
| | - Jack Fabrizio
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | - Kan Bao
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
- U.S. Department of Agriculture-Agriculture Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | - Michael Mazourek
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
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Nie H, Kim M, Lee S, Lim S, Lee MS, Kim JH, Noh SJ, Park SW, Kim ST, Shin AY, Lee Y, Kwon SY. High-quality genome assembly and genetic mapping reveal a gene regulating flesh color in watermelon ( Citrullus lanatus). FRONTIERS IN PLANT SCIENCE 2023; 14:1142856. [PMID: 36938051 PMCID: PMC10014564 DOI: 10.3389/fpls.2023.1142856] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
The unique color and type characteristics of watermelon fruits are regulated by many molecular mechanisms. However, it still needs to be combined with more abundant genetic data to fine-tune the positioning. We assembled genomes of two Korean inbred watermelon lines (cv. 242-1 and 159-1) with unique color and fruit-type characteristics and identified 23,921 and 24,451 protein-coding genes in the two genomes, respectively. To obtain more precise results for further study, we resequenced one individual of each parental line and an F2 population composed of 87 individuals. This identified 1,539 single-nucleotide polymorphisms (SNPs) and 80 InDel markers that provided a high-density genetic linkage map with a total length of 3,036.9 cM. Quantitative trait locus mapping identified 15 QTLs for watermelon fruit quality-related traits, including β-carotene and lycopene content in fruit flesh, fruit shape index, skin thickness, flesh color, and rind color. By investigating the mapping intervals, we identified 33 candidate genes containing variants in the coding sequence. Among them, Cla97C01G008760 was annotated as a phytoene synthase with a single-nucleotide variant (A → G) in the first exon at 9,539,129 bp of chromosome 1 that resulted in the conversion of a lysine to glutamic acid, indicating that this gene might regulate flesh color changes at the protein level. These findings not only prove the importance of a phytoene synthase gene in pigmentation but also explain an important reason for the color change of watermelon flesh.
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Affiliation(s)
- Hualin Nie
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Moonkyo Kim
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
- Division of Life Science, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Sanghee Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Biosystems and Bioengineering Program, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Sohee Lim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Mi Sun Lee
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Ju Hyeok Kim
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Sol Ji Noh
- Watermelon and Strawberry Research Institute, Chungcheongbuk-do Agricultural Research and Extension Services, Cheongju, Republic of Korea
| | - Seong Won Park
- Watermelon and Strawberry Research Institute, Chungcheongbuk-do Agricultural Research and Extension Services, Cheongju, Republic of Korea
| | - Sang-Tae Kim
- Department of Medical and Biological Sciences, Catholic University of Korea, Bucheon, Republic of Korea
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioinformatics, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, University of Science and Technology, Daejeon, Republic of Korea
| | - Yi Lee
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Biosystems and Bioengineering Program, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
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30
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Kaur H, Manchanda P, Kumar P, Dhall RK, Chhuneja P, Weng Y. Genome-wide identification and characterization of parthenocarpic fruit set-related gene homologs in cucumber (Cucumis sativus L.). Sci Rep 2023; 13:2403. [PMID: 36765113 PMCID: PMC9918540 DOI: 10.1038/s41598-023-29660-3] [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: 07/21/2022] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Cucumber (Cucumis sativus L.), a major horticultural crop, in the family Cucurbitaceae is grown and consumed globally. Parthenocarpy is an ideal trait for many fruit and vegetables which produces seedless fruit desired by consumers. The seedlessness occurs when fruit develops without fertilization which can be either natural or induced. So far, a limited number of genes regulating parthenocarpic fruit set have been reported in several fruit or vegetable crops, most of which are involved in hormone biosynthesis or signalling. Although parthenocarpic cucumber has been widely used in commercial production for a long time; its genetic basis is not well understood. In this study, we retrieved thirty five parthenocarpy fruit-set related genes (PRGs) from bibliomic data in various plants. Thirty-five PRG homologs were identified in the cucumber genome via homology-based search. An in silico analysis was performed on phylogenetic tree, exon-intron structure, cis-regulatory elements in the promoter region, and conserved domains of their deduced proteins, which provided insights into the genetic make-up of parthenocarpy-related genes in cucumber. Simple sequence repeat (SSR) sequences were mined in these PRGs, and 31 SSR markers were designed. SSR genotyping identified three SSRs in two polymorphic genes. Quantitative real-time PCR of selected genes was conducted in five cucumber lines with varying degrees of parthenocarpic fruit set capacities, which revealed possible association of their expression with parthenocarpy. The results revealed that homologs CsWD40 and CsPIN-4 could be considered potential genes for determination of parthenocarpy as these genes showed parental polymorphism and differential gene expression in case of parthenocarpic and non-parthenocarpic parents.
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Affiliation(s)
- Harleen Kaur
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Pooja Manchanda
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India.
| | - Pankaj Kumar
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Rajinder Kumar Dhall
- Department of Vegetable Science, College of Horticulture and Forestry, Punjab Agricultural University, Ludhiana, 141004, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Yiqun Weng
- USDA-ARS Vegetable Crops Research Unit, Department of Horticulture, University of Wisconsin, Madison, WI, 53706, USA
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31
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Dinan L, Lafont F, Lafont R. The Distribution of Phytoecdysteroids among Terrestrial Vascular Plants: A Comparison of Two Databases and Discussion of the Implications for Plant/Insect Interactions and Plant Protection. PLANTS (BASEL, SWITZERLAND) 2023; 12:776. [PMID: 36840124 PMCID: PMC9967490 DOI: 10.3390/plants12040776] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/26/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
Phytoecdysteroids are a class of plant secondary compounds which are present in a wide diversity of vascular plant species, where they contribute to a reduction in invertebrate predation. Over the past 55 years, a significant body of heterogeneous literature on the presence, identities and/or quantities of ecdysteroids in plant species has accumulated, resulting in the compilation of a first database, the Ecdybase Literature Survey (ELS; 4908 entries, covering 2842 species). A second extensive database on the distribution of ecdysteroids in vascular plants is available as the Exeter Survey (ES; 4540 entries, covering 4155 species), which used standardised extraction and analysis methods to survey seeds/spores. We compare the usefulness of these two databases to provide information on the occurrence of phytoecdysteroids at the order/family levels in relation to the recent molecular classifications of gymnosperms, pteridophytes/lycophytes and angiosperms. The study, in conjunction with the other published literature, provides insights into the distribution of phytoecdysteroids in the plant world, their role in plant protection in nature and their potential future contribution to crop protection. Furthermore, it will assist future investigations in the chemotaxonomy of phytoecdysteroids and other classes of plant secondary compounds.
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32
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Jenny LA, Shapiro LR, Davis CC, Jonathan Davies T, Pierce NE, Meineke E. Herbarium specimens reveal herbivory patterns across the genus Cucurbita. AMERICAN JOURNAL OF BOTANY 2023; 110:e16126. [PMID: 36633920 DOI: 10.1002/ajb2.16126] [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: 07/02/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
PREMISE Quantifying how closely related plant species differ in susceptibility to insect herbivory is important for understanding the variation in evolutionary pressures on plant functional traits. However, empirically measuring in situ variation in herbivory spanning the geographic range of a plant-insect complex is logistically difficult. Recently, new methods have been developed using herbarium specimens to investigate patterns in plant-insect symbioses across large geographic scales. Such investigations provide insights into how accelerated anthropogenic changes may impact plant-insect interactions that are of ecological or agricultural importance. METHODS Here, we analyze 274 pressed herbarium samples to investigate variation in herbivory damage in 13 different species of the economically important plant genus Cucurbita (Cucurbitaceae). This collection is composed of specimens of wild, undomesticated Cucurbita that were collected from across their native range, and Cucurbita cultivars collected from both within their native range and from locations where they have been introduced for agriculture in temperate North America. RESULTS Herbivory is common on individuals of all Cucurbita species collected throughout their geographic ranges. However, estimates of herbivory varied considerably among individuals, with mesophytic species accruing more insect damage than xerophytic species, and wild specimens having more herbivory than specimens collected from human-managed habitats. CONCLUSIONS Our study suggests that long-term evolutionary changes in habitat from xeric to mesic climates and wild to human-managed habitats may mediate the levels of herbivory pressure from coevolved herbivores. Future investigations into the potential factors that contribute to herbivory may inform the management of domesticated crop plants and their insect herbivores.
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Affiliation(s)
- Laura A Jenny
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
| | - Lori R Shapiro
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, 27695, United States
| | - Charles C Davis
- Harvard University Herbaria, Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
| | - T Jonathan Davies
- Departments of Botany, and Forest & Conservation Sciences, University of British Columbia, Vancouver, British Columbia, BC V6T 1Z4, Canada
- African Centre for DNA Barcoding, University of Johannesburg, Johannesburg, Gauteng, 2028, South Africa
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
| | - Emily Meineke
- Department of Entomology and Nematology, University of California, Davis, Davis, California, 95616, United States
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Yang Y, Zhang B, Bao Y, Huang P, Li J, Li R, Zhao Q. Chromosome-Level Genome Assembly of Herpetospermum pedunculosum (Cucurbitaceae). Genome Biol Evol 2023; 15:6991395. [PMID: 36652386 PMCID: PMC9897187 DOI: 10.1093/gbe/evad005] [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: 11/27/2022] [Revised: 12/23/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
This study presents a chromosome-level reference genome assembly of a traditional Tibetan medicinal plant, Herpetospermum pedunculosum belonging to the Cucurbitaceae family. Following a combined PacBio high-fidelity sequencing and Hi-C analysis, a final H. pedunculosum genome assembly, 804.11 Mb in length was obtained, 90.45% of which was anchored into ten pseudochromosomes with a contig N50 of 24.39 Mb. In addition, 579.55 Mb repetitive sequences and 23,924 high-confidence protein-coding genes were annotated. Phylogenetic analysis revealed that H. pedunculosum was sister to a clade formed by cucumber, zucchini, and wax gourd. Further whole-genome duplication analysis revealed no recent polyploidization event in the H. pedunculosum genome. The high-quality H. pedunculosum genome presented here will be highly useful in investigating the molecular mechanisms underlying the biosynthesis of its active compounds and adaptation strategies to the extreme environment. It will also provide great insights into comparative genomic studies of Cucurbitaceae and flowering plants.
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Affiliation(s)
- Yixi Yang
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, China,School of Food and Biological Engineering, Chengdu University, China
| | - Bowen Zhang
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, China,School of Food and Biological Engineering, Chengdu University, China
| | - Ying Bao
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, China,School of Food and Biological Engineering, Chengdu University, China
| | - Peng Huang
- Tibet Rhodiola Pharmaceutical Holding Company, Lhasa, China
| | - Jian Li
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, China,School of Basic Medical Sciences, Chengdu University, China
| | - Rui Li
- Corresponding authors: E-mails: ;
| | - Qi Zhao
- Corresponding authors: E-mails: ;
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Cai L, Pan R, Zeng Q, Zhang X, Zeng R, Zhu Q. The complete plastome sequence of Momordica cochinchinensis (Cucurbitaceae). Mitochondrial DNA B Resour 2023; 8:329-332. [PMID: 36876141 PMCID: PMC9980024 DOI: 10.1080/23802359.2023.2181649] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Momordica cochinchinensis (Lour.) Spreng. is an important medicinal plant that is used to treat various diseases in South and Southeast Asia. In this study, the complete plastome of M. cochinchinensis was sequenced and found to exhibit a total length of 158,955 bp, with a large single copy (LSC) region of 87,924 bp and a small single copy (SSC) region of 18,479 bp, as well as with two inverted repeats (IRs) that were both 26,726 bp in length. In total, 129 genes were detected, comprising 86 protein-encoding genes, 8 ribosomal RNA (rRNA) genes, and 35 transfer RNA (tRNA) genes. Furthermore, the inferred phylogenetic tree confirmed that M. cochinchinensis belongs to the genus Momordica in the Cucurbitaceae family. The research results will be used for authenticating M. cochinchinensis plant materials and for analyzing the genetic diversity and phylogenetic relationships in Momordica.
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Affiliation(s)
- Lijuan Cai
- Nanchang Business College, Jiangxi Agricultural University, Gongqing, P. R. China
| | - Rao Pan
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Qun Zeng
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Xiaoyan Zhang
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Rongbin Zeng
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Qianglong Zhu
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P. R. China
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35
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Yang S, Sun Z, Zhang G, Wang L, Zhong Q. Identification of the key metabolites and related genes network modules highly associated with the nutrients and taste components among different Pepino (Solanum muricatum) cultivars. Food Res Int 2023; 163:112287. [PMID: 36596193 DOI: 10.1016/j.foodres.2022.112287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 11/27/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
There is considerable knowledge about plant compounds that produce flavor, scent, and aroma. Aside from the similarities, however, groups of plant-produced nutrients and taste components have little in common with each other. Network analysis holds promise for metabolic gene discovery, which is especially important in plant systems where metabolic networks are not yet fully resolved. To bridge this gap, we propose a joint model of gene regulation and metabolic reactions in two different pepino varieties. Differential metabolomics analysis is carried out for detection of eventual interaction of compound. We adopted a multi-omics approach to profile the transcriptome and metabolome analyze differences in phenolic acids, flavonoids, organic acids, lipids, alkaloids, and sugars between LOF and SRF. The two most predominant classes of metabolites are phenolic acids and lipids in pepino. Overall results show enrichment in most DEGs was carbohydrate and biosynthesis of secondary metabolites pathway. Results of DEMs predominantly comprised N-p-coumaroyl agmatine and tryptamine, and significant differences were observed in their expression between LOF and SRF. Integrated DEMs and DEGs specific networks were constructed by combining two types of networks: transcriptional regulatory networks composed of interactions between DEMs and the regulated genes, and pepino metabolite-metabolite interaction networks. Newly discovered features, such as DEGs (USPA, UBE2 and DELLA) involved in the production of secondary metabolites are found in coregulated gene clusters. Moreover, lipid metabolites were most involved in DEMs correlations by OPLS-DA while identifying a significant number of DEGs co-regulated by SENP1, HMGCS et al. These results further that the metabolite discrepancies result from characterized the nutrients and taste components between two pepino genotype. Among the possible causes of the differences between species in pepino metabolite concentrations is co-regulated by these DEGs, continue to suggest that novel features of metabolite biosynthetic pathway remain to be uncovered. Finally, the integrated metabolome and transcriptome analyses have revealed that many important metabolic pathways are regulated at the transcriptional level. The metabolites content differences observed among varieties of the same species mainly originates from different regulated genes and enzymes expression. Overall, this study provides new insights into the underlying causes of differences in the plant metabolites and suggests that genetic data can be used to improve its nutrients and taste components.
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Affiliation(s)
- Shipeng Yang
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China; College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100, China
| | - Zhu Sun
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China
| | - Guangnan Zhang
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China
| | - Lihui Wang
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China
| | - Qiwen Zhong
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China.
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de Lima MMF, Anselmo DHAL, Silva R, Nunes GHS, Fulco UL, Vasconcelos MS, Mello VD. A Bayesian Analysis of Plant DNA Length Distribution via κ-Statistics. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1225. [PMID: 36141111 PMCID: PMC9497530 DOI: 10.3390/e24091225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
We report an analysis of the distribution of lengths of plant DNA (exons). Three species of Cucurbitaceae were investigated. In our study, we used two distinct κ distribution functions, namely, κ-Maxwellian and double-κ, to fit the length distributions. To determine which distribution has the best fitting, we made a Bayesian analysis of the models. Furthermore, we filtered the data, removing outliers, through a box plot analysis. Our findings show that the sum of κ-exponentials is the most appropriate to adjust the distribution curves and that the values of the κ parameter do not undergo considerable changes after filtering. Furthermore, for the analyzed species, there is a tendency for the κ parameter to lay within the interval (0.27;0.43).
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Affiliation(s)
- Maxsuel M. F. de Lima
- Departamento de Física, Universidade do Estado do Rio Grande do Norte, Natal 59072-970, RN, Brazil
| | - Dory H. A. L. Anselmo
- Departamento de Física, Universidade do Estado do Rio Grande do Norte, Natal 59072-970, RN, Brazil
- Departamento de Física, Universidade Federal do Rio Grande do Norte, Natal 59072-970, RN, Brazil
| | - Raimundo Silva
- Departamento de Física, Universidade do Estado do Rio Grande do Norte, Natal 59072-970, RN, Brazil
- Departamento de Física, Universidade Federal do Rio Grande do Norte, Natal 59072-970, RN, Brazil
| | - Glauber H. S. Nunes
- Departamento de Ciências Vegetais, Universidade Federal Rural do Semi-Árido, Mossoró 59625-900, RN, Brazil
| | - Umberto L. Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal 59072-970, RN, Brazil
| | - Manoel S. Vasconcelos
- Departamento de Física, Universidade Federal do Rio Grande do Norte, Natal 59072-970, RN, Brazil
| | - Vamberto D. Mello
- Departamento de Física, Universidade do Estado do Rio Grande do Norte, Natal 59072-970, RN, Brazil
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Almohaimeed HM, Al-Zahrani MH, Almuhayawi MS, Algaidi SA, Batawi AH, Baz HA, Mohammedsaleh ZM, Baz NA, Saleh FM, Ayuob N. Accelerating Effect of Cucurbita pepo L. Fruit Extract on Excisional Wound Healing in Depressed Rats Is Mediated through Its Anti-Inflammatory and Antioxidant Effects. Nutrients 2022; 14:3336. [PMID: 36014842 PMCID: PMC9415108 DOI: 10.3390/nu14163336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/19/2022] Open
Abstract
Background: Chronic stress can hinder wound healing as it suppresses both the cellular and innate immune responses. Objectives: The study aims to assess the effectiveness of the administration of topical and oral Cucurbita pepo L. (CP) ethanolic extract in prompting excisional wound healing in rats exposed to chronic stress, and to explain how it works. Materials and methods: Fifty albino rats assigned to five groups (n = 10) were utilized in this study. The chronic unpredictable mild stress (CUMS) model was used for 4 weeks to induce depressive-like behavior in rats, and a forced swim test and corticosterone were assessed to confirm its occurrence. During the experiment, an excisional wound was induced in the rats and followed. Oxidant/antioxidants status and pro-inflammatory cytokines levels were measured in the serum and wound area. Gene expression of pro-inflammatory cytokines was also assessed using RT-PCR. Wound closure histopathological changes and immunohistochemical expression of CD68, CD3, and CD4 at the wound area was assessed. Results: The administration of CP, both orally and topically, significantly reduced (p < 0.001) the depressive-like behavior and corticosterone and pro-inflammatory cytokines levels, while it significantly up-regulated the antioxidant activity compared to the untreated and topically CP-treated groups. Both topically CP-treated and combined CP-treated groups showed complete re-epithelialization, reduced inflammatory cells infiltration, collagen fibers deposition, and significantly increased CD3, CD4 positive T cells count, with a superior effect in the combined CP-treated groups. Conclusion: Cucurbita pepo L., administrated both topically and orally, can enhance the wound healing process in rats with depressive-like behavior mostly through the antioxidant, anti-inflammatory, and antidepressant activities observed in this study.
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Affiliation(s)
- Hailah M. Almohaimeed
- Department of Basic Science, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Maryam Hassan Al-Zahrani
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mohammed Saad Almuhayawi
- Department of Medical Microbiology & Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Yousef Abdullatif Jameel Chair of Prophetic Medicine Applications (YAJCPMA), Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Sami Awda Algaidi
- Department of Anatomy, Taibah University, Medina 42353, Saudi Arabia
| | - Ashwaq H. Batawi
- Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Hasan Ahmed Baz
- Clinical Toxicology, Faculty of Medicine, Umm Al Qura University/King Abdullah Medical City, Mecca 24211, Saudi Arabia
| | - Zuhair M. Mohammedsaleh
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Nhal Ahmed Baz
- Department of Periodontist, King Abdullah Medical City, Mecca 24211, Saudi Arabia
| | - Fayez M. Saleh
- Department of Medical Microbiology, Faculty of Medicine, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Nasra Ayuob
- Department of Medical Histology, Faculty of Medicine, Damietta University, Damietta 34517, Egypt
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Pérez-Escobar OA, Tusso S, Przelomska NAS, Wu S, Ryan P, Nesbitt M, Silber MV, Preick M, Fei Z, Hofreiter M, Chomicki G, Renner SS. Genome sequencing of up to 6,000-yr-old Citrullus seeds reveals use of a bitter-fleshed species prior to watermelon domestication. Mol Biol Evol 2022; 39:6652436. [PMID: 35907246 PMCID: PMC9387916 DOI: 10.1093/molbev/msac168] [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] [Indexed: 11/17/2022] Open
Abstract
Iconographic evidence from Egypt suggests that watermelon pulp was consumed there as a dessert by 4,360 BP. Earlier archaeobotanical evidence comes from seeds from Neolithic settlements in Libya, but whether these were watermelons with sweet pulp or other forms is unknown. We generated genome sequences from 6,000- and 3,300-year-old seeds from Libya and Sudan, and from worldwide herbarium collections made between 1824 and 2019, and analyzed these data together with resequenced genomes from important germplasm collections for a total of 131 accessions. Phylogenomic and population-genomic analyses reveal that (1) much of the nuclear genome of both ancient seeds is traceable to West African seed-use “egusi-type” watermelon (Citrullus mucosospermus) rather than domesticated pulp-use watermelon (Citrullus lanatus ssp. vulgaris); (2) the 6,000-year-old watermelon likely had bitter pulp and greenish-white flesh as today found in C. mucosospermus, given alleles in the bitterness regulators ClBT and in the red color marker LYCB; and (3) both ancient genomes showed admixture from C. mucosospermus, C. lanatus ssp. cordophanus, C. lanatus ssp. vulgaris, and even South African Citrullus amarus, and evident introgression between the Libyan seed (UMB-6) and populations of C. lanatus. An unexpected new insight is that Citrullus appears to have initially been collected or cultivated for its seeds, not its flesh, consistent with seed damage patterns induced by human teeth in the oldest Libyan material.
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Affiliation(s)
| | - Sergio Tusso
- Faculty of Biology, Division of Genetics, University of Munich (LMU), 82152 Planegg- Martinsried, Germany
| | | | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | | | - Mark Nesbitt
- Royal Botanic Gardens, Kew, TW9 3AE, United Kingdom
| | - Martina V Silber
- Faculty of Biology, Systematic Botany and Mycology, University of Munich (LMU), 80638 Munich, Germany
| | - Michaela Preick
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY 14853, USA.,USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Michael Hofreiter
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Guillaume Chomicki
- Ecology and Evolutionary Biology, School of Bioscience, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Susanne S Renner
- Faculty of Biology, Systematic Botany and Mycology, University of Munich (LMU), 80638 Munich, Germany.,Department of Biology, Washington University, Saint Louis, MO 63130, USA
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The Divergence of Chromosome Structures and 45S Ribosomal DNA Organization in Cucumis debilis Inferred by Comparative Molecular Cytogenetic Mapping. PLANTS 2022; 11:plants11151960. [PMID: 35956438 PMCID: PMC9370355 DOI: 10.3390/plants11151960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/09/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022]
Abstract
Cucumis debilis W.J.de Wilde & Duyfjes is an annual and monoecious plant. This species is endemic to Southeast Asia, particularly Vietnam. However, C. debilis is rarely studied, and no detailed information is available regarding its basic chromosome number, 45S ribosomal DNA (rDNA) status, and divergence among other Cucumis species. In this study, we characterized the morphological characters and determined and investigated the basic chromosome number and chromosomal distribution of 45S rDNA of C. debilis using the fluorescent in situ hybridization (FISH) technique. A maximum likelihood tree was constructed by combining the chloroplast and internal transcribed spacer of 45S rDNAs to infer its relationship within Cucumis. C. debilis had an oval fruit shape, green fruit peel, and protrusion-like white spots during the immature fruit stage. FISH analysis using 45S rDNA probe showed three pairs of 45S rDNA loci located at the terminal region in C. debilis, similar to C. hystrix. Meanwhile, two, two, and five pairs of 45S rDNA loci were observed for C. melo, C. metuliferus, and C. sativus, respectively. One melon (P90) and cucumber accessions exhibited different chromosomal localizations compared with other members of Cucumis. The majority of Cucumis species showed the terminal location of 45S rDNA, but melon P90 and cucumber exhibited terminal–interstitial and all interstitial orientations of 45S rDNA loci. Based on molecular cytogenetics and phylogenetic evidence, C. debilis is more closely related to cucumber than melon. Therefore, C. debilis may serve as a potential parental accession for genetic improvement of cucumber through interspecific hybridization.
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40
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Lin X, Zhang N, Song H, Lin K, Pang E. Population-specific, recent positive selection signatures in cultivated Cucumis sativus L. (cucumber). G3 GENES|GENOMES|GENETICS 2022; 12:6585339. [PMID: 35554526 PMCID: PMC9258548 DOI: 10.1093/g3journal/jkac119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022]
Abstract
Population-specific, positive selection promotes the diversity of populations and drives local adaptations in the population. However, little is known about population-specific, recent positive selection in the populations of cultivated cucumber (Cucumis sativus L.). Based on a genomic variation map of individuals worldwide, we implemented a Fisher’s combination method by combining 4 haplotype-based approaches: integrated haplotype score (iHS), number of segregating sites by length (nSL), cross-population extended haplotype homozygosity (XP-EHH), and Rsb. Overall, we detected 331, 2,147, and 3,772 population-specific, recent positive selective sites in the East Asian, Eurasian, and Xishuangbanna populations, respectively. Moreover, we found that these sites were related to processes for reproduction, response to abiotic and biotic stress, and regulation of developmental processes, indicating adaptations to their microenvironments. Meanwhile, the selective genes associated with traits of fruits were also observed, such as the gene related to the shorter fruit length in the Eurasian population and the gene controlling flesh thickness in the Xishuangbanna population. In addition, we noticed that soft sweeps were common in the East Asian and Xishuangbanna populations. Genes involved in hard or soft sweeps were related to developmental regulation and abiotic and biotic stress resistance. Our study offers a comprehensive candidate dataset of population-specific, selective signatures in cultivated cucumber populations. Our methods provide guidance for the analysis of population-specific, positive selection. These findings will help explore the biological mechanisms of adaptation and domestication of cucumber.
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Affiliation(s)
- Xinrui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University , Beijing 100875, China
| | - Ning Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University , Beijing 100875, China
| | - Hongtao Song
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University , Beijing 100875, China
| | - Kui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University , Beijing 100875, China
| | - Erli Pang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University , Beijing 100875, China
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41
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Cornelius ML, Haber AI, Weber DC. Host Finding Behavior of the Parasitoid Hadronotus pennsylvanicus (Hymenoptera: Scelionidae) for Egg Masses of the Squash Bugs Anasa tristis and Anasa armigera (Hemiptera: Coreidae) in Squash and Cucumber Fields. ENVIRONMENTAL ENTOMOLOGY 2022; 51:537-544. [PMID: 35429162 DOI: 10.1093/ee/nvac018] [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: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Parasitoid foraging behavior is affected by habitat and host plant differences. Egg parasitoids also use a combination of oviposition-induced and host-derived cues to find host eggs. This study compared parasitism by Hadronotus pennsylvanicus (Ashmead) (Hymenoptera: Scelionidae) on two squash bug species, Anasa tristis (DeGeer) and Anasa armigera Say (Hemiptera: Coreidae), by placing sentinel squash and cucumber plants with egg masses of either of the two squash bug species in squash and cucumber fields in a 3-way factorial design. Host density of wild A. tristis egg masses in squash fields may have influenced parasitoid foraging behavior on sentinel plants. In the 3-way factorial design, parasitism was higher on sentinel squash plants and in squash fields overall. However, parasitism on A. armigera egg masses was highest on sentinel cucumber plants in squash fields and parasitism on A. tristis egg masses was higher on sentinel squash plants in either squash or cucumber fields and lowest on sentinel cucumber plants in cucumber fields. Results suggest that parasitoids were able to specifically orient to the combination of host plant and host cues associated with A. tristis egg masses on sentinel squash plants, but that they were more responsive to plant-induced cues associated with cucumber when searching for A. armigera egg masses. Parasitoids appear to utilize different combinations of host plant and host cues when searching for eggs of the two squash bug species.
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Affiliation(s)
- Mary L Cornelius
- Invasive Insect Biocontrol and Behavior Laboratory, USDA Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
| | - Ariela I Haber
- Invasive Insect Biocontrol and Behavior Laboratory, USDA Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
- Invasive Insect Biocontrol and Behavior Laboratory, USDA Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
| | - Donald C Weber
- Invasive Insect Biocontrol and Behavior Laboratory, USDA Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
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Shah IH, Ashraf M, Khan AR, Manzoor MA, Hayat K, Arif S, Sabir IA, Abdullah M, Niu Q, Zhang Y. Controllable synthesis and stabilization of Tamarix aphylla-mediated copper oxide nanoparticles for the management of Fusarium wilt on musk melon. 3 Biotech 2022; 12:128. [PMID: 35601642 PMCID: PMC9120281 DOI: 10.1007/s13205-022-03189-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/26/2022] [Indexed: 11/01/2022] Open
Abstract
Excessive use of pesticides and mineral fertilizers poses a serious threat to ecoenvironment sustainability and human health. Nano pesticides or Nano fungicides have attained great attention in the field of agriculture due to their unique characteristics, by improving crop growth with enhancing pathogenesis-related defense system. However, there is a need to develop a sustainable mechanism for the synthesis of fungicides which replace the chemical pesticides to avoid their hazardous impact. Here in, Tamarix aphylla mediated CuO-Nanoparticles (NPs) were synthesized, characterized and their activity was evaluated under in-vitro and in-vivo conditions. The structural and elemental analysis of NPs were carried out by using X-ray powder diffraction (XRD), Fourier transformed infrared spectroscopy (FTIR), UV-visible spectrophotometer, Scanning electron microscope (SEM) and Transmission electron microscope (TEM). In the greenhouse, at an optimum concentration of 50 mg/L reduced disease severity very effectively and enhanced plant growth. Application of NPs also assisted in the induction of systemic response of defense-related genes in melon. Under In vitro condition at 100 mg/L significantly reduced mycelial growth (84.5%) by directly acting on the pathogenic cell wall. Our work confirmed that dosedependent concentration of T. aphylla extract based biological CuO-NPs enhance plant growth and help to effectively resist against F. oxysporum infection. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03189-0.
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Affiliation(s)
- Iftikhar Hussain Shah
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 People’s Republic of China
| | - Muhammad Ashraf
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 People’s Republic of China
| | - Ali Raza Khan
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, People’s Republic of China
| | - Muhammad Aamir Manzoor
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Kashif Hayat
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 People’s Republic of China
| | - Samiah Arif
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 People’s Republic of China
| | - Irfan Ali Sabir
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 People’s Republic of China
| | - Muhammad Abdullah
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072 Australia
| | - Qingliang Niu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 People’s Republic of China
| | - Yidong Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 People’s Republic of China
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Wang Y, Lei Z, Ye R, Zhou W, Zhou Y, Zou Z, Li J, Yi L, Dai Z. Effects of Cadmium on Physiochemistry and Bioactive Substances of Muskmelon ( Cucumis melo L.). Molecules 2022; 27:molecules27092913. [PMID: 35566265 PMCID: PMC9101123 DOI: 10.3390/molecules27092913] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 02/05/2023] Open
Abstract
Muskmelon pedicel is the fruit stalk of muskmelon and one of the traditional Chinese medicines, which can be used to treat jaundice, diabetes and neuropathy. However, in recent years, agricultural soil heavy metal cadmium (Cd) pollution has become serious, coupled with the imperfect sales management of herbal medicine, increasing the potential health risk of contaminated herbal medicine in the human body. In this paper, the comprehensive quality of contaminated muskmelon was tested. The results showed that Cd stress significantly inhibited the growth of muskmelon plants, reduced the anthocyanin and chlorophyll contents, and increased the fruit size and sweetness of muskmelon. In addition, heavy metal Cd can also cause oxidative stress in plants, resulting in a series of changes in antioxidant enzyme activities. In the experimental group, the content of polyphenols and saponins increased by 27.02% and 23.92%, respectively, after high-concentration Cd treatment, which may be a mechanism of plant resistance to stress. This paper reveals that the content of bioactive substances in Chinese herbal medicine is high, but the harm in heavy metals cannot be underestimated, which should be paid attention to by relevant departments.
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Affiliation(s)
- Yunqiang Wang
- Institute of Economic Crops, Hubei Academy of Agricultural Science, Wuhan 430064, China; (Y.W.); (W.Z.); (L.Y.)
- Vegetable Germplasm Innovation and Genetic Improvement Key Laboratory of Hubei Province, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Zhen Lei
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China; (Z.L.); (R.Y.); (Y.Z.); (Z.Z.)
| | - Rongbin Ye
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China; (Z.L.); (R.Y.); (Y.Z.); (Z.Z.)
| | - Wei Zhou
- Institute of Economic Crops, Hubei Academy of Agricultural Science, Wuhan 430064, China; (Y.W.); (W.Z.); (L.Y.)
- Vegetable Germplasm Innovation and Genetic Improvement Key Laboratory of Hubei Province, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Ying Zhou
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China; (Z.L.); (R.Y.); (Y.Z.); (Z.Z.)
| | - Zhengkang Zou
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China; (Z.L.); (R.Y.); (Y.Z.); (Z.Z.)
| | - Junli Li
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China; (Z.L.); (R.Y.); (Y.Z.); (Z.Z.)
- Correspondence: (J.L.); (Z.D.)
| | - Licong Yi
- Institute of Economic Crops, Hubei Academy of Agricultural Science, Wuhan 430064, China; (Y.W.); (W.Z.); (L.Y.)
- Vegetable Germplasm Innovation and Genetic Improvement Key Laboratory of Hubei Province, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Zhaoyi Dai
- Institute of Economic Crops, Hubei Academy of Agricultural Science, Wuhan 430064, China; (Y.W.); (W.Z.); (L.Y.)
- Vegetable Germplasm Innovation and Genetic Improvement Key Laboratory of Hubei Province, Hubei Academy of Agricultural Science, Wuhan 430064, China
- Correspondence: (J.L.); (Z.D.)
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Bhowmick BK, Jha S. A critical review on cytogenetics of Cucurbitaceae with updates on Indian taxa. COMPARATIVE CYTOGENETICS 2022; 16:93-125. [PMID: 36761811 PMCID: PMC9849056 DOI: 10.3897/compcytogen.v16.i2.79033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/16/2022] [Indexed: 06/13/2023]
Abstract
The cytogenetic relationships in the species of Cucurbitaceae are becoming immensely important to answer questions pertaining to genome evolution. Here, a simplified and updated data resource on cytogenetics of Cucurbitaceae is presented on the basis of foundational parameters (basic, zygotic and gametic chromosome numbers, ploidy, genome size, karyotype) and molecular cytogenetics. We have revised and collated our own findings on seven agriculturally important Indian cucurbit species in a comparative account with the globally published reports. Chromosome count (of around 19% species) shows nearly three-fold differences while genome size (of nearly 5% species) shows 5.84-fold differences across the species. There is no significant correlation between chromosome numbers and nuclear genome sizes. The possible trend of evolution is discussed here based on molecular cytogenetics data, especially the types and distribution of nucleolus organizer regions (NORs). The review supersedes the scopes of general chromosome databases and invites scopes for continuous updates. The offline resource serves as an exclusive toolkit for research and breeding communities across the globe and also opens scope for future establishment of web-database on Cucurbitaceae cytogenetics.
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Affiliation(s)
- Biplab Kumar Bhowmick
- Department of Botany, Scottish Church College, 1&3, Urquhart Square, Kolkata-700006, West Bengal, IndiaScottish Church CollegeKolkataIndia
| | - Sumita Jha
- Plant Cytogenetics and Biotechnology Laboratory, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, West Bengal, IndiaUniversity of CalcuttaKolkataIndia
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45
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Donati L, Bertin S, Gentili A, Luigi M, Taglienti A, Manglli A, Tiberini A, Brasili E, Sciubba F, Pasqua G, Ferretti L. Effects of Organic Biostimulants Added with Zeolite on Zucchini Squash Plants Infected by Tomato Leaf Curl New Delhi Virus. Viruses 2022; 14:v14030607. [PMID: 35337014 PMCID: PMC8952782 DOI: 10.3390/v14030607] [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: 01/17/2022] [Revised: 03/08/2022] [Accepted: 03/11/2022] [Indexed: 11/16/2022] Open
Abstract
The use of organic substances in integrated pest management can contribute to human- and environment-safe crop production. In the present work, a combination of organic biostimulants (Fullcrhum Alert and BioVeg 500) and an inorganic corroborant (Clinogold, zeolite) was tested for the effects on the plant response to the quarantine pest tomato leaf curl New Delhi virus (ToLCNDV). Biostimulants were applied to healthy and infected greenhouse-grown zucchini plants, and the vegetative parameters and viral titer were evaluated. Although no antiviral effects were observed in terms of both virus replication and symptom expression, these biostimulants were shown to influence plant fitness. A significant increase in biomass and in leaf, flower, and fruit production was induced in both healthy and infected plants. Biostimulants also enhanced the production of metabolites commonly involved in plant response to virus infection, such as carbohydrates, phenylpropanoids and free amino acids. These results encourage new field trials to evaluate the actual productivity of infected plants after treatments and the possible application of organic biostimulants in agriculture.
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Affiliation(s)
- Livia Donati
- Council for Agricultural Research and Economics–Research Centre for Plant Protection and Certification, 00156 Rome, Italy; (S.B.); (A.G.); (M.L.); (A.T.); (A.M.); (A.T.); (L.F.)
- Correspondence:
| | - Sabrina Bertin
- Council for Agricultural Research and Economics–Research Centre for Plant Protection and Certification, 00156 Rome, Italy; (S.B.); (A.G.); (M.L.); (A.T.); (A.M.); (A.T.); (L.F.)
| | - Andrea Gentili
- Council for Agricultural Research and Economics–Research Centre for Plant Protection and Certification, 00156 Rome, Italy; (S.B.); (A.G.); (M.L.); (A.T.); (A.M.); (A.T.); (L.F.)
| | - Marta Luigi
- Council for Agricultural Research and Economics–Research Centre for Plant Protection and Certification, 00156 Rome, Italy; (S.B.); (A.G.); (M.L.); (A.T.); (A.M.); (A.T.); (L.F.)
| | - Anna Taglienti
- Council for Agricultural Research and Economics–Research Centre for Plant Protection and Certification, 00156 Rome, Italy; (S.B.); (A.G.); (M.L.); (A.T.); (A.M.); (A.T.); (L.F.)
| | - Ariana Manglli
- Council for Agricultural Research and Economics–Research Centre for Plant Protection and Certification, 00156 Rome, Italy; (S.B.); (A.G.); (M.L.); (A.T.); (A.M.); (A.T.); (L.F.)
| | - Antonio Tiberini
- Council for Agricultural Research and Economics–Research Centre for Plant Protection and Certification, 00156 Rome, Italy; (S.B.); (A.G.); (M.L.); (A.T.); (A.M.); (A.T.); (L.F.)
| | - Elisa Brasili
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy; (E.B.); (F.S.); (G.P.)
- NMR-based Metabolomics Laboratory (NMLab), Sapienza University of Rome, 00185 Rome, Italy
| | - Fabio Sciubba
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy; (E.B.); (F.S.); (G.P.)
- NMR-based Metabolomics Laboratory (NMLab), Sapienza University of Rome, 00185 Rome, Italy
| | - Gabriella Pasqua
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy; (E.B.); (F.S.); (G.P.)
- NMR-based Metabolomics Laboratory (NMLab), Sapienza University of Rome, 00185 Rome, Italy
| | - Luca Ferretti
- Council for Agricultural Research and Economics–Research Centre for Plant Protection and Certification, 00156 Rome, Italy; (S.B.); (A.G.); (M.L.); (A.T.); (A.M.); (A.T.); (L.F.)
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Bellini G, Erfmeier A, Schrieber K. No Support for the Neolithic Plant Invasion Hypothesis: Invasive Species From Eurasia Do Not Perform Better Under Agropastoral Disturbance in Early Life Stages Than Invaders From Other Continents. FRONTIERS IN PLANT SCIENCE 2022; 13:801750. [PMID: 35222466 PMCID: PMC8874271 DOI: 10.3389/fpls.2022.801750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Pre-adaptation to disturbance is an important driver of biological invasions in human-altered ecosystems. Agropastoralism is one of the oldest forms of landscape management. It surged 12,000 years ago in Western Asia and it was then imported to Europe starting 8,000 years ago. The Neolithic Plant Invasion hypothesis suggests that Eurasian plants succeed at invading agroecosystems worldwide thanks to their adaptation to agropastoralism, which derives from these species' long co-evolution with such practice. Plant species from Western Asia are predicted to have the highest degree of adaptation to agropastoralism, since they have co-evolved with such practice for several millennia more than European plants, and non-Eurasian species should be poorly adapted due to their relatively short exposure. However, this Eurocentric perspective largely ignores that several other cultures around the world independently developed and implemented agropastoralism through history, which challenges this hypothesized superior adaptation of Eurasian species. Here, we tested whether the early-life performance of invasive plants under disturbance depends on their geographical origin and the associated assumed exposure time to agropastoralism. We selected 30 species divided into three groups: exposure long, native to Western Asia; exposure medium, native to Central Europe; exposure short, native to America. Three soil disturbance treatments (control/compaction/tilling) combined with two space occupancy levels (available/occupied) were applied to monospecific experimental units (n = 900), each containing 50 seeds. We predicted that Eurasian species would benefit more from disturbance in terms of germination and seedling performance than species with shorter assumed exposure to agropastoralism, and that this effect would be stronger when space is occupied. Contrary to these expectations, all species groups profited equally from disturbance, while non-Eurasian species were most hampered by space occupancy. For germination success and speed, exposure long species had higher values than exposure short species, regardless of the disturbance treatment. These results do not support that Eurasian species possess a higher adaptation to agropastoralism, but rather that non-Eurasian species can cope just as well with the associated disturbances. We discuss how future experiments that address the complex relationships between species interactions, plant life-phases and the quality of disturbance can help to understand the role of land-use history in plant invasion success.
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Affiliation(s)
- Ginevra Bellini
- Department of Geobotany, Institute for Ecosystem Research, Kiel University, Kiel, Germany
- Cluster of Excellence ROOTS, Kiel University, Kiel, Germany
| | - Alexandra Erfmeier
- Department of Geobotany, Institute for Ecosystem Research, Kiel University, Kiel, Germany
- Cluster of Excellence ROOTS, Kiel University, Kiel, Germany
| | - Karin Schrieber
- Department of Geobotany, Institute for Ecosystem Research, Kiel University, Kiel, Germany
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Pichot C, Djari A, Tran J, Verdenaud M, Marande W, Huneau C, Gautier V, Latrasse D, Arribat S, Sommard V, Troadec C, Poncet C, Bendahmane M, Szecsi J, Dogimont C, Salse J, Benhamed M, Zouine M, Boualem A, Bendahmane A. Cantaloupe melon genome reveals 3D chromatin features and structural relationship with the ancestral cucurbitaceae karyotype. iScience 2022; 25:103696. [PMID: 35059606 PMCID: PMC8760558 DOI: 10.1016/j.isci.2021.103696] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/01/2021] [Accepted: 12/20/2021] [Indexed: 11/21/2022] Open
Abstract
Cucumis melo displays a large diversity of horticultural groups with cantaloupe melon the most cultivated type. Using a combination of single-molecule sequencing, 10X Genomics link-reads, high-density optical and genetic maps, and chromosome conformation capture (Hi-C), we assembled a chromosome scale C. melo var. cantalupensis Charentais mono genome. Integration of RNA-seq, MeDip-seq, ChIP-seq, and Hi-C data revealed a widespread compartmentalization of the melon genome, segregating constitutive heterochromatin and euchromatin. Genome-wide comparative and evolutionary analysis between melon botanical groups identified Charentais mono genome increasingly more divergent from Harukei-3 (reticulatus), Payzawat (inodorus), and HS (ssp. agrestis) genomes. To assess the paleohistory of the Cucurbitaceae, we reconstructed the ancestral Cucurbitaceae karyotype and compared it to sequenced cucurbit genomes. In contrast to other species that experienced massive chromosome shuffling, melon has retained the ancestral genome structure. We provide comprehensive genomic resources and new insights in the diversity of melon horticultural groups and evolution of cucurbits. We provide a chromosome scale C. melo var. cantalupensis Charentais mono genome Epigenomic analysis revealed a widespread compartmentalization of the melon genome We reconstructed the ancestral Cucurbitaceae karyotype Melon has retained the ancestral Cucurbitaceae genome structure
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Affiliation(s)
- Clement Pichot
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Anis Djari
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France
| | - Joseph Tran
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Marion Verdenaud
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - William Marande
- INRAE, Centre National de Ressources Génomiques Végétales, 31326 Castanet-Tolosan, France
| | - Cecile Huneau
- INRAE-UCA UMR 1095 GDEC, 5 chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - Veronique Gautier
- INRAE-UCA UMR 1095 GDEC, 5 chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Sandrine Arribat
- INRAE, Centre National de Ressources Génomiques Végétales, 31326 Castanet-Tolosan, France
| | - Vivien Sommard
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Christelle Troadec
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Charles Poncet
- INRAE-UCA UMR 1095 GDEC, 5 chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, INRAE, CNRS, Université Lyon 1-ENSL, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France
| | - Judit Szecsi
- Laboratoire Reproduction et Développement des Plantes, INRAE, CNRS, Université Lyon 1-ENSL, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France
| | - Catherine Dogimont
- INRAE GAFL, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet, France
| | - Jerome Salse
- INRAE-UCA UMR 1095 GDEC, 5 chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Mohamed Zouine
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France
| | - Adnane Boualem
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Abdelhafid Bendahmane
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Corresponding author
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Ramalhete C, Gonçalves BMF, Barbosa F, Duarte N, Ferreira MJU. Momordica balsamina: phytochemistry and pharmacological potential of a gifted species. PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2022; 21:617-646. [PMID: 35153639 PMCID: PMC8821832 DOI: 10.1007/s11101-022-09802-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 01/09/2022] [Indexed: 05/07/2023]
Abstract
Momordica balsamina L. (Cucurbitaceae), frequently named balsam apple, southern balsam pear or African pumpkin, is a vegetable with high nutritional value, being mostly used as food in sub-Saharan Africa. It has also been largely used in traditional medicine to treat several diseases, such as malaria fevers and diabetes. As a member of the Cucurbitaceae family, the main constituents are cucurbitane-type triterpenoids, with different oxidation patterns, named cucurbitacins. This review aims at summarizing our contribution to the phytochemical study of M. balsamina and the evaluation of the isolated cucurbitacins and derivatives as multidrug resistance reversers in cancer cells and bacteria. In this way, the selective antiproliferative activity against multidrug resistant cancer cells of cucurbitacins obtained from M. balsamina, their ability as P-glycoprotein inhibitors in cancer cells overexpressing this ABC transporter, as well as efflux pump inhibitors in resistant bacteria strains are reviewed. Moreover, the in vitro antimalarial activity of cucurbitacins and acyl derivatives against the blood and liver-stages of Plasmodium strains, and the in vivo activity of selected compounds is also reviewed. Besides our work, edible and medicinal uses, and other studies mainly reporting the biological activities of M. balsamina extracts, such as antidiabetic, antibacterial, anti-inflammatory, and antioxidant properties are also addressed.
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Affiliation(s)
- Cátia Ramalhete
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
- ATLÂNTICA – Instituto Universitário, Fábrica da Pólvora de Barcarena, Barcarena, Oeiras, 2730-036 Portugal
| | - Bruno M. F. Gonçalves
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Filipa Barbosa
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Noélia Duarte
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Maria-José U. Ferreira
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
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Ježek J, Mirtič K, Rešetič N, Hodnik JJ, Vergles Rataj A. The effect of pumpkin seed cake and ground cloves (Syzygium aromaticum) supplementation on gastrointestinal nematode egg shedding in sheep. Parasite 2021; 28:78. [PMID: 34870589 PMCID: PMC8647689 DOI: 10.1051/parasite/2021076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 11/15/2021] [Indexed: 11/14/2022] Open
Abstract
The aim of this study was to evaluate the effect of feed additives (pumpkin seed cake and cloves) on the egg excretion of gastrointestinal nematodes (GIN) in sheep. Thirty ewes naturally infected with GIN were randomly selected from a flock and assigned to the following groups of 10 animals each: clove group (received 1.8 g ground cloves/ewe/day, for 7 days), pumpkin seed cake group (200 g pumpkin seed cake/ewe/day, for 7 days) and control group. Before starting the study, on day 0, and 5 days after the 7-day supplementation, on day 12, the body condition and FAMACHA scores were assessed and individual faecal egg counts (FEC) were performed. The mean body condition and the FAMACHA scores did not change significantly between day 0 and 12 with the exception of a significantly deteriorated FAMACHA score in the clove group. The percentage reduction of FEC was 40.7% on day 12 in the clove group and 52.9% in the pumpkin seed cake group. In the control group, FEC increased by 8.7%. A coproculture of faecal samples from four of the most infected animals on day 0 revealed Trichostrongylus spp. larvae L3 in all four selected ewes, Ostertagia spp. and Cooperia spp. in three and Haemonchus contortus in one ewe. These results are promising and encourage further studies aimed to evaluate the possibility that these plant supplements could be a complementary method for parasite control, thus reducing the need for chemotherapy.
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Ogundare SA, Moodley V, Amaku JF, Ogunmoye AO, Atewolara-Odule OC, Olubomehin OO, Awokoya KN, Sanyaolu NO, Ibikunle AA, van Zyl WE. Nanocrystalline cellulose derived from melon seed shell (Citrullus colocynthis L.) for reduction and stabilization of silver nanoparticles: Synthesis and catalytic activity. CARBOHYDRATE POLYMER TECHNOLOGIES AND APPLICATIONS 2021. [DOI: 10.1016/j.carpta.2021.100134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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