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Huang W, Xu B, Guo W, Huang Z, Li Y, Wu W. De novo genome assembly and population genomics of a shrub tree Barthea barthei (Hance) krass provide insights into the adaptive color variations. FRONTIERS IN PLANT SCIENCE 2024; 15:1365686. [PMID: 38751846 PMCID: PMC11094225 DOI: 10.3389/fpls.2024.1365686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Flower color is a classic example of an ecologically important trait under selection in plants. Understanding the genetic mechanisms underlying shifts in flower color can provide key insights into ecological speciation. In this study, we investigated the genetic basis of flower color divergence in Barthea barthei, a shrub tree species exhibiting natural variation in flower color. We assembled a high-quality genome assembly for B. barthei with a contig N50 of 2.39 Mb and a scaffold N50 of 16.21 Mb. The assembly was annotated with 46,430 protein-coding genes and 1,560 non-coding RNAs. Genome synteny analysis revealed two recent tetraploidization events in B. barthei, estimated to have occurred at approximately 17 and 63 million years ago. These tetraploidization events resulted in massive duplicated gene content, with over 70% of genes retained in collinear blocks. Gene family members of the core regulators of the MBW complex were significantly expanded in B. barthei compared to Arabidopsis, suggesting that these duplications may have provided raw genetic material for the evolution of novel regulatory interactions and the diversification of anthocyanin pigmentation. Transcriptome profiling of B. barthei flowers revealed differential expression of 9 transcription factors related to anthocyanin biosynthesis between the two ecotypes. Six of these differentially expressed transcription factors were identified as high-confidence candidates for adaptive evolution based on positive selection signals. This study provides insights into the genetic basis of flower color divergence and the evolutionary mechanisms underlying ecological adaptation in plants.
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Affiliation(s)
- Weicheng Huang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- South China Botanical Garden, Chinese Academy of Science, Guangzhou, China
| | - Bin Xu
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Wei Guo
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Zecheng Huang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yongquan Li
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wei Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
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Ramanauskas K, Igić B. kakapo: easy extraction and annotation of genes from raw RNA-seq reads. PeerJ 2023; 11:e16456. [PMID: 38034874 PMCID: PMC10688300 DOI: 10.7717/peerj.16456] [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: 01/20/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023] Open
Abstract
kakapo (kākāpō) is a Python-based pipeline that allows users to extract and assemble one or more specified genes or gene families. It flexibly uses original RNA-seq read or GenBank SRA accession inputs without performing global assembly of entire transcriptomes or metatranscriptomes. The pipeline identifies open reading frames in the assembled gene transcripts and annotates them. It optionally filters raw reads for ribosomal, plastid, and mitochondrial reads, or reads belonging to non-target organisms (e.g., viral, bacterial, human). kakapo can be employed for targeted assembly, to extract arbitrary loci, such as those commonly used for phylogenetic inference in systematics or candidate genes and gene families in phylogenomic and metagenomic studies. We provide example applications and discuss how its use can offset the declining value of GenBank's single-gene databases and help assemble datasets for a variety of phylogenetic analyses.
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Affiliation(s)
- Karolis Ramanauskas
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Boris Igić
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States of America
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Petrone-Mendoza E, Vergara-Silva F, Olson ME. Plant morpho evo-devo. TRENDS IN PLANT SCIENCE 2023; 28:1257-1276. [PMID: 37423784 DOI: 10.1016/j.tplants.2023.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 06/02/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023]
Abstract
Evo-devo is often thought of as being the study of which genes underlie which phenotypes. However, evo-devo is much more than this, especially in plant science. In leaf scars along stems, cell changes across wood growth rings, or flowers along inflorescences, plants trace a record of their own development. Plant morpho evo-devo provides data that genes could never furnish on themes such as heterochrony, the evolution of temporal phenotypes, modularity, and phenotype-first evolution. As plant science surges into increasingly -omic realms, it is essential to keep plant morpho evo-devo in full view as an honored member of the evo-devo canon, ensuring that plant scientists can, wherever they are, generate fundamental insights at the appropriate level of biological organization.
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Affiliation(s)
- Emilio Petrone-Mendoza
- Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n de Ciudad Universitaria, Ciudad de México 04510, México; Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, C.P. 04510, CDMX, México
| | - Francisco Vergara-Silva
- Laboratorio de Teoría Evolutiva e Historia de la Ciencia, Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mark E Olson
- Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n de Ciudad Universitaria, Ciudad de México 04510, México.
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Qiu Y, Cai C, Mo X, Zhao X, Wu L, Liu F, Li R, Liu C, Chen J, Tian M. Transcriptome and metabolome analysis reveals the effect of flavonoids on flower color variation in Dendrobium nobile Lindl. FRONTIERS IN PLANT SCIENCE 2023; 14:1220507. [PMID: 37680360 PMCID: PMC10481954 DOI: 10.3389/fpls.2023.1220507] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/08/2023] [Indexed: 09/09/2023]
Abstract
Introduction Dendrobium nobile L. is a rare orchid plant with high medicinal and ornamentalvalue, and extremely few genetic species resources are remaining in nature. In the normal purple flower population, a type of population material with a white flower variation phenotype has been discovered, and through pigment component determination, flavonoids were preliminarily found to be the main reason for the variation. Methods This study mainly explored the different genes and metabolites at different flowering stages and analysed the flower color variation mechanism through transcriptome- and flavonoid-targeted metabolomics. The experimental materials consisted of two different flower color phenotypes, purple flower (PF) and white flower (WF), observed during three different periods. Results and discussion The results identified 1382, 2421 and 989 differentially expressed genes (DEGs) in the white flower variety compared with the purple flower variety at S1 (bud stage), S2 (chromogenic stage) and S3 (flowering stage), respectively. Among these, 27 genes enriched in the ko00941, ko00942, ko00943 and ko00944 pathways were screened as potential functional genes affecting flavonoid synthesis and flower color. Further analysis revealed that 15 genes are potential functional genes that lead to flavonoid changes and flower color variations. The metabolomics results at S3 found 129 differentially accumulated metabolites (DAMs), which included 8 anthocyanin metabolites, all of which (with the exception of delphinidin-3-o-(2'''-o-malonyl) sophoroside-5-o-glucoside) were found at lower amounts in the WF variety compared with the PF variety, indicating that a decrease in the anthocyanin content was the main reason for the inability to form purple flowers. Therefore, the changes in 19 flavone and 62 flavonol metabolites were considered the main reasons for the formation of white flowers. In this study, valuable materials responsible for flower color variation in D. nobile were identified and further analyzed the main pathways and potential genes affecting changes in flavonoids and the flower color. This study provides a material basis and theoretical support for the hybridization and molecular-assisted breeding of D. nobile.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ji Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Mengliang Tian
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
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Wong DCJ, Pichersky E, Peakall R. Many different flowers make a bouquet: Lessons from specialized metabolite diversity in plant-pollinator interactions. CURRENT OPINION IN PLANT BIOLOGY 2023; 73:102332. [PMID: 36652780 DOI: 10.1016/j.pbi.2022.102332] [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: 10/07/2022] [Revised: 12/04/2022] [Accepted: 12/08/2022] [Indexed: 06/10/2023]
Abstract
Flowering plants have evolved extraordinarily diverse metabolites that underpin the floral visual and olfactory signals enabling plant-pollinator interactions. In some cases, these metabolites also provide unusual rewards that specific pollinators depend on. While some metabolites are shared by most flowering plants, many have evolved in restricted lineages in response to the specific selection pressures encountered within different niches. The latter are designated as specialized metabolites. Recent investigations continue to uncover a growing repertoire of unusual specialized metabolites. Increased accessibility to cutting-edge multi-omics technologies (e.g. genome, transcriptome, proteome, metabolome) is now opening new doors to simultaneously uncover the molecular basis of their synthesis and their evolution across diverse plant lineages. Drawing upon the recent literature, this perspective discusses these aspects and, where known, their ecological and evolutionary relevance. A primer on omics-guided approaches to discover the genetic and biochemical basis of functional specialized metabolites is also provided.
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Affiliation(s)
- Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia.
| | - Eran Pichersky
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Rod Peakall
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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Xu R, Luo M, Xu J, Wang M, Huang B, Miao Y, Liu D. Integrative Analysis of Metabolomic and Transcriptomic Data Reveals the Mechanism of Color Formation in Corms of Pinellia ternata. Int J Mol Sci 2023; 24:ijms24097990. [PMID: 37175702 PMCID: PMC10178707 DOI: 10.3390/ijms24097990] [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: 03/08/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Pinellia ternata (Thunb.) Breit. (P. ternata) is a very important plant that is commonly used in traditional Chinese medicine. Its corms can be used as medicine and function to alleviate cough, headache, and phlegm. The epidermis of P. ternata corms is often light yellow to yellow in color; however, within the range of P. ternata found in JingZhou City in Hubei Province, China, there is a form of P. ternata in which the epidermis of the corm is red. We found that the total flavonoid content of red P. ternata corms is significantly higher than that of yellow P. ternata corms. The objective of this study was to understand the molecular mechanisms behind the difference in epidermal color between the two forms of P. ternata. The results showed that a high content of anthocyanidin was responsible for the red epidermal color in P. ternata, and 15 metabolites, including cyanidin-3-O-rutinoside-5-O-glucoside, cyanidin-3-O-glucoside, and cyanidin-3-O-rutinoside, were screened as potential color markers in P. ternata through metabolomic analysis. Based on an analysis of the transcriptome, seven genes, including PtCHS1, PtCHS2, PtCHI1, PtDFR5, PtANS, PtUPD-GT2, and PtUPD-GT3, were found to have important effects on the biosynthesis of anthocyanins in the P. ternata corm epidermis. Furthermore, two transcription factors (TFs), bHLH1 and bHLH2, may have regulatory functions in the biosynthesis of anthocyanins in red P. ternata corms. Using an integrative analysis of the metabolomic and transcriptomic data, we identified five genes, PtCHI, PtDFR2, PtUPD-GT1, PtUPD-GT2, and PtUPD-GT3, that may play important roles in the presence of the red epidermis color in P. ternata corms.
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Affiliation(s)
- Rong Xu
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Ming Luo
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Jiawei Xu
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Mingxing Wang
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Bisheng Huang
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Yuhuan Miao
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Dahui Liu
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan 430065, China
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Yuan L, Niu H, Yun Y, Tian J, Lao F, Liao X, Gao Z, Ren D, Zhou L. Analysis of coloration characteristics of Tunisian soft-seed pomegranate arils based on transcriptome and metabolome. Food Chem 2022; 370:131270. [PMID: 34788951 DOI: 10.1016/j.foodchem.2021.131270] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 01/10/2023]
Abstract
In this study, combining metabolome and transcriptome, color related attributes and phenolic compositions of Tunisian pomegranate arils from 7 Chinese regions at same developing stage were studied. The total anthocyanin (TAC), flavonoids, and percent polymeric color (PPC) were ranged at 8.93-28.41 mg/100 g arils, 37.55-69.72 mg/100 g arils, and 3.38-21.96%, respectively. In total, 51 phenolic compounds were characterized, most of which were markedly higher in reddish-purple pomegranate arils than those levels in reddish pomegranate arils. In contrast, the accumulation of tannins was significantly higher in reddish pomegranate arils. Among the 49 differentially expressed genes, 8 and 5 genes were matched to β-glucosidase and peroxidase, respectively. Correlation analysis showed that PPC was negatively correlated with 10 phenolic metabolites and TAC, positively correlated with L*, polymeric color, and 1 gene (|r| > 0.7, p < 0.01). Our results provide new insights for understanding the difference in coloration of pomegranate arils.
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Affiliation(s)
- Lei Yuan
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province 650500, China
| | - Huihui Niu
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province 650500, China
| | - Yurou Yun
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province 650500, China
| | - Jun Tian
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province 650500, China
| | - Fei Lao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiaojun Liao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Zhengqing Gao
- Yunnan Institute of Horticultural Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, Yunnan Province, China
| | - Dabing Ren
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province 650500, China
| | - Linyan Zhou
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province 650500, China.
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Beyond Purple Tomatoes: Combined Strategies Targeting Anthocyanins to Generate Crimson, Magenta, and Indigo Fruit. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7090327] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The range of colours of many flowers and fruits is largely due to variations in the types of anthocyanins produced. The degree of hydroxylation on the B-ring affects the hue of these pigments, causing a shift from the orange end of the visible spectrum to the blue end. Besides colour, this modification can also affect other properties of anthocyanins, including the ability to protect the plant against different stresses or, when included in the human diet, to provide benefits for disease prevention. The level of hydroxylation of the B-ring is determined by the activity of two key hydroxylases, F3′H and F3′5′H, and by the substrate preference of DFR, an enzyme acting downstream in the biosynthetic pathway. We show that, in tomato, a strategy based on fruit-specific engineering of three regulatory genes (AmDel, AmRos1, AtMYB12) and a single biosynthetic gene (AmDFR), together with the availability of a specific mutation (f3′5′h), results in the generation of three different varieties producing high levels of anthocyanins with different levels of hydroxylation. These tomatoes show distinctive colours and mimic the classes of anthocyanins found in natural berries, thus providing unique near-isogenic material for different studies.
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Astuti G, Barone G, Di Gristina E, Domina G, Giacò A, Orsenigo S, Peruzzi L. Chromosome numbers for the Italian flora: 11. ITALIAN BOTANIST 2021. [DOI: 10.3897/italianbotanist.11.70173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this contribution, new chromosome data obtained on material collected in Italy are presented. It includes counts for Centaurea aegusae, Hieracium racemosum subsp. lucanum, H. australe subsp. australe, Lysimachia arvensis subsp. arvensis, Micromeria graeca subsp. graeca, and M. graeca subsp. consentina.
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Donadio G, Mensitieri F, Santoro V, Parisi V, Bellone ML, De Tommasi N, Izzo V, Dal Piaz F. Interactions with Microbial Proteins Driving the Antibacterial Activity of Flavonoids. Pharmaceutics 2021; 13:660. [PMID: 34062983 PMCID: PMC8147964 DOI: 10.3390/pharmaceutics13050660] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 12/14/2022] Open
Abstract
Flavonoids are among the most abundant natural bioactive compounds produced by plants. Many different activities have been reported for these secondary metabolites against numerous cells and systems. One of the most interesting is certainly the antimicrobial, which is stimulated through various molecular mechanisms. In fact, flavonoids are effective both in directly damaging the envelope of Gram-negative and Gram-positive bacteria but also by acting toward specific molecular targets essential for the survival of these microorganisms. The purpose of this paper is to present an overview of the most interesting results obtained in the research focused on the study of the interactions between flavonoids and bacterial proteins. Despite the great structural heterogeneity of these plant metabolites, it is interesting to observe that many flavonoids affect the same cellular pathways. Furthermore, it is evident that some of these compounds interact with more than one target, producing multiple effects. Taken together, the reported data demonstrate the great potential of flavonoids in developing innovative systems, which can help address the increasingly serious problem of antibiotic resistance.
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Affiliation(s)
- Giuliana Donadio
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (G.D.); (V.S.); (V.P.); (M.L.B.); (N.D.T.)
| | - Francesca Mensitieri
- Department of Medicine and Surgery, University of Salerno, 84082 Baronissi, Italy; (F.M.); (V.I.)
| | - Valentina Santoro
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (G.D.); (V.S.); (V.P.); (M.L.B.); (N.D.T.)
| | - Valentina Parisi
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (G.D.); (V.S.); (V.P.); (M.L.B.); (N.D.T.)
- PhD Program in Drug Discovery and Development, Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy
| | - Maria Laura Bellone
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (G.D.); (V.S.); (V.P.); (M.L.B.); (N.D.T.)
- PhD Program in Drug Discovery and Development, Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy
| | - Nunziatina De Tommasi
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (G.D.); (V.S.); (V.P.); (M.L.B.); (N.D.T.)
| | - Viviana Izzo
- Department of Medicine and Surgery, University of Salerno, 84082 Baronissi, Italy; (F.M.); (V.I.)
| | - Fabrizio Dal Piaz
- Department of Medicine and Surgery, University of Salerno, 84082 Baronissi, Italy; (F.M.); (V.I.)
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