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Article: Mozambican

Navarini, Luciano / Scaglione, Davide / Del Terra, Lorenzo / Scalabrin, Simone / Mavuque, Lopes / Turello, Luca / Nguenha, Rafael / Luongo, Gianluca

AoB PLANTS

2024 Volume 16, Issue 2, Page(s) plae004

Abstract: Mozambique does not have a tradition of ... ...

Abstract	Mozambique does not have a tradition of farming
Language	English
Publishing date	2024-02-06
Publishing country	England
Document type	Journal Article
ZDB-ID	2555823-7
ISSN	2041-2851
ISSN	2041-2851
DOI	10.1093/aobpla/plae004
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Article: The oleosin gene family in coffee: Analysis of oleosomes, oleosins and lipid-related gene expression during germination of Coffea arabica seeds

Marin, Veronica / Del Terra, Lorenzo / Crisafulli, Paola / Navarini, Luciano

Plant gene. 2020 Dec., v. 24

2020

Abstract: Little information is available about lipid metabolism in Coffea arabica L. seeds, which have an oil content between 11 and 16% w/w. This is surprising given the involvement of lipids in the physical, chemical, and physiological properties of the coffee ... ...

Abstract	Little information is available about lipid metabolism in Coffea arabica L. seeds, which have an oil content between 11 and 16% w/w. This is surprising given the involvement of lipids in the physical, chemical, and physiological properties of the coffee beverage. To shed light on this subject, freshly harvested C. arabica seeds were sampled at different stages of germination. Oleosomes (the organelles responsible for lipid storage) were extracted and their structure was observed by differential interference-contrast microscopy. Triacylglycerol content of oleosomes was analyzed by thin-layer chromatography, and the protein fraction was evaluated by gel electrophoresis. A review of available genomic data on oleosin and lipase genes was performed, and expression of genes related to lipid metabolism was measured by Real-Time PCR.The results drew a coherent picture of coffee seed germination, revealing that oleosins have the highest concentration after 14 days of germination, followed by a marked decrease. This was backed up by molecular observations, showing how oleosin genes were downregulated after 6–9 days of germination, while genes related to lipid degradation were upregulated from day 9 onwards. Morphological evidence supported these findings, as after 14 days embryo growth became significant and cotyledons started to invade the endosperm and metabolize seed reserves. The present research will be an important first step in better understanding the biology of oleosomes in Coffea arabica L. and in elucidating the role of lipid metabolism in green coffee quality.
Keywords	Coffea arabica ; carboxylic ester hydrolases ; coffee (beverage) ; endosperm ; gel electrophoresis ; gene expression ; genes ; genomics ; lipid bodies ; lipid content ; lipid metabolism ; microscopy ; oleosin ; seed germination ; thin layer chromatography ; triacylglycerols
Language	English
Dates of publication	2020-12
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-AP-2-clean
ISSN	2352-4073
DOI	10.1016/j.plgene.2020.100263
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm.

Scalabrin, Simone / Magris, Gabriele / Liva, Mario / Vitulo, Nicola / Vidotto, Michele / Scaglione, Davide / Del Terra, Lorenzo / Ruosi, Manuela Rosanna / Navarini, Luciano / Pellegrino, Gloria / Berny Mier Y Teran, Jorge Carlos / Toniutti, Lucile / Suggi Liverani, Furio / Cerutti, Mario / Di Gaspero, Gabriele / Morgante, Michele

Nature communications

2024 Volume 15, Issue 1, Page(s) 463

Abstract: In order to better understand the mechanisms generating genetic diversity in the recent allotetraploid species Coffea arabica, here we present a chromosome-level assembly obtained with long read technology. Two genomic compartments with different ... ...

Abstract	In order to better understand the mechanisms generating genetic diversity in the recent allotetraploid species Coffea arabica, here we present a chromosome-level assembly obtained with long read technology. Two genomic compartments with different structural and functional properties are identified in the two homoeologous genomes. The resequencing data from a large set of accessions reveals low intraspecific diversity in the center of origin of the species. Across a limited number of genomic regions, diversity increases in some cultivated genotypes to levels similar to those observed within one of the progenitor species, Coffea canephora, presumably as a consequence of introgressions deriving from the so-called Timor hybrid. It also reveals that, in addition to few, early-occurring exchanges between homoeologous chromosomes, there are numerous recent chromosomal aberrations including aneuploidies, deletions, duplications and exchanges. These events are still polymorphic in the germplasm and could represent a fundamental source of genetic variation in such a lowly variable species.
MeSH term(s)	Coffea ; Chromosome Aberrations ; Aneuploidy ; Genomics ; Chromosomes
Language	English
Publishing date	2024-01-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-44449-8
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Article ; Online: Aquaporins in Coffea arabica L.: Identification, expression, and impacts on plant water relations and hydraulics.

Miniussi, Matilda / Del Terra, Lorenzo / Savi, Tadeja / Pallavicini, Alberto / Nardini, Andrea

Plant physiology and biochemistry : PPB

2015 Volume 95, Page(s) 92–102

Abstract: Plant aquaporins (AQPs) are involved in the transport of water and other small solutes across cell membranes, and thus play major roles in the regulation of plant water balance, as well as in growth regulation and response to abiotic stress factors. ... ...

Abstract	Plant aquaporins (AQPs) are involved in the transport of water and other small solutes across cell membranes, and thus play major roles in the regulation of plant water balance, as well as in growth regulation and response to abiotic stress factors. Limited information is currently available about the presence and role of AQPs in Coffea arabica L., despite the economic importance of the species and its vulnerability to drought stress. We identified candidate AQP genes by screening a proprietary C. arabica transcriptome database, resulting in the identification of nine putative aquaporins. A phylogenetic analysis based on previously characterized AQPs from Arabidopsis thaliana and Solanum tuberosum allowed to assign the putative coffee AQP sequences to the Tonoplast (TIP) and Plasma membrane (PIP) subfamilies. The possible functional role of coffee AQPs was explored by measuring hydraulic conductance and aquaporin gene expression on leaf and root tissues of two-year-old plants (C. arabica cv. Pacamara) subjected to different experimental conditions. In a first experiment, we tested plants for root and leaf hydraulic conductance both before dawn and at mid-day, to check the eventual impact of light on AQP activity and plant hydraulics. In a second experiment, we measured plant hydraulic responses to different water stress levels as eventually affected by changes in AQPs expression levels. Our results shed light on the possible roles of AQPs in the regulation of C. arabica hydraulics and water balance, opening promising research lines to improve the sustainability of coffee cultivation under global climate change scenarios.
MeSH term(s)	Aquaporins/biosynthesis ; Aquaporins/genetics ; Arabidopsis/genetics ; Arabidopsis/metabolism ; Coffea/genetics ; Coffea/metabolism ; Gene Expression Regulation, Plant/physiology ; Phylogeny ; Plant Proteins/biosynthesis ; Plant Proteins/genetics ; Solanum tuberosum/genetics ; Solanum tuberosum/metabolism
Chemical Substances	Aquaporins ; Plant Proteins
Language	English
Publishing date	2015-07-26
Publishing country	France
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	742978-2
ISSN	1873-2690 ; 0981-9428
ISSN (online)	1873-2690
ISSN	0981-9428
DOI	10.1016/j.plaphy.2015.07.024
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Article: Functional characterization of three Coffea arabica L. monoterpene synthases: Insights into the enzymatic machinery of coffee aroma

Del Terra, Lorenzo / Alberto Pallavicini / Elisa Asquini / Furio Suggi Liverani / Giorgio Graziosi / Luciano Navarini / Valentina Lonzarich

Phytochemistry. 2013 May, v. 89

2013

Abstract: The chemical composition of the coffee beverage is extremely complex, being made up of hundreds of volatile and non-volatile compounds, many of which are generated in the thermal reactions that occur during the roasting process. However, in the raw ... ...

Abstract	The chemical composition of the coffee beverage is extremely complex, being made up of hundreds of volatile and non-volatile compounds, many of which are generated in the thermal reactions that occur during the roasting process. However, in the raw coffee bean there are also compounds that survive roasting and are therefore extracted into the beverage. Monoterpenes are an example of this category, as their presence has been reported in the coffee flower, fruit, seed, roasted bean and in the beverage aroma.The present work describes the isolation, heterologous expression and functional characterization of three Coffea arabica cDNAs coding for monoterpene synthases. RNA was purified from C. arabica (cv. Catuai Red) flowers, seeds and fruits at 4 successive ripening stages. Degenerate primers were designed on the most conserved regions of the monoterpene synthase gene family, and then used to isolate monoterpene synthase-like sequences from the cDNA libraries. After 5′- and 3′-RACE, the complete transcripts of 4 putative C. arabica monoterpene synthases (CofarTPS) were obtained. Gene expression in different tissues and developmental stages was analysed. After heterologous expression in Escherichia coli, enzyme activity and substrate specificity were evaluated in vitro by incubation of the recombinant proteins with geranyl pyrophosphate (GPP), geranylgeranyl pyrophosphate (GGPP) and farnesyl pyrophosphate (FPP), precursors respectively of mono-, di- and sesquiterpenes. The reaction products were characterized by HS-SPME GC–MS. CofarTPS1 was classified as a limonene synthase gene, while CofarTPS2 and 3 showed lower activity with the production of linalool and β-myrcene.
MeSH term(s)	Amino Acid Sequence ; Biocatalysis ; Cloning, Molecular ; Coffea/chemistry/enzymology/genetics ; DNA, Complementary/genetics ; Gene Expression Regulation, Plant ; Intramolecular Lyases/chemistry/genetics/isolation & purification/metabolism ; Molecular Sequence Data ; Odors/analysis
Keywords	beans ; cDNA libraries ; chemical composition ; Coffea arabica ; coffee (beverage) ; coffee beans ; complementary DNA ; developmental stages ; enzyme activity ; Escherichia coli ; flowers ; fruits ; gas chromatography ; gene expression ; genes ; linalool ; mass spectrometry ; odors ; recombinant proteins ; ripening ; RNA ; roasting ; seeds ; sesquiterpenoids ; substrate specificity
Language	English
Dates of publication	2013-05
Size	p. 6-14.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	208884-8
ISSN	1873-3700 ; 0031-9422
ISSN (online)	1873-3700
ISSN	0031-9422
DOI	10.1016/j.phytochem.2013.01.005
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Article ; Online: Lipase activity and antioxidant capacity in coffee (Coffea arabica L.) seeds during germination.

Patui, Sonia / Clincon, Luisa / Peresson, Carlo / Zancani, Marco / Conte, Lanfranco / Del Terra, Lorenzo / Navarini, Luciano / Vianello, Angelo / Braidot, Enrico

Plant science : an international journal of experimental plant biology

2014 Volume 219-220, Page(s) 19–25

Abstract: In this paper, lipase activity was characterized in coffee (Coffea arabica L.) seeds to determine its involvement in lipid degradation during germination. The lipase activity, evaluated by a colorimetric method, was already present before imbibition of ... ...

Abstract	In this paper, lipase activity was characterized in coffee (Coffea arabica L.) seeds to determine its involvement in lipid degradation during germination. The lipase activity, evaluated by a colorimetric method, was already present before imbibition of seeds and was further induced during the germination process. The activity showed a biphasic behaviour, which was similar in seeds either with or without endocarp (parchment), even though the phenomenon showed a delay in the former. The enzymatic activity was inhibited by tetrahydrolipstatin (THL), a selective and irreversible inhibitor of lipases, and by a polyclonal antibody raised against purified alkaline lipase from castor bean. The immunochemical analysis evidenced a protein of ca. 60 kDa, cross-reacting with an anti-lipase antibody, in coffee samples obtained from seeds of both types. Gas chromatographic analyses of free fatty acid (FFA) content confirmed the differences shown in the lipolytic activity of the samples with or without parchment, since FFA levels increased more rapidly in samples without parchment. Finally, the analyses of the antioxidant capacity showed that the presence of parchment was crucial for lowering the oxidation of the lipophylic fraction, being the seeds with parchment less prone to oxidation processes.
MeSH term(s)	Antioxidants/metabolism ; Chromatography, Gas ; Coffea/enzymology ; Germination ; Lipase/metabolism ; Lipid Metabolism ; Plant Proteins/metabolism ; Seeds/enzymology
Chemical Substances	Antioxidants ; Plant Proteins ; Lipase (EC 3.1.1.3)
Language	English
Publishing date	2014-01-03
Publishing country	Ireland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	742010-9
ISSN	1873-2259 ; 0168-9452
ISSN (online)	1873-2259
ISSN	0168-9452
DOI	10.1016/j.plantsci.2013.12.014
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Article ; Online: Functional characterization of three Coffea arabica L. monoterpene synthases: insights into the enzymatic machinery of coffee aroma.

Del Terra, Lorenzo / Lonzarich, Valentina / Asquini, Elisa / Navarini, Luciano / Graziosi, Giorgio / Suggi Liverani, Furio / Pallavicini, Alberto

Phytochemistry

2013 Volume 89, Page(s) 6–14

Abstract	The chemical composition of the coffee beverage is extremely complex, being made up of hundreds of volatile and non-volatile compounds, many of which are generated in the thermal reactions that occur during the roasting process. However, in the raw coffee bean there are also compounds that survive roasting and are therefore extracted into the beverage. Monoterpenes are an example of this category, as their presence has been reported in the coffee flower, fruit, seed, roasted bean and in the beverage aroma. The present work describes the isolation, heterologous expression and functional characterization of three Coffea arabica cDNAs coding for monoterpene synthases. RNA was purified from C. arabica (cv. Catuai Red) flowers, seeds and fruits at 4 successive ripening stages. Degenerate primers were designed on the most conserved regions of the monoterpene synthase gene family, and then used to isolate monoterpene synthase-like sequences from the cDNA libraries. After 5'- and 3'-RACE, the complete transcripts of 4 putative C. arabica monoterpene synthases (CofarTPS) were obtained. Gene expression in different tissues and developmental stages was analysed. After heterologous expression in Escherichia coli, enzyme activity and substrate specificity were evaluated in vitro by incubation of the recombinant proteins with geranyl pyrophosphate (GPP), geranylgeranyl pyrophosphate (GGPP) and farnesyl pyrophosphate (FPP), precursors respectively of mono-, di- and sesquiterpenes. The reaction products were characterized by HS-SPME GC-MS. CofarTPS1 was classified as a limonene synthase gene, while CofarTPS2 and 3 showed lower activity with the production of linalool and β-myrcene.
MeSH term(s)	Amino Acid Sequence ; Biocatalysis ; Cloning, Molecular ; Coffea/chemistry ; Coffea/enzymology ; Coffea/genetics ; DNA, Complementary/genetics ; Gene Expression Regulation, Plant ; Intramolecular Lyases/chemistry ; Intramolecular Lyases/genetics ; Intramolecular Lyases/isolation & purification ; Intramolecular Lyases/metabolism ; Molecular Sequence Data ; Odorants/analysis
Chemical Substances	DNA, Complementary ; Intramolecular Lyases (EC 5.5.-) ; pinene cyclase I (EC 5.5.-)
Language	English
Publishing date	2013-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208884-8
ISSN	1873-3700 ; 0031-9422
ISSN (online)	1873-3700
ISSN	0031-9422
DOI	10.1016/j.phytochem.2013.01.005
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Article ; Online: A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm.

Scalabrin, Simone / Toniutti, Lucile / Di Gaspero, Gabriele / Scaglione, Davide / Magris, Gabriele / Vidotto, Michele / Pinosio, Sara / Cattonaro, Federica / Magni, Federica / Jurman, Irena / Cerutti, Mario / Suggi Liverani, Furio / Navarini, Luciano / Del Terra, Lorenzo / Pellegrino, Gloria / Ruosi, Manuela Rosanna / Vitulo, Nicola / Valle, Giorgio / Pallavicini, Alberto /

Graziosi, Giorgio / Klein, Patricia E / Bentley, Nolan / Murray, Seth / Solano, William / Al Hakimi, Amin / Schilling, Timothy / Montagnon, Christophe / Morgante, Michele / Bertrand, Benoit

Scientific reports

2020 Volume 10, Issue 1, Page(s) 4642

Abstract: The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in ... ...

Abstract	The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma's D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors.
MeSH term(s)	Coffea/genetics ; Coffea/growth & development ; Costa Rica ; Crops, Agricultural/genetics ; Crops, Agricultural/growth & development ; Genome Size ; Genome, Plant ; Polymorphism, Single Nucleotide ; Tetraploidy ; Whole Genome Sequencing/methods ; Yemen
Language	English
Publishing date	2020-03-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-61216-7
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Article: Differential responses of Coffea arabica L. leaves and roots to chemically induced systemic acquired resistance.

De Nardi, Barbara / Dreos, René / Del Terra, Lorenzo / Martellossi, Chiara / Asquini, Elisa / Tornincasa, Patrizia / Gasperini, Debora / Pacchioni, Beniamina / Rathinavelu, Rajkumar / Pallavicini, Alberto / Graziosi, Giorgio

Genome

2006 Volume 49, Issue 12, Page(s) 1594–1605

Abstract: Coffea arabica is susceptible to several pests and diseases, some of which affect the leaves and roots. Systemic acquired resistance (SAR) is the main defence mechanism activated in plants in response to pathogen attack. Here, we report the effects of ... ...

Abstract	Coffea arabica is susceptible to several pests and diseases, some of which affect the leaves and roots. Systemic acquired resistance (SAR) is the main defence mechanism activated in plants in response to pathogen attack. Here, we report the effects of benzo(1,2,3)thiadiazole-7-carbothioic acid-S-methyl ester (BTH), a SAR chemical inducer, on the expression profile of C. arabica. Two cDNA libraries were constructed from the mRNA isolated from leaves and embryonic roots to create 1587 nonredundant expressed sequence tags (ESTs). We developed a cDNA microarray containing 1506 ESTs from the leaves and embryonic roots, and 48 NBS-LRR (nucleotide-binding site leucine-rich repeat) gene fragments derived from 2 specific genomic libraries. Competitive hybridization between untreated and BTH-treated leaves resulted in 55 genes that were significantly overexpressed and 16 genes that were significantly underexpressed. In the roots, 37 and 42 genes were over and underexpressed, respectively. A general shift in metabolism from housekeeping to defence occurred in the leaves and roots after BTH treatment. We observed a systemic increase in pathogenesis-related protein synthesis, in the oxidative burst, and in the cell wall strengthening processes. Moreover, responses in the roots and leaves varied significantly.
MeSH term(s)	Coffea/drug effects ; Coffea/genetics ; Coffea/immunology ; Expressed Sequence Tags ; Gene Expression Regulation, Plant/drug effects ; Genes, Plant/physiology ; Immunity, Innate/drug effects ; Immunity, Innate/genetics ; Oligonucleotide Array Sequence Analysis ; Plant Leaves/drug effects ; Plant Leaves/genetics ; Plant Roots/drug effects ; Plant Roots/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Thiadiazoles/pharmacology
Chemical Substances	Thiadiazoles ; S-methyl benzo(1,2,3)thiadiazole-7-carbothioate (BCW6119347)
Language	English
Publishing date	2006-12
Publishing country	Canada
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639031-6
ISSN	1480-3321 ; 0831-2796
ISSN (online)	1480-3321
ISSN	0831-2796
DOI	10.1139/g06-125
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Article: Functional characterization of three Coffea arabica L. monoterpene synthases: Insights into the enzymatic machinery of coffee aroma

Del Terra, Lorenzo / Lonzarich, Valentina / Asquini, Elisa / Navarini, Luciano / Graziosi, Giorgio / Suggi Liverani, Furio / Pallavicini, Alberto

Phytochemistry

Volume v. 89

Abstract	The chemical composition of the coffee beverage is extremely complex, being made up of hundreds of volatile and non-volatile compounds, many of which are generated in the thermal reactions that occur during the roasting process. However, in the raw coffee bean there are also compounds that survive roasting and are therefore extracted into the beverage. Monoterpenes are an example of this category, as their presence has been reported in the coffee flower, fruit, seed, roasted bean and in the beverage aroma. The present work describes the isolation, heterologous expression and functional characterization of three Coffea arabica cDNAs coding for monoterpene synthases. RNA was purified from C. arabica (cv. Catuai Red) flowers, seeds and fruits at 4 successive ripening stages. Degenerate primers were designed on the most conserved regions of the monoterpene synthase gene family, and then used to isolate monoterpene synthase-like sequences from the cDNA libraries. After 5′- and 3′-RACE, the complete transcripts of 4 putative C. arabica monoterpene synthases (CofarTPS) were obtained. Gene expression in different tissues and developmental stages was analysed. After heterologous expression in Escherichia coli, enzyme activity and substrate specificity were evaluated in vitro by incubation of the recombinant proteins with geranyl pyrophosphate (GPP), geranylgeranyl pyrophosphate (GGPP) and farnesyl pyrophosphate (FPP), precursors respectively of mono-, di- and sesquiterpenes. The reaction products were characterized by HS-SPME GC–MS. CofarTPS1 was classified as a limonene synthase gene, while CofarTPS2 and 3 showed lower activity with the production of linalool and β-myrcene.
Keywords	genes ; odors ; developmental stages ; gas chromatography ; sesquiterpenoids ; roasting ; beans ; enzyme activity ; Escherichia coli ; seeds ; flowers ; coffee (beverage) ; chemical composition ; linalool ; substrate specificity ; coffee beans ; ripening ; fruits ; recombinant proteins ; RNA ; mass spectrometry ; complementary DNA ; cDNA libraries ; gene expression ; Coffea arabica
Language	English
Document type	Article
ISSN	0031-9422
Database	AGRIS - International Information System for the Agricultural Sciences and Technology

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