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Perla Hamon - One of the best experts on this subject based on the ideXlab platform.
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WCSdb: a database of wild Coffea species.
Database : the journal of biological databases and curation, 2020Co-Authors: Romain Guyot, Perla Hamon, Emmanuel Couturon, Nathalie Raharimalala, Jean-jacques Rakotomalala, Sreenath Lakkanna, Sylvie-annabel Sabatier, Antoine Affouard, Pierre BonnetAbstract:Coffee is a beverage enjoyed by millions of people worldwide and an important commodity for millions of people. Beside the two cultivated species (Coffea arabica and Coffea canephora), the 139 wild coffee species/taxa belonging to the Coffea genus are largely unknown to coffee scientists and breeders although these species may be crucial for future coffee crop development to face climate changes. Here we present the Wild Coffee Species database (WCSdb) hosted by Pl@ntNet platform (http://publish.plantnet-project.org/project/wildcofdb_en), providing information for 141 coffee species/taxa, for which 84 contain a photo gallery and 82 contain sequencing data (genotyping-by-sequencing, chloroplast or whole genome sequences). The objective of this database is to better understand and characterize the species (identification, morphology, biochemical compounds, genetic diversity and sequence data) in order to better protect and promote them. Database url http://publish.plantnet-project.org/project/wildcofdb_en.
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Photo bank for: WCSdb: A database of Wild Coffea Species
2020Co-Authors: Romain Guyot, Perla Hamon, Emmanuel Couturon, Nathalie Raharimalala, Jean-jacques RakotomalalaAbstract:Coffee is a beverage enjoyed by millions of people worldwide and an important commodity for millions of people. Beside the two cultivated species (Coffea arabica and Coffea canephora), the 139 wild coffee species belong to the Coffea genus are largely unknown to coffee scientists and breeders although these species may be crucial for future coffee crop development to face climate changes. Here we present the Wild Coffee Species database hosted by PlantNet platform (http://publish.plantnet-project.org/project/wildcofdb_en), providing information for 140 coffee species, for which 84 contain a photo gallery and 82 contain sequencing data (GBS, chloroplast or whole genome sequences). The objective of this database is to better understand and characterize the species (identification, morphology, biochemical compounds, genetic diversity, sequence data) in order to better protect and promote them.
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Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species
PLoS ONE, 2019Co-Authors: Christophe Guyeux, Dominique Crouzillat, Romain Guyot, Jean Charr, Hue T Tran, Agnelo Furtado, Robert J Henry, Perla HamonAbstract:Chloroplast sequences are widely used for phylogenetic analysis due to their high degree of conservation in plants. Whole chloroplast genomes can now be readily obtained for plant species using new sequencing methods, giving invaluable data for plant evolution However new annotation methods are required for the efficient analysis of this data to deliver high quality phylogenetic analyses. In this study, the two main tools for chloroplast genome annotation were compared. More consistent detection and annotation of genes were produced with GeSeq when compared to the currently used Dogma. This suggests that the annotation of most of the previously annotated chloroplast genomes should now be updated. GeSeq was applied to species related to coffee, including 16 species of the Coffea and Psilanthus genera to reconstruct the ancestral chloroplast genomes and to evaluate their phylogenetic relationships. Eight genes in the plant chloroplast pan genome (consisting of 92 genes) were always absent in the coffee species analyzed. Notably, the two main cultivated coffee species (i.e. Arabica and Robusta) did not group into the same clade and differ in their pattern of gene evolution. While Arabica coffee (Coffea arabica) belongs to the Coffea genus, Robusta coffee (Coffea canephora) is associated with the Psilanthus genus. A more extensive survey of related species is required to determine if this is a unique attribute of Robusta coffee or a more widespread feature of coffee tree species.
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High genetic diversity of in situ and ex situ populations of Madagascan coffee species: further implications for the management of coffee genetic resources
Tree Genetics and Genomes, 2013Co-Authors: Domohina Andrianasolo, Jean-jacques Rakotomalala, Sylvie-annabel Sabatier, Serge Hamon, Aaron Davis, Norosoa Razafinarivo, Perla HamonAbstract:The genetic diversity of endemic Madagascan Coffea species has not received any considerable attention, despite the high extinction threat facing most of the species on the island. In order to address this shortfall, we assessed and compared the genetic diversity and allelic richness of ex situ and in situ populations for four selected species, and 18 ex situ populations maintained at the Kianjavato Coffee Research Station. We also investigated the possibility of in situ and ex situ hybridization events for Madagascan coffee, both within and between species. For these purposes, we used 18 nuclear microsatellite markers, on a total of 37 Coffea populations (4 in situ and 33 ex situ) representing a total of 398 genotypes (96 in situ and 302 ex situ) for 23 species. Our study showed (1) strong differentiation between Madagascan Coffea species; (2) good differentiation between all the populations studied, including those from the same locality (even when the area of the locality was restricted); (3) good evidence for both in situ and ex situ hybridization, although in situ hybridization appeared to be limited; (4) much higher genetic diversity within in situ collections compared to ex situ collections; and (5) that, despite limitations, the Kianjavato Coffee Research Station collection is an extremely valuable resource of Madagascan coffee germplasm. Recommendations for in situ and ex situ germplasm conservation are discussed
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Advances in Coffea Genomics
Advances in Botanical Research, 2010Co-Authors: A. De Kochko, Perla Hamon, Alan Carvalho Andrade, Dominique Crouzillat, Romain Guyot, Claudine Campa, Lukas A. Mueller, Sélastique Akaffou, Ray Ming, Valérie PoncetAbstract:Abstract Coffee is the second most valuable commodity exported by developing countries. The Coffea genus comprises over 103 species but coffee production uses only two species throughout the tropics: Coffea canephora, which is self-sterile and diploid and better known as Robusta, and C. arabica, which is self-fertile and tetraploid. With the arrival of new analytical technologies and the start of genome sequencing projects, it was clearly time to review the state of the art of coffee genetics and genomics. In the first part of this chapter, we present the main results concerning genetic diversity and phylogeny – the most advanced fields – based on large molecular marker sets, such as random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs), intersimple sequence repeat (ISSR), single sequence repeats (SSRs), or conserved orthologue set (COS), which are mainly polymerase chain reaction (PCR) based. These markers also enable the construction of genetic maps and the identification of quantitative trait loci (QTLs) for both morphological and biochemical traits. In the second part, after reviewing current knowledge on variation in coffee genome size and insights into cytogenetics, we focus on currently available genomic resources and web facilities. Large sets of expressed sequences tags (ESTs) and bacterial artificial chromosome (BAC) libraries for both C. canephora and C. arabica have been obtained along with information on genes and specific metabolic pathways. In the final section, we describe recently designed tools and their ultimate goal, which is to facilitate the sequencing, assembly and annotation of the first Coffea genome. We are at the gate of a new era of scientific approaches to coffee that should lead to a better understanding of phylogenetic relationships and genome evolution within the genus. Finally, taken together, this information should help develop improved varieties to meet the new challenges represented by ongoing radical changes in the environment.
Serge Hamon - One of the best experts on this subject based on the ideXlab platform.
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High genetic diversity of in situ and ex situ populations of Madagascan coffee species: further implications for the management of coffee genetic resources
Tree Genetics and Genomes, 2013Co-Authors: Domohina Andrianasolo, Jean-jacques Rakotomalala, Sylvie-annabel Sabatier, Serge Hamon, Aaron Davis, Norosoa Razafinarivo, Perla HamonAbstract:The genetic diversity of endemic Madagascan Coffea species has not received any considerable attention, despite the high extinction threat facing most of the species on the island. In order to address this shortfall, we assessed and compared the genetic diversity and allelic richness of ex situ and in situ populations for four selected species, and 18 ex situ populations maintained at the Kianjavato Coffee Research Station. We also investigated the possibility of in situ and ex situ hybridization events for Madagascan coffee, both within and between species. For these purposes, we used 18 nuclear microsatellite markers, on a total of 37 Coffea populations (4 in situ and 33 ex situ) representing a total of 398 genotypes (96 in situ and 302 ex situ) for 23 species. Our study showed (1) strong differentiation between Madagascan Coffea species; (2) good differentiation between all the populations studied, including those from the same locality (even when the area of the locality was restricted); (3) good evidence for both in situ and ex situ hybridization, although in situ hybridization appeared to be limited; (4) much higher genetic diversity within in situ collections compared to ex situ collections; and (5) that, despite limitations, the Kianjavato Coffee Research Station collection is an extremely valuable resource of Madagascan coffee germplasm. Recommendations for in situ and ex situ germplasm conservation are discussed
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Use of high-resolution satellite imagery in an integrated model to predict the distribution of shade coffee tree hybrid zones
Remote Sensing of Environment, 2010Co-Authors: Christine Gomez, A. De Kochko, Valérie Poncet, Serge Hamon, M. Mangeas, M. Petit, C. Corbane, D. Le Pierres, M. DespinoyAbstract:In New Caledonia (21 S, 165 E), shade-grown coffee plantations were abandoned for economic reasons in the middle of the 20th century. Coffee species (Coffee arabica, C canephora and C liberica) were introduced from Africa in the late 19th century, they survived in the wild and spontaneously cross-hybridized. Coffee species were originally planted in native forest in association with leguminous trees (mostly introduced species) to improve their growth. Thus the canopy cover over rustic shade coffee plantations is heterogeneous with a majority of large crowns, attributed to leguminous trees. The aim of this study was to identify suitable areas for coffee inter-specific hybridization in New Caledonia using field based environmental parameters and remotely sensed predictors. Due to the complex structure of tropical vegetation, remote sensing imagery needs to be spatially accurate and to have the appropriate bands for monitoring vegetation cover. Quickbird panchromatic (black and white) imagery at 0.6 to 0.7 m spatial resolutions and multispectral imagery at 2.4 m spatial resolution were pansharpened and used for this study. The two most suitable remotely sensed indicators, canopy heterogeneity and tree crown size, were acquired by the sequential use of tree crown detection (neural network), image processing (such as textural analysis) and classification. All models were supervised and trained on learning data determined by human expertise. The final model has two remotely sensed indicators and three physical parameters based on the Digital Elevation Model: elevation, slope and water flow accumulation. Using these five predictive variables as inputs, two modelling methods, a decision tree and a neural network, were implemented. The decision tree, which showed 96.9% accuracy on the test set, revealed the involvement of ecological parameters in the hybridization of Coffea species. We showed that hybrid zones could be characterized by combinations of modalities, underlining the complexity of the environment concerned. For instance, forest heterogeneity and large crown size, steep slopes (>53.5%) and elevation between 194 and 429 m asl, are favourable factors for Coffea inter-specific hybridization. The application of the neural network on the whole area gave a predictive map that distinguished the most suitable areas by means of a nonlinear continuous indicator. The map provides a confidence level for each area. The most favourable areas were geographically localized, providing a clue for the detection and conservation of favourable areas for Coffea species neo-diversity.
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Trigonelline and sucrose diversity in wild Coffea species
Food Chemistry, 2004Co-Authors: Claudine Campa, Stéphane Dussert, J.f. Ballester, Sylvie Doulbeau, Serge Hamon, M. NoirotAbstract:Trigonelline and sucrose are two coffee aroma precursors. Contents of these compounds are higher in Coffea arabica than in Coffea canephora green beans and this could be the main explanation for consumers' preference for C. arabica coffee. This is the first evaluation of sucrose and trigonelline contents involving 14 species and six new taxa not yet botanically characterised. Trigonelline and sucrose contents varied between species from 0.39% to 1.77% dry matter basis (dmb) and from 3.8% to 10.7% dmb, respectively. C. canephora could be improved through both compounds by crosses with Coffea eugenioides.
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Inheritance of coffee bean sucrose content in the interspecific cross Coffea pseudozanguebariae × Coffea liberica 'dewevrei'.
Plant Breeding, 2000Co-Authors: Sylvie Doulbeau, Bernard Guyot, André Charrier, Serge Hamon, Sélastique Akaffou, Jacques Louarn, Michel NoirotAbstract:The sucrose content of coffee bean is an important component of the coffee flavour: the higher the sucrose content in green beans, the more intense coffee cup flavour: Beans of the anciently cultivated cultivar Coffea liberica‘dewevrei’ have low levels of sucrose compared with beans of the wild species Coffea pseudozanguebariae. In the present study, the inheritance of the sucrose accumulation in the interspecific cross C. pseudozanguebariae×C. liberica‘dewevrei’ was examined. The sucrose content was measured in mature beans of both parental species, and in F1 and backcross hybrids using high-pressure liquid chromatography coupled to pulsed amperometric detection. The sucrose accumulation in all but one hybrid, showed genetic additivity. A segregation distortion was identified in the offspring of the backcross to C pseudozanguebariae. There was no year effect and only a low genotype × year interaction. Consequences for breeding, in relation to the coffee cup taste improvement, are discussed.
Jean-jacques Rakotomalala - One of the best experts on this subject based on the ideXlab platform.
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WCSdb: a database of wild Coffea species.
Database : the journal of biological databases and curation, 2020Co-Authors: Romain Guyot, Perla Hamon, Emmanuel Couturon, Nathalie Raharimalala, Jean-jacques Rakotomalala, Sreenath Lakkanna, Sylvie-annabel Sabatier, Antoine Affouard, Pierre BonnetAbstract:Coffee is a beverage enjoyed by millions of people worldwide and an important commodity for millions of people. Beside the two cultivated species (Coffea arabica and Coffea canephora), the 139 wild coffee species/taxa belonging to the Coffea genus are largely unknown to coffee scientists and breeders although these species may be crucial for future coffee crop development to face climate changes. Here we present the Wild Coffee Species database (WCSdb) hosted by Pl@ntNet platform (http://publish.plantnet-project.org/project/wildcofdb_en), providing information for 141 coffee species/taxa, for which 84 contain a photo gallery and 82 contain sequencing data (genotyping-by-sequencing, chloroplast or whole genome sequences). The objective of this database is to better understand and characterize the species (identification, morphology, biochemical compounds, genetic diversity and sequence data) in order to better protect and promote them. Database url http://publish.plantnet-project.org/project/wildcofdb_en.
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Photo bank for: WCSdb: A database of Wild Coffea Species
2020Co-Authors: Romain Guyot, Perla Hamon, Emmanuel Couturon, Nathalie Raharimalala, Jean-jacques RakotomalalaAbstract:Coffee is a beverage enjoyed by millions of people worldwide and an important commodity for millions of people. Beside the two cultivated species (Coffea arabica and Coffea canephora), the 139 wild coffee species belong to the Coffea genus are largely unknown to coffee scientists and breeders although these species may be crucial for future coffee crop development to face climate changes. Here we present the Wild Coffee Species database hosted by PlantNet platform (http://publish.plantnet-project.org/project/wildcofdb_en), providing information for 140 coffee species, for which 84 contain a photo gallery and 82 contain sequencing data (GBS, chloroplast or whole genome sequences). The objective of this database is to better understand and characterize the species (identification, morphology, biochemical compounds, genetic diversity, sequence data) in order to better protect and promote them.
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Complex evolutionary history of coffees revealed by full plastid genomes and 28,800 nuclear SNP analyses, with particular emphasis on Coffea canephora (Robusta coffee)
Molecular Phylogenetics and Evolution, 2020Co-Authors: Jean Charr, Dominique Crouzillat, Christophe Guyeux, Piet Stoffelen, Jean-jacques Rakotomalala, Andrea Garavito, Patrick Descombes, Coralie Fournier, Eva Raharimalala, Steven JanssensAbstract:For decades coffees were associated with the genus Coffea. In 2011, the closely related genus Psilanthus was subsumed into Coffea. However, results obtained in 2017-based on 28,800 nuclear SNPs-indicated that there is not substantial phylogenetic support for this incorporation. In addition, a recent study of 16 plastid fullgenome sequences highlighted an incongruous placement of Coffea canephora (Robusta coffee) between maternal and nuclear trees. In this study, similar global features of the plastid genomes of Psilanthus and Coffea are observed. In agreement with morphological and physiological traits, the nuclear phylogenetic tree clearly separates Psilanthus from Coffea (with exception to C. rhamnifolia, closer to Psilanthus than to Coffea). In contrast, the maternal molecular tree was incongruent with both morphological and nuclear differentiation, with four main clades observed, two of which include both Psilanthus and Coffea species, and two with either Psilanthus or Coffea species. Interestingly, Coffea and Psilanthus taxa sampled in West and Central Africa are members of the same group. Several mechanisms such as the retention of ancestral polymorphisms due to incomplete lineage sorting, hybridization leading to homoploidy (without chromosome doubling) and alloploidy (for C. arabica) are involved in the evolutionary history of the coffee species. While sharing similar morphological characteristics, the genetic relationships within C. canephora have shown that some populations are well differentiated and genetically isolated. Given the position of its closely-related species, we may also consider C. canephora to be undergoing a long process of speciation with an intermediate step of (sub-)speciation.
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High genetic diversity of in situ and ex situ populations of Madagascan coffee species: further implications for the management of coffee genetic resources
Tree Genetics and Genomes, 2013Co-Authors: Domohina Andrianasolo, Jean-jacques Rakotomalala, Sylvie-annabel Sabatier, Serge Hamon, Aaron Davis, Norosoa Razafinarivo, Perla HamonAbstract:The genetic diversity of endemic Madagascan Coffea species has not received any considerable attention, despite the high extinction threat facing most of the species on the island. In order to address this shortfall, we assessed and compared the genetic diversity and allelic richness of ex situ and in situ populations for four selected species, and 18 ex situ populations maintained at the Kianjavato Coffee Research Station. We also investigated the possibility of in situ and ex situ hybridization events for Madagascan coffee, both within and between species. For these purposes, we used 18 nuclear microsatellite markers, on a total of 37 Coffea populations (4 in situ and 33 ex situ) representing a total of 398 genotypes (96 in situ and 302 ex situ) for 23 species. Our study showed (1) strong differentiation between Madagascan Coffea species; (2) good differentiation between all the populations studied, including those from the same locality (even when the area of the locality was restricted); (3) good evidence for both in situ and ex situ hybridization, although in situ hybridization appeared to be limited; (4) much higher genetic diversity within in situ collections compared to ex situ collections; and (5) that, despite limitations, the Kianjavato Coffee Research Station collection is an extremely valuable resource of Madagascan coffee germplasm. Recommendations for in situ and ex situ germplasm conservation are discussed
M. Noirot - One of the best experts on this subject based on the ideXlab platform.
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Trigonelline and sucrose diversity in wild Coffea species
Food Chemistry, 2004Co-Authors: Claudine Campa, Stéphane Dussert, J.f. Ballester, Sylvie Doulbeau, Serge Hamon, M. NoirotAbstract:Trigonelline and sucrose are two coffee aroma precursors. Contents of these compounds are higher in Coffea arabica than in Coffea canephora green beans and this could be the main explanation for consumers' preference for C. arabica coffee. This is the first evaluation of sucrose and trigonelline contents involving 14 species and six new taxa not yet botanically characterised. Trigonelline and sucrose contents varied between species from 0.39% to 1.77% dry matter basis (dmb) and from 3.8% to 10.7% dmb, respectively. C. canephora could be improved through both compounds by crosses with Coffea eugenioides.
Reginald H. Wilson - One of the best experts on this subject based on the ideXlab platform.
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Discrimination of Arabica and Robusta in instant coffee by Fourier transform infrared spectroscopy and chemometrics
Journal of Agricultural and Food Chemistry, 1996Co-Authors: Romain Briandet, E. Katherine Kemsley, Reginald H. WilsonAbstract:Two species of coffee bean have acquired worldwide economic importance: these are, Coffea Arabica and Coffea Canephora variant Robusta. Arabica beans are valued most highly by the trade, as they are considered to have a finer flavor than Robusta. In this work, Fourier transform infrared spectroscopy is explored as a rapid alternative to wet chemical methods for authentication and quantification of coffee products. Principal component analysis (PCA) is applied to spectra of freeze-dried instant coffees, acquired by DRIFT (diffuse reflection infrared Fourier transform) and ATR (attenuated total reflection) sampling techniques, and reveals clustering according to coffee species. Linear discriminant analysis of the principal component scores yields 100% correct classifications for both training and test samples. The chemical origin of the discrimination is explored through interpretation of the PCA loadings. Partial least squares regression is applied to spectra of Arabica and Robusta blends to determine the relative content of each species. Internal cross-validation gives a correlation coefficient of 0.99 and a standard error of prediction of 1.20% (w/w), illustrating the potential of the method for industrial off-line quality control analysis.
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Discrimination between Coffea arabica and Coffea canephora variant robusta beans using infrared spectroscopy
Food Chemistry, 1995Co-Authors: E.k. Kemsley, S Ruault, Reginald H. WilsonAbstract:The seed or ‘bean’ of the coffee plant is an important crop, grown commercially across the world. Two species are commonly cultivated: Coffea arabica and Coffea canephora variant robusta. Analytical techniques for species identification, in particular of coffee products such as ground or ‘instant’ coffees, are of great importance. In this paper, mid-infrared spectroscopy is proposed as a rapid alternative to existing authentication methods, which are often time-consuming or difficult to implement successfully. A Fourier-transform infrared spectrometer is used for this work, equipped with a diffuse reflectance accessory. Statistical procedures comprising principal components analysis and classical discriminant analysis are applied to spectra of ground roast arabica and robusta beans, and results presented which demonstrate that the species of such samples can readily be identified.