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PLoS ONE 01/2013; 8(2). · 4.09 Impact Factor
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Angélique D'Hont,
France Denoeud,
Jean-Marc Aury,
Franc-Christophe Baurens,
Françoise Carreel,
Olivier Garsmeur,
Benjamin Noel,
Stéphanie Bocs,
Gaëtan Droc,
Mathieu Rouard, [......],
Mouna Jeridi,
Jaroslav Dolezel,
Nicolas Roux, Ange-Marie Risterucci,
Jean Weissenbach,
Manuel Ruiz,
Jean-Christophe Glaszmann,
Francis Quétier,
Nabila Yahiaoui,
Patrick Wincker
[show abstract]
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ABSTRACT: Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish). Pests and diseases have gradually become adapted, representing an imminent danger for global banana production. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon-eudicotyledon divergence.
Nature 07/2012; 488(7410):213-7. · 36.28 Impact Factor
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Claire Billot,
Ronan Rivallan,
Mbaye Ndoye Sall,
Daniel Fonceka,
Monique Deu,
Jean-Christophe Glaszmann,
Jean-Louis Noyer,
Jean-François Rami, Ange-Marie Risterucci,
Patrick Wincker,
Puna Ramu,
Charles T Hash
[show abstract]
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ABSTRACT: • Premise of the study: Discrepancies in terms of genotyping data are frequently observed when comparing simple sequence repeat (SSR) data sets across genotyping technologies and laboratories. This technical concern introduces biases that hamper any synthetic studies or comparison of genetic diversity between collections. To prevent this for Sorghum bicolor, we developed a control kit of 48 SSR markers. • Methods and Results: One hundred seventeen markers were selected along the genome to provide coverage across the length of all 10 sorghum linkage groups. They were tested for polymorphism and reproducibility across two laboratories (Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement [CIRAD], France, and International Crops Research Institute for the Semi-Arid Tropics [ICRISAT], India) using two commonly used genotyping technologies (polyacrylamide gel-based technology with LI-COR sequencing machines and capillary systems with ABI sequencing apparatus) with DNA samples from a diverse set of 48 S. bicolor accessions. • Conclusions: A kit for diversity analysis (http://sat.cirad.fr/sat/sorghum_SSR_kit/) was developed. It contains information on 48 technically robust sorghum microsatellite markers and 10 DNA controls. It can further be used to calibrate sorghum SSR genotyping data acquired with different technologies and compare those to genetic diversity references.
American Journal of Botany 05/2012; 99(6):e245-50. · 2.66 Impact Factor
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Olivier Fouet,
Mathilde Allegre,
Xavier Argout,
Mélanie Jeanneau,
Arnaud Lemainque,
Sylvana Pavek,
Anne Boland, Ange Marie Risterucci,
Gaston Loor,
Mathias Tahi,
Xavier Sabau,
Brigitte Courtois,
Claire Lanaud
[show abstract]
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ABSTRACT: Theobroma cacao L. is a major cash crop for tropical countries, providing incomes for 14 million small farmers. Establishing sustainable
disease resistance and maintaining cocoa qualities are among the major objectives of breeding programs. To enrich the high-density
genetic map, useful for all cocoa genetic studies, with gene-based markers, a recently produced large EST resource was mined
to develop expressed sequence tag-based simple sequence repeat markers (EST-SSRs) defined in genes with a putative known function.
A set of 174 polymorphic EST-SSRs was identified from a selection of 314 non-redundant EST-SSRs with a putative known function.
Of them, 115 loci were mapped on the cocoa reference map. This new map contains 582 codominant markers arranged in ten linkage
groups corresponding to the haploid number of chromosomes. An average interval between markers of 1.3cM was found, with approximately
one SSR every 2cM. This new set of EST-SSRs includes 14 candidate genes for plant resistance or cocoa qualities. The percentage
of polymorphic SSRs varied depending on the different gene regions from which they originated, with respectively 54%, 69%,
and 82% of polymorphic EST-SSRs originating from coding sequences, and from the non-coding untranslated 5′UTR and 3′UTR regions.
This new map contains a set of 384 SSR markers that are easily transferable across different mapping populations and useful
for all genetic analyses in T. cacao. The new set of EST-SSRs will be a useful tool for studying the functional diversity of populations and for carrying out
association mapping studies.
Keywords
Theobroma cacao
–EST-SSR–Genetic map–Candidate genes
Tree Genetics & Genomes 04/2012; 7(4):799-817. · 2.34 Impact Factor
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Maria Marcano,
Sonia Morales,
Maria Theresa Hoyer,
Brigitte Courtois, Ange Marie Risterucci,
Olivier Fouet,
Tatiana Pugh,
Emile Cros,
Ventura Gonzalez,
Manuel Dagert,
Claire Lanaud
[show abstract]
[hide abstract]
ABSTRACT: The selection of productive varieties of modern Criollo cocoa, showing fine aromatic qualities in their beans, is of major
interest for some producing countries, such as Venezuela. Cultivated populations of Modern Criollo or Trinitario varieties
may be suitable for admixture mapping analysis, as large blocks of alleles derived from two identified divergent ancestors,
recently admixed, are still preserved, after a few generations of recombination, similar to experimental mapping progenies.
Two hundred and fifty-seven individuals from a cultivated population of Modern Criollo were selected and analysed with 92
microsatellite markers distributed along the genome. This population exhibited a wide range of variability for yield factors
and morphological features. Population structure analysis identified two main subgroups corresponding to the admixture from
the two ancestors Criollo and Forastero. Several significant associations between markers and phenotypic data (yield factors
and morphological traits) were identified by a least squares general linear model (GLM) taking into account the population
structure and the percentage of admixture of each individual. Results were compared with classical QTL analyses previously
reported for other cacao populations. Most markers associated to quantitative traits were very close to QTLs detected formerly
for the same traits. Associations were also identified between markers and several qualitative traits including the red pigmentation
observed in different organs, mainly associated to common markers in linkage group 4.
Tree Genetics & Genomes 04/2012; 5(2):329-337. · 2.34 Impact Factor
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[show abstract]
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ABSTRACT: Ecuador's economic history has been closely linked to Theobroma cacao L cultivation, and specifically to the native fine flavour Nacional cocoa variety. The original Nacional cocoa trees are presently in danger of extinction due to foreign germplasm introductions. In a previous work, a few non-introgressed Nacional types were identified as potential founders of the modern Ecuadorian cocoa population, but so far their origin could not be formally identified. In order to determine the putative centre of origin of Nacional and trace its domestication history, we used 80 simple sequence repeat (SSR) markers to analyse the relationships between these potential Nacional founders and 169 wild and cultivated cocoa accessions from South and Central America. The highest genetic similarity was observed between the Nacional pool and some wild genotypes from the southern Amazonian region of Ecuador, sampled along the Yacuambi, Nangaritza and Zamora rivers in Zamora Chinchipe province. This result was confirmed by a parentage analysis. Based on our results and on data about pre-Columbian civilization and Spanish colonization history of Ecuador, we determined, for the first time, the possible centre of origin and migration events of the Nacional variety from the Amazonian area until its arrival in the coastal provinces. As large unexplored forest areas still exist in the southern part of the Ecuadorian Amazonian region, our findings could provide clues as to where precious new genetic resources could be collected, and subsequently used to improve the flavour and disease resistance of modern Ecuadorian cocoa varieties.
PLoS ONE 01/2012; 7(11):e48438. · 4.09 Impact Factor
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Xavier Perrier,
Edmond De Langhe,
Mark Donohue,
Carol Lentfer,
Luc Vrydaghs,
Frédéric Bakry,
Françoise Carreel,
Isabelle Hippolyte,
Jean-Pierre Horry,
Christophe Jenny,
Vincent Lebot, Ange-Marie Risterucci,
Kodjo Tomekpe,
Hugues Doutrelepont,
Terry Ball,
Jason Manwaring,
Pierre de Maret,
Tim Denham
[show abstract]
[hide abstract]
ABSTRACT: Original multidisciplinary research hereby clarifies the complex geodomestication pathways that generated the vast range of banana cultivars (cvs). Genetic analyses identify the wild ancestors of modern-day cvs and elucidate several key stages of domestication for different cv groups. Archaeology and linguistics shed light on the historical roles of people in the movement and cultivation of bananas from New Guinea to West Africa during the Holocene. The historical reconstruction of domestication processes is essential for breeding programs seeking to diversify and improve banana cvs for the future.
Proceedings of the National Academy of Sciences 07/2011; 108(28):11311-8. · 9.68 Impact Factor
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Xavier Argout,
Jerome Salse,
Jean-Marc Aury,
Mark J Guiltinan,
Gaetan Droc,
Jerome Gouzy,
Mathilde Allegre,
Cristian Chaparro,
Thierry Legavre,
Siela N Maximova, [......],
Ismael Kebe,
Pierre Costet,
Rod Wing,
W Richard McCombie,
Emmanuel Guiderdoni,
Francis Quetier,
Olivier Panaud,
Patrick Wincker,
Stephanie Bocs,
Claire Lanaud
[show abstract]
[hide abstract]
ABSTRACT: We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions.
Nature Genetics 02/2011; 43(2):101-8. · 35.53 Impact Factor
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Isabelle Hippolyte,
Frederic Bakry,
Marc Seguin,
Laetitia Gardes,
Ronan Rivallan, Ange-Marie Risterucci,
Christophe Jenny,
Xavier Perrier,
Françoise Carreel,
Xavier Argout, [......],
Didier Mbéguié-A-Mbéguié,
Takashi Matsumoto,
Veronique De Bernardinis,
Eric Huttner,
Andrzej Kilian,
Franc-Christophe Baurens,
Angélique D'Hont,
François Cote,
Brigitte Courtois,
Jean-Christophe Glaszmann
[show abstract]
[hide abstract]
ABSTRACT: The genus Musa is a large species complex which includes cultivars at diploid and triploid levels. These sterile and vegetatively propagated cultivars are based on the A genome from Musa acuminata, exclusively for sweet bananas such as Cavendish, or associated with the B genome (Musa balbisiana) in cooking bananas such as Plantain varieties. In M. acuminata cultivars, structural heterozygosity is thought to be one of the main causes of sterility, which is essential for obtaining seedless fruits but hampers breeding. Only partial genetic maps are presently available due to chromosomal rearrangements within the parents of the mapping populations. This causes large segregation distortions inducing pseudo-linkages and difficulties in ordering markers in the linkage groups. The present study aims at producing a saturated linkage map of M. acuminata, taking into account hypotheses on the structural heterozygosity of the parents.
An F1 progeny of 180 individuals was obtained from a cross between two genetically distant accessions of M. acuminata, 'Borneo' and 'Pisang Lilin' (P. Lilin). Based on the gametic recombination of each parent, two parental maps composed of SSR and DArT markers were established. A significant proportion of the markers (21.7%) deviated (p < 0.05) from the expected Mendelian ratios. These skewed markers were distributed in different linkage groups for each parent. To solve some complex ordering of the markers on linkage groups, we associated tools such as tree-like graphic representations, recombination frequency statistics and cytogenetical studies to identify structural rearrangements and build parsimonious linkage group order. An illustration of such an approach is given for the P. Lilin parent.
We propose a synthetic map with 11 linkage groups containing 489 markers (167 SSRs and 322 DArTs) covering 1197 cM. This first saturated map is proposed as a "reference Musa map" for further analyses. We also propose two complete parental maps with interpretations of structural rearrangements localized on the linkage groups. The structural heterozygosity in P. Lilin is hypothesized to result from a duplication likely accompanied by an inversion on another chromosome. This paper also illustrates a methodological approach, transferable to other species, to investigate the mapping of structural rearrangements and determine their consequences on marker segregation.
BMC Plant Biology 04/2010; 10:65. · 3.45 Impact Factor
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Isabelle Hippolyte,
Frederic Bakry,
Marc Seguin,
Laetitia Gardes,
Ronan Rivallan, Ange-Marie Risterucci,
Christophe Jenny,
Xavier Perrier,
Françoise Carreel,
Xavier Argout, [......],
Didier Mbéguié-A-Mbéguié,
Takashi Matsumoto,
De Bernardinis Veronique,
Eric Huttner,
Andrzej Kilian,
Franc-Christophe Baurens,
Angélique D'Hont,
François Cote,
Brigitte Courtois,
Jean-Christophe Glaszmann
[show abstract]
[hide abstract]
ABSTRACT: Abstract
Background
The genus Musa is a large species complex which includes cultivars at diploid and triploid levels. These sterile and vegetatively propagated cultivars are based on the A genome from Musa acuminata , exclusively for sweet bananas such as Cavendish, or associated with the B genome ( Musa balbisiana ) in cooking bananas such as Plantain varieties. In M. acuminata cultivars, structural heterozygosity is thought to be one of the main causes of sterility, which is essential for obtaining seedless fruits but hampers breeding. Only partial genetic maps are presently available due to chromosomal rearrangements within the parents of the mapping populations. This causes large segregation distortions inducing pseudo-linkages and difficulties in ordering markers in the linkage groups. The present study aims at producing a saturated linkage map of M. acuminata , taking into account hypotheses on the structural heterozygosity of the parents.
Results
An F<sub>1 </sub>progeny of 180 individuals was obtained from a cross between two genetically distant accessions of M. acuminata , 'Borneo' and 'Pisang Lilin' (P. Lilin). Based on the gametic recombination of each parent, two parental maps composed of SSR and DArT markers were established. A significant proportion of the markers (21.7%) deviated (p < 0.05) from the expected Mendelian ratios. These skewed markers were distributed in different linkage groups for each parent. To solve some complex ordering of the markers on linkage groups, we associated tools such as tree-like graphic representations, recombination frequency statistics and cytogenetical studies to identify structural rearrangements and build parsimonious linkage group order. An illustration of such an approach is given for the P. Lilin parent.
Conclusions
We propose a synthetic map with 11 linkage groups containing 489 markers (167 SSRs and 322 DArTs) covering 1197 cM. This first saturated map is proposed as a "reference Musa map" for further analyses. We also propose two complete parental maps with interpretations of structural rearrangements localized on the linkage groups. The structural heterozygosity in P. Lilin is hypothesized to result from a duplication likely accompanied by an inversion on another chromosome. This paper also illustrates a methodological approach, transferable to other species, to investigate the mapping of structural rearrangements and determine their consequences on marker segregation.
BMC Plant Biology. 01/2010;
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[show abstract]
[hide abstract]
ABSTRACT: Diversity Arrays Technology (DArT) is a DNA hybridisation-based molecular marker technique that can detect simultaneously variation at numerous genomic loci without sequence information. This efficiency makes it a potential tool for a quick and powerful assessment of the structure of germplasm collections. This article demonstrates the usefulness of DArT markers for genetic diversity analyses of Musa spp. genotypes. We developed four complexity reduction methods to generate DArT genomic representations and we tested their performance using 48 reference Musa genotypes. For these four complexity reduction methods, DArT markers displayed high polymorphism information content. We selected the two methods which generated the most polymorphic genomic representations (PstI/BstNI 16.8%, PstI/TaqI 16.1%) to analyze a panel of 168 Musa genotypes from two of the most important field collections of Musa in the world: Cirad (Neufchateau, Guadeloupe), and IITA (Ibadan, Nigeria). Since most edible cultivars are derived from two wild species, Musa acuminata (A genome) and Musa balbisiana (B genome), the study is restricted mostly to accessions of these two species and those derived from them. The genomic origin of the markers can help resolving the pedigree of valuable genotypes of unknown origin. A total of 836 markers were identified and used for genotyping. Ten percent of them were specific to the A genome and enabled targeting this genome portion in relatedness analysis among diverse ploidy constitutions. DArT markers revealed genetic relationships among Musa genotype consistent with those provided by the other markers technologies, but at a significantly higher resolution and speed and reduced cost.
Theoretical and Applied Genetics 09/2009; 119(6):1093-103. · 3.30 Impact Factor
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Xavier Argout,
Olivier Fouet,
Patrick Wincker,
Karina Gramacho,
Thierry Legavre,
Xavier Sabau, Ange Marie Risterucci,
Corinne Da Silva,
Julio Cascardo,
Mathilde Allegre, [......],
Manuel Ruiz,
Laurence Alemanno,
Regina Machado,
Wilberth Phillips,
Ray Schnell,
Martin Gilmour,
Eric Rosenquist,
David Butler,
Siela Maximova,
Claire Lanaud
[show abstract]
[hide abstract]
ABSTRACT: Theobroma cacao L., is a tree originated from the tropical rainforest of South America. It is one of the major cash crops for many tropical countries. T. cacao is mainly produced on smallholdings, providing resources for 14 million farmers. Disease resistance and T. cacao quality improvement are two important challenges for all actors of cocoa and chocolate production. T. cacao is seriously affected by pests and fungal diseases, responsible for more than 40% yield losses and quality improvement, nutritional and organoleptic, is also important for consumers. An international collaboration was formed to develop an EST genomic resource database for cacao.
Fifty-six cDNA libraries were constructed from different organs, different genotypes and different environmental conditions. A total of 149,650 valid EST sequences were generated corresponding to 48,594 unigenes, 12,692 contigs and 35,902 singletons. A total of 29,849 unigenes shared significant homology with public sequences from other species.Gene Ontology (GO) annotation was applied to distribute the ESTs among the main GO categories.A specific information system (ESTtik) was constructed to process, store and manage this EST collection allowing the user to query a database.To check the representativeness of our EST collection, we looked for the genes known to be involved in two different metabolic pathways extensively studied in other plant species and important for T. cacao qualities: the flavonoid and the terpene pathways. Most of the enzymes described in other crops for these two metabolic pathways were found in our EST collection.A large collection of new genetic markers was provided by this ESTs collection.
This EST collection displays a good representation of the T. cacao transcriptome, suitable for analysis of biochemical pathways based on oligonucleotide microarrays derived from these ESTs. It will provide numerous genetic markers that will allow the construction of a high density gene map of T. cacao. This EST collection represents a unique and important molecular resource for T. cacao study and improvement, facilitating the discovery of candidate genes for important T. cacao trait variation.
BMC Genomics 11/2008; 9:512. · 4.07 Impact Factor
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Maria Marcano,
Tatiana Pugh,
Emile Cros,
Sonia Morales,
Elvis A Portillo Páez,
Brigitte Courtois,
Jean Christophe Glaszmann,
Jan M M Engels,
Wilbert Phillips,
Carlos Astorga, Ange Marie Risterucci,
Olivier Fouet,
Ventura González,
Kai Rosenberg,
Isabelle Vallat,
Manuel Dagert,
Claire Lanaud
[show abstract]
[hide abstract]
ABSTRACT: A sound understanding of crop history can provide the basis for deriving novel genetic information through admixture mapping. We confirmed this, by using characterization data from an international collection of cocoa, collected 25 years ago, and from a contemporary plantation. We focus on the trees derived from three centuries of admixture between Meso-American Criollo and South American Forastero genomes. In both cacao sets of individuals, linkage disequilibrium extended over long genetic distances along chromosome regions, as expected in populations derived from recent admixture. Based on loose genome scans, genomic regions involved in useful traits were identified. Fifteen genomic regions involved in seed and fruit weight variation were highlighted. They correspond to ten previously identified QTLs and five novel ones. Admixture mapping can help to add value to genetic resources and thus, help to encourage investment in their conservation.
Theoretical and Applied Genetics 04/2007; 114(5):877-84. · 3.30 Impact Factor
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[show abstract]
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ABSTRACT: Disease resistance and defence gene analog (RGA/DGA) sequences were isolated in cocoa using a PCR approach with degenerate primers designed from conserved domains of plant resistance and defence genes: the NBS (nucleotide binding site) motif present in a number of resistance genes such as the tobacco N, sub-domains of plant serine/threonine kinases such as the Pto tomato gene, and conserved domains of two defence gene families: pathogenesis-related proteins (PR) of classes 2 and 5. Nucleotide identity between thirty six sequences isolated from cocoa and known resistance or defence genes varied from 58 to 80%. Amino acid sequences translated from corresponding coding sequences produced sequences without stop codons, except for one NBS –like sequence. Most of the RGAs could be mapped on the cocoa genome and three clusters of genes could be observed : NBS-like sequences clustered in two regions located on chromosomes 7 and 10, Pto-like sequences mapped in five genome regions of which one, located on chromosome 4, corresponded to a cluster of five different sequences. PR2-like sequences mapped in two regions located on chromosome 5 and 9 respectively. An enrichment of the genetic map with microsatellite markers allowed us to identify several co-localisations of RGAs, DGAs and QTL for resistance to Phytophthora detected in several progenies, particularly on chromosome 4 where a cluster of Pto-like sequences and 4 QTL for resistance to Phytophthora were observed. Many other serious diseases affect cocoa and the candidate genes, isolated in this study, could be of broader interest in cocoa disease management.
Molecular Breeding 01/2004; 13(3):211-227. · 2.85 Impact Factor
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Xavier Argout,
Jerome Salse,
Jean-Marc Aury,
Gaetan Droc,
Jerome Gouzy,
Mathilde Allegre,
Cristian Chaparro,
Thierry Legavre,
Mark Guiltinan,
Siela Maximova, [......],
Ismael Kebe,
Pierre Costet,
Rod Wing,
W Richard McCombie,
Emmanuel Guiderdoni,
Francis Quetier,
Olivier Panaud,
Patrick Wincker,
Stephanie Sidibe-Bocs,
Claire Lanaud
[show abstract]
[hide abstract]
ABSTRACT: We sequenced and assembled the genome of _Theobroma cacao_, an economically important tropical fruit tree crop that is the source of chocolate. The assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of them anchored on the 10 _T. cacao_ chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example flavonoid-related genes. It also provides a major source of candidate genes for _T. cacao_ disease resistance and quality improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten _T. cacao_ chromosomes were shaped from an ancestor through eleven chromosome fusions. The _T. cacao_ genome can be considered as a simple living relic of higher plant evolution.
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