The Experts below are selected from a list of 4305 Experts worldwide ranked by ideXlab platform
Pierre Lagoda - One of the best experts on this subject based on the ideXlab platform.
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diploid Musa Acuminata genetic diversity assayed with sequence tagged microsatellite sites
Electrophoresis, 1998Co-Authors: Agnès Grapin, Jean-louis Noyer, Françoise Carreel, Dominique Dambier, Franc-christophe Baurens, Claire Lanaud, Pierre LagodaAbstract:The sequence-tagged microsatellite site (STMS) discrimination potential was explored using nine microsatellite primer pairs. STMS polymorphism was assayed by nonradioactive urea-polyacrylamide gel electrophoresis. Genetic relationships were examined among 59 genotypes of wild or cultivated accessions of diploid Musa Acuminata. The organization of the subspecies was confirmed and some clone relationships were clarified.
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Diploid Musa Acuminata genetic diversity assayed with sequence‐tagged microsatellite sites
Electrophoresis, 1998Co-Authors: Agnès Grapin, Jean-louis Noyer, Françoise Carreel, Dominique Dambier, Franc-christophe Baurens, Claire Lanaud, Pierre LagodaAbstract:The sequence-tagged microsatellite site (STMS) discrimination potential was explored using nine microsatellite primer pairs. STMS polymorphism was assayed by nonradioactive urea-polyacrylamide gel electrophoresis. Genetic relationships were examined among 59 genotypes of wild or cultivated accessions of diploid Musa Acuminata. The organization of the subspecies was confirmed and some clone relationships were clarified.
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The saturated map of diploid banana (Musa Acuminata)
1997Co-Authors: Jean-louis Noyer, Dominique Dambier, Claire Lanaud, Pierre LagodaAbstract:The first saturated map, based on a selfed progeny (89 individuals) from a highly fertile synthetic AA diploid banana cultivar (M53), displaying a BLSD 'resistant' phenotype, is being presented. More than three hundred markers are linked in 11 linkage groups representing the genome (2n=22) of Musa Acuminata; Roughly one third of the markers are co-dominant RFLPs (hundred) and microsatellites (thirty). In particular, the efficacy of polymorphic microsatellite markers for mapping the banana genome with rapid and simple methods is pointed out. Two thirds of the markers are dominant AFLPs. Particularities for a mapping job in banana are discussed. Due to Acuminata sub-species specific translocations, a sizeable number of markers present high distortion levels. A 'frame-map' based on evenly spaced co-dominant markers is proposed. (Texte integral)
Franc-christophe Baurens - One of the best experts on this subject based on the ideXlab platform.
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Three new genome assemblies support a rapid radiation in Musa Acuminata (wild banana)
Genome Biology and Evolution, 2018Co-Authors: Gaëtan Droc, Franc-christophe Baurens, Alberto Cenci, Julie Sardos, Björn Geigle, Mark Hibbins, Nabila Yahiaoui, Vincent Berry, Matthew W. Hahn, Angélique D'hontAbstract:Edible bananas result from interspecific hybridization between Musa Acuminata and Musa balbisiana, as well as among subspecies in M. Acuminata. Four particular M. Acuminata subspecies have been proposed as the main contributors of edible bananas, all of which radiated in a short period of time in southeastern Asia. Clarifying the evolution of these lineages at a whole-genome scale is therefore an important step toward understanding the domestication and diversification of this crop. This study reports the de novo genome assembly and gene annotation of a representative genotype from three different subspecies of M. Acuminata. These data are combined with the previously published genome of the fourth subspecies to investigate phylogenetic relationships. Analyses of shared and unique gene families reveal that the four subspecies are quite homogenous, with a core genome representing at least 50% of all genes and very few M. Acuminata species-specific gene families. Multiple alignments indicate high sequence identity between homologous single copy-genes, supporting the close relationships of these lineages. Interestingly, phylogenomic analyses demonstrate high levels of gene tree discordance, due to both incomplete lineage sorting and introgression. This pattern suggests rapid radiation within Musa Acuminata subspecies that occurred after the divergence with M. balbisiana. Introgression between M. a. ssp. malaccensis and M. a. ssp. burmannica was detected across the genome, though multiple approaches to resolve the subspecies tree converged on the same topology. To support evolutionary and functional analyses, we introduce the PanMusa database, which enables researchers to exploration of individual gene families and trees.
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Improvement of the banana "Musa Acuminata" reference sequence using NGS data and semi-automated bioinformatics methods.
BMC genomics, 2016Co-Authors: Guillaume Martin, Franc-christophe Baurens, Gaëtan Droc, Mathieu Rouard, Alberto Cenci, Andrzej Kilian, Alex Hastie, Jaroslav Doležel, Jean-marc Aury, Adriana AlbertiAbstract:Recent advances in genomics indicate functional significance of a majority of genome sequences and their long range interactions. As a detailed examination of genome organization and function requires very high quality genome sequence, the objective of this study was to improve reference genome assembly of banana (Musa Acuminata). We have developed a modular bioinformatics pipeline to improve genome sequence assemblies, which can handle various types of data. The pipeline comprises several semi-automated tools. However, unlike classical automated tools that are based on global parameters, the semi-automated tools proposed an expert mode for a user who can decide on suggested improvements through local compromises. The pipeline was used to improve the draft genome sequence of Musa Acuminata. Genotyping by sequencing (GBS) of a segregating population and paired-end sequencing were used to detect and correct scaffold misassemblies. Long insert size paired-end reads identified scaffold junctions and fusions missed by automated assembly methods. GBS markers were used to anchor scaffolds to pseudo-molecules with a new bioinformatics approach that avoids the tedious step of marker ordering during genetic map construction. Furthermore, a genome map was constructed and used to assemble scaffolds into super scaffolds. Finally, a consensus gene annotation was projected on the new assembly from two pre-existing annotations. This approach reduced the total Musa scaffold number from 7513 to 1532 (i.e. by 80 %), with an N50 that increased from 1.3 Mb (65 scaffolds) to 3.0 Mb (26 scaffolds). 89.5 % of the assembly was anchored to the 11 Musa chromosomes compared to the previous 70 %. Unknown sites (N) were reduced from 17.3 to 10.0 %. The release of the Musa Acuminata reference genome version 2 provides a platform for detailed analysis of banana genome variation, function and evolution. Bioinformatics tools developed in this work can be used to improve genome sequence assemblies in other species.
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diploid Musa Acuminata genetic diversity assayed with sequence tagged microsatellite sites
Electrophoresis, 1998Co-Authors: Agnès Grapin, Jean-louis Noyer, Françoise Carreel, Dominique Dambier, Franc-christophe Baurens, Claire Lanaud, Pierre LagodaAbstract:The sequence-tagged microsatellite site (STMS) discrimination potential was explored using nine microsatellite primer pairs. STMS polymorphism was assayed by nonradioactive urea-polyacrylamide gel electrophoresis. Genetic relationships were examined among 59 genotypes of wild or cultivated accessions of diploid Musa Acuminata. The organization of the subspecies was confirmed and some clone relationships were clarified.
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Diploid Musa Acuminata genetic diversity assayed with sequence‐tagged microsatellite sites
Electrophoresis, 1998Co-Authors: Agnès Grapin, Jean-louis Noyer, Françoise Carreel, Dominique Dambier, Franc-christophe Baurens, Claire Lanaud, Pierre LagodaAbstract:The sequence-tagged microsatellite site (STMS) discrimination potential was explored using nine microsatellite primer pairs. STMS polymorphism was assayed by nonradioactive urea-polyacrylamide gel electrophoresis. Genetic relationships were examined among 59 genotypes of wild or cultivated accessions of diploid Musa Acuminata. The organization of the subspecies was confirmed and some clone relationships were clarified.
Agnès Grapin - One of the best experts on this subject based on the ideXlab platform.
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diploid Musa Acuminata genetic diversity assayed with sequence tagged microsatellite sites
Electrophoresis, 1998Co-Authors: Agnès Grapin, Jean-louis Noyer, Françoise Carreel, Dominique Dambier, Franc-christophe Baurens, Claire Lanaud, Pierre LagodaAbstract:The sequence-tagged microsatellite site (STMS) discrimination potential was explored using nine microsatellite primer pairs. STMS polymorphism was assayed by nonradioactive urea-polyacrylamide gel electrophoresis. Genetic relationships were examined among 59 genotypes of wild or cultivated accessions of diploid Musa Acuminata. The organization of the subspecies was confirmed and some clone relationships were clarified.
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Diploid Musa Acuminata genetic diversity assayed with sequence‐tagged microsatellite sites
Electrophoresis, 1998Co-Authors: Agnès Grapin, Jean-louis Noyer, Françoise Carreel, Dominique Dambier, Franc-christophe Baurens, Claire Lanaud, Pierre LagodaAbstract:The sequence-tagged microsatellite site (STMS) discrimination potential was explored using nine microsatellite primer pairs. STMS polymorphism was assayed by nonradioactive urea-polyacrylamide gel electrophoresis. Genetic relationships were examined among 59 genotypes of wild or cultivated accessions of diploid Musa Acuminata. The organization of the subspecies was confirmed and some clone relationships were clarified.
Dominique Dambier - One of the best experts on this subject based on the ideXlab platform.
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diploid Musa Acuminata genetic diversity assayed with sequence tagged microsatellite sites
Electrophoresis, 1998Co-Authors: Agnès Grapin, Jean-louis Noyer, Françoise Carreel, Dominique Dambier, Franc-christophe Baurens, Claire Lanaud, Pierre LagodaAbstract:The sequence-tagged microsatellite site (STMS) discrimination potential was explored using nine microsatellite primer pairs. STMS polymorphism was assayed by nonradioactive urea-polyacrylamide gel electrophoresis. Genetic relationships were examined among 59 genotypes of wild or cultivated accessions of diploid Musa Acuminata. The organization of the subspecies was confirmed and some clone relationships were clarified.
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Diploid Musa Acuminata genetic diversity assayed with sequence‐tagged microsatellite sites
Electrophoresis, 1998Co-Authors: Agnès Grapin, Jean-louis Noyer, Françoise Carreel, Dominique Dambier, Franc-christophe Baurens, Claire Lanaud, Pierre LagodaAbstract:The sequence-tagged microsatellite site (STMS) discrimination potential was explored using nine microsatellite primer pairs. STMS polymorphism was assayed by nonradioactive urea-polyacrylamide gel electrophoresis. Genetic relationships were examined among 59 genotypes of wild or cultivated accessions of diploid Musa Acuminata. The organization of the subspecies was confirmed and some clone relationships were clarified.
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The saturated map of diploid banana (Musa Acuminata)
1997Co-Authors: Jean-louis Noyer, Dominique Dambier, Claire Lanaud, Pierre LagodaAbstract:The first saturated map, based on a selfed progeny (89 individuals) from a highly fertile synthetic AA diploid banana cultivar (M53), displaying a BLSD 'resistant' phenotype, is being presented. More than three hundred markers are linked in 11 linkage groups representing the genome (2n=22) of Musa Acuminata; Roughly one third of the markers are co-dominant RFLPs (hundred) and microsatellites (thirty). In particular, the efficacy of polymorphic microsatellite markers for mapping the banana genome with rapid and simple methods is pointed out. Two thirds of the markers are dominant AFLPs. Particularities for a mapping job in banana are discussed. Due to Acuminata sub-species specific translocations, a sizeable number of markers present high distortion levels. A 'frame-map' based on evenly spaced co-dominant markers is proposed. (Texte integral)
Françoise Carreel - One of the best experts on this subject based on the ideXlab platform.
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diploid Musa Acuminata genetic diversity assayed with sequence tagged microsatellite sites
Electrophoresis, 1998Co-Authors: Agnès Grapin, Jean-louis Noyer, Françoise Carreel, Dominique Dambier, Franc-christophe Baurens, Claire Lanaud, Pierre LagodaAbstract:The sequence-tagged microsatellite site (STMS) discrimination potential was explored using nine microsatellite primer pairs. STMS polymorphism was assayed by nonradioactive urea-polyacrylamide gel electrophoresis. Genetic relationships were examined among 59 genotypes of wild or cultivated accessions of diploid Musa Acuminata. The organization of the subspecies was confirmed and some clone relationships were clarified.
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Diploid Musa Acuminata genetic diversity assayed with sequence‐tagged microsatellite sites
Electrophoresis, 1998Co-Authors: Agnès Grapin, Jean-louis Noyer, Françoise Carreel, Dominique Dambier, Franc-christophe Baurens, Claire Lanaud, Pierre LagodaAbstract:The sequence-tagged microsatellite site (STMS) discrimination potential was explored using nine microsatellite primer pairs. STMS polymorphism was assayed by nonradioactive urea-polyacrylamide gel electrophoresis. Genetic relationships were examined among 59 genotypes of wild or cultivated accessions of diploid Musa Acuminata. The organization of the subspecies was confirmed and some clone relationships were clarified.
