المؤلفون: Martin, Guillaume, Baurens, Franc-Christophe, Labadie, Karine, Hervouet, Catherine, Salmon, Frédéric, Marius, Franck, Paulo-De-La-Reberdiere, Nilda, van den Houwe, Ines, Aury, Jean-Marc, d’Hont, Angélique, Yahiaoui, Nabila

المساهمون: Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage Evry (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), The Alliance of Bioversity International and International Center for Tropical Agriculture (CIAT) Belgique, Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) Rome (Alliance), Consultative Group on International Agricultural Research CGIAR (CGIAR)-Consultative Group on International Agricultural Research CGIAR (CGIAR), Laboratoire de Bioinformatique pour la Génomique et la Biodiversité (LBGB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage Evry (GENOSCOPE), This work was supported by the France Génomique (ANR-10-INBS-0009) project DYNAMO, the Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) and the Agropolis Fondation (ID 1504-006) ‘GenomeHarvest’ project through the French Investissements d’Avenir program (Labex Agro: ANR- 10-LABX-0001)., ANR-10-INBS-0009,France Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)

المصدر: ISSN: 0305-7364.

مصطلحات موضوعية: Musa acuminata, Musa balbisiana, Musa schizocarpa, banana cultivars, Mchare, parentage, unreduced gamete, polyploid, whole genome approach, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]

الوصف: International audience ; Background and Aims: Cultivated bananas resulted from inter(sub)specific hybridizations involving Musa species and subspecies (M. acuminata subspecies, M. schizocarpa, M. balbisiana) and the subsequent selection, centuries ago, of hybrids with parthenocarpic, seedless fruits. Cultivars have low fertility and are vegetatively propagated, forming groups of somaclones. Relatively few of them, mainly triploids, are grown on a large scale and characterization of their parental relationships may be useful for breeding strategies. Here we investigate parental relationships and gamete-type contributions among diploid and polyploid banana cultivars.Methods: We used SNP genotyping data from whole-genome sequencing of 178 banana individuals, including 111 cultivars, 55 wild bananas and 12 synthetic F1 hybrids. We analysed the proportion of SNP sites in accordance with direct parentage with a global statistic and along chromosomes for selected individuals.Key Results: We characterized parentage relationships for 7 diploid cultivars, 11 triploid cultivars and 1 tetraploid cultivar. Results showed that both diploid and triploid cultivars could have contributed gametes to other banana cultivars. Diploids may have contributed 1x or 2x gametes and triploids 1x to 3x gametes. The Mchare diploid cultivar group, nowadays only found in East Africa, was found as parent of two diploid and eight triploid cultivars. In five of its identified triploid offspring, corresponding to main export or locally popular dessert bananas, Mchare contributed a 2x gamete with full genome restitution without recombination. Analyses of remaining haplotypes in these Mchare offspring suggested ancestral pedigree relationships between different interspecific banana cultivars.Conclusions: The current cultivated banana resulted from different pathways of formation, with implication of recombined or un-recombined unreduced gametes produced by diploid or triploid cultivars. Identification of dessert banana’s parents and the types of ...

العلاقة: info:eu-repo/semantics/altIdentifier/pmid/37267450; hal-04361041; https://hal.science/hal-04361041Test; https://hal.science/hal-04361041/documentTest; https://hal.science/hal-04361041/file/mcad065.pdfTest; PUBMED: 37267450; WOS: 001010221400001

الإتاحة: https://doi.org/10.1093/aob/mcad065Test
https://hal.science/hal-04361041Test
https://hal.science/hal-04361041/documentTest
https://hal.science/hal-04361041/file/mcad065.pdfTest

المؤلفون: Belser, Caroline, Baurens, Franc-Christophe, Noël, Benjamin, Martin, Guillaume, Cruaud, Corinne, Istace, Benjamin, Yahiaoui, Nabila, Labadie, Karine, Hribova, Eva, Dolezel, Jaroslav, Lemainque, Arnaud, Wincker, Patrick, D'Hont, Angélique, Aury, Jean-Marc

المصدر: Communications Biology

مصطلحات موضوعية: F30 - Génétique et amélioration des plantes, phytogénétique, Génome, Télomères, Biotechnologie végétale, génomique, Musa acuminata, http://aims.fao.org/aos/agrovoc/c_49985Test, http://aims.fao.org/aos/agrovoc/c_3224Test, http://aims.fao.org/aos/agrovoc/c_abdfcd4cTest, http://aims.fao.org/aos/agrovoc/c_27590Test, http://aims.fao.org/aos/agrovoc/c_92382Test, http://aims.fao.org/aos/agrovoc/c_4994Test

الوصف: Long-read technologies hold the promise to obtain more complete genome assemblies and to make them easier. Coupled with long-range technologies, they can reveal the architecture of complex regions, like centromeres or rDNA clusters. These technologies also make it possible to know the complete organization of chromosomes, which remained complicated before even when using genetic maps. However, generating a gapless and telomere-to-telomere assembly is still not trivial, and requires a combination of several technologies and the choice of suitable software. Here, we report a chromosome-scale assembly of a banana genome (Musa acuminata) generated using Oxford Nanopore long-reads. We generated a genome coverage of 177X from a single PromethION flowcell with near 17X with reads longer than 75 kbp. From the 11 chromosomes, 5 were entirely reconstructed in a single contig from telomere to telomere, revealing for the first time the content of complex regions like centromeres or clusters of paralogous genes.

وصف الملف: text

العلاقة: http://agritrop.cirad.fr/599053Test/; Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing. Belser Caroline, Baurens Franc-Christophe, Noël Benjamin, Martin Guillaume, Cruaud Corinne, Istace Benjamin, Yahiaoui Nabila, Labadie Karine, Hribova Eva, Dolezel Jaroslav, Lemainque Arnaud, Wincker Patrick, D'Hont Angélique, Aury Jean-Marc. 2021. Communications Biology, 4:1047, 12 p.https://doi.org/10.1038/s42003-021-02559-3Test; http://agritrop.cirad.fr/599053/1/Belser%20et%20al%202021_Telomere-to-telomere%20gapless%20chromosomes%20of%20banana%20using%20nanopore%20sequencing.pdfTest

الإتاحة: https://doi.org/10.1038/s42003-021-02559-3Test
http://agritrop.cirad.fr/599053Test/
http://agritrop.cirad.fr/599053/1/Belser%20et%20al%202021_Telomere-to-telomere%20gapless%20chromosomes%20of%20banana%20using%20nanopore%20sequencing.pdfTest

المؤلفون: Martin, Guillaume, Cardi, Céline, Sarah, Gautier, Ricci, Sébastien, Jenny, Christophe, Fondi, Emmanuel, Perrier, Xavier, Glaszmann, Jean-Christophe, d'Hont, Angélique, Yahiaoui, Nabila

المساهمون: Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), African Center for Research on Bananas and Plantains = Centre Africain de Recherches sur Bananiers et Plantains (CARBAP), French National Research Agency (ANR) : 0900-001, ANR-10-LABX-0001-01, French National Research Agency (ANR) : ANR-10-LABX-0001-01, 1504-006, CGIAR Research Programme on Roots, Tubers, and Bananas (RTB), CIRAD - UMR AGAP HPC Data Center of the South Green Bioinfor-matics platform, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)

المصدر: ISSN: 0960-7412.

مصطلحات موضوعية: genome ancestry, diversity, hybridization, Musa acuminata, admixture, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology

الوصف: UT Early access ; International audience ; Hybridizations between closely related species commonly occur in the domestication process of many crops. Banana cultivars are derived from such hybridizations between species and subspecies of the Musa genus that have diverged in various tropical Southeast Asian regions and archipelagos. Among the diploid and triploid hybrids generated, those with seedless parthenocarpic fruits were selected by humans and thereafter dispersed through vegetative propagation. Musa acuminata subspecies contribute to most of these cultivars. We analyzed sequence data from 14 M. acuminata wild accessions and 10 M. acuminata-based cultivars, including diploids and one triploid, to characterize the ancestral origins along their chromosomes. We used multivariate analysis and single nucleotide polymorphism clustering and identified five ancestral groups as contributors to these cultivars. Four of these corresponded to known M. acuminata subspecies. A fifth group, found only in cultivars, was defined based on the 'Pisang Madu' cultivar and represented two uncharacterized genetic pools. Diverse ancestral contributions along cultivar chromosomes were found, resulting in mosaics with at least three and up to five ancestries. The commercially important triploid Cavendish banana cultivar had contributions from at least one of the uncharacterized genetic pools and three known M. acuminata subspecies. Our results highlighted that cultivated banana origins are more complex than expected - involving multiple hybridization steps - and also that major wild banana ancestors have yet to be identified. This study revealed the extent to which admixture has framed the evolution and domestication of a crop plant.

العلاقة: info:eu-repo/semantics/altIdentifier/pmid/31930580; hal-02628306; https://hal.inrae.fr/hal-02628306Test; https://hal.inrae.fr/hal-02628306/documentTest; https://hal.inrae.fr/hal-02628306/file/publis20-agap-003_martin_genome_1.pdfTest; PRODINRA: 496720; PUBMED: 31930580; WOS: 000516834300001

الإتاحة: https://doi.org/10.1111/tpj.14683Test
https://hal.inrae.fr/hal-02628306Test
https://hal.inrae.fr/hal-02628306/documentTest
https://hal.inrae.fr/hal-02628306/file/publis20-agap-003_martin_genome_1.pdfTest

المؤلفون: Martin, Guillaume, Baurens, Franc-Christophe, Hervouet, Catherine, Salmon, Frédéric, Delos, Jean-Marie Eric, Labadie, Karine, Perdereau, Aude, Mournet, Pierre, Blois, Louis, Dupouy, Marion, Carreel, Françoise, Ricci, Sebastien, Lemainque, Arnaud, Yahiaoui, Nabila, D'Hont, Angélique

المصدر: Plant Journal

مصطلحات موضوعية: F30 - Génétique et amélioration des plantes, Musa acuminata, Translocation chromosomique, translocation réciproque, Évolution, Recombinaison, http://aims.fao.org/aos/agrovoc/c_4994Test, http://aims.fao.org/aos/agrovoc/c_24003Test, http://aims.fao.org/aos/agrovoc/c_1d4ba39dTest, http://aims.fao.org/aos/agrovoc/c_2745Test, http://aims.fao.org/aos/agrovoc/c_6475Test

الوصف: Chromosome rearrangements and the way that they impact genetic differentiation and speciation have long raised questions from evolutionary biologists. They are also a major concern for breeders because of their bearing on chromosome recombination. Banana is a major crop that derives from inter(sub)specific hybridizations between various once geographically isolated Musa species and subspecies. We sequenced 155 accessions, including banana cultivars and representatives of Musa diversity, and genotyped‐by‐sequencing 1059 individuals from 11 progenies. We precisely characterized six large reciprocal translocations and showed that they emerged in different (sub)species of Musa acuminata, the main contributor to currently cultivated bananas. Most diploid and triploid cultivars analyzed were structurally heterozygous for 1 to 4 M. acuminata translocations, highlighting their complex origin. We showed that all translocations induced a recombination reduction of variable intensity and extent depending on the translocations, involving only the breakpoint regions, a chromosome arm, or an entire chromosome. The translocated chromosomes were found preferentially transmitted in many cases. We explore and discuss the possible mechanisms involved in this preferential transmission and its impact on translocation colonization.

وصف الملف: text

العلاقة: http://agritrop.cirad.fr/596991Test/; Chromosome reciprocal translocations have accompanied subspecies evolution in bananas. Martin Guillaume, Baurens Franc-Christophe, Hervouet Catherine, Salmon Frédéric, Delos Jean-Marie Eric, Labadie Karine, Perdereau Aude, Mournet Pierre, Blois Louis, Dupouy Marion, Carreel Françoise, Ricci Sebastien, Lemainque Arnaud, Yahiaoui Nabila, D'Hont Angélique. 2020. Plant Journal, 104 : 1698-1711.https://doi.org/10.1111/tpj.15031Test; http://agritrop.cirad.fr/596991/7/596991.pdfTest

الإتاحة: https://doi.org/10.1111/tpj.15031Test
http://agritrop.cirad.fr/596991Test/
http://agritrop.cirad.fr/596991/7/596991.pdfTest

المؤلفون: Dupouy, Marion, Baurens, Franc-Christophe, Derouault, Paco, Hervouet, Catherine, Cardi, Céline, Cruaud, Corinne, Istace, Benjamin, Labadie, Karine, Guiougou, Chantal, Toubi, Lyonel, Salmon, Frederic, Mournet, Pierre, Rouard, Mathieu, Yahiaoui, Nabila, Lemainque, Arnaud, Martin, Guillaume, d'Hont, Angélique

المساهمون: Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Paris-Saclay, CGIAR, French National Research Agency (ANR) : 1504-006 Labex, Agro:ANR-10LABX-0001-01, French National Research Agency (ANR) : ANR-10INBS-09, CGIAR Research Programme on Roots, Tubers and Bananas (RTB), ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), ANR-10-INBS-0009,France Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010)

المصدر: ISSN: 0305-7364.

مصطلحات موضوعية: banana, chromosomal rearrangement, reciprocal translocation, paired-end sequencing, genotyping by sequencing, Musa acuminata, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology

الوصف: International audience ; Background and Aims Banana cultivars are derived from hybridizations involving Musa acuminata subspecies. The latter diverged following geographical isolation in distinct South-east Asian continental regions and islands. Observation of chromosome pairing irregularities in meiosis of hybrids between these subspecies suggested the presence of large chromosomal structural variations. The aim of this study was to characterize such rearrangements. Methods Marker (single nucleotide polymorphism) segregation in a self-progeny of the 'Calcutta 4' accession and mate-pair sequencing were used to search for chromosomal rearrangements in comparison with the M. acuminata ssp. malaccensis genome reference sequence. Signature segment junctions of the revealed chromosome structures were identified and searched in whole-genome sequencing data from 123 wild and cultivated Musa accessions. Key Results Two large reciprocal translocations were characterized in the seedy banana M. acuminata ssp. burmannicoides 'Calcutta 4' accession. One consisted of an exchange of a 240 kb distal region of chromosome 2 with a 7.2 Mb distal region of chromosome 8. The other involved an exchange of a 20.8 Mb distal region of chromosome 1 with a 11.6 Mb distal region of chromosome 9. Both translocations were found only in wild accessions belonging to the burmannicoides/burmannica/siamea subspecies. Only two of the 87 cultivars analysed displayed the 2/8 translocation, while none displayed the 1/9 translocation. Conclusion Two large reciprocal translocations were identified that probably originated in the burmannica genetic group. Accurate characterization of these translocations should enhance the use of this disease resistance-rich burmannica group in breeding programmes.

العلاقة: info:eu-repo/semantics/altIdentifier/pmid/31241133; hal-02627570; https://hal.inrae.fr/hal-02627570Test; https://hal.inrae.fr/hal-02627570/documentTest; https://hal.inrae.fr/hal-02627570/file/Publis19-agap-029_dupouy_two_1.pdfTest; PRODINRA: 489101; PUBMED: 31241133; WOS: 000493045000015

الإتاحة: https://doi.org/10.1093/aob/mcz078Test
https://hal.inrae.fr/hal-02627570Test
https://hal.inrae.fr/hal-02627570/documentTest
https://hal.inrae.fr/hal-02627570/file/Publis19-agap-029_dupouy_two_1.pdfTest

المؤلفون: Rouard, Mathieu, Droc, Gaëtan, Martin, Guillaume, Sardos, Julie, Hueber, Yann, Guignon, Valentin, Cenci, Alberto, Geigle, B., Hibbins, M.S., Yahiaoui, Nabila, Baurens, Franc-Christophe, Berry, Vinvent, Hahn, M.W., D'Hont, Angélique, Roux, Nicolas

المصدر: Genome Biology and Evolution

مصطلحات موضوعية: F30 - Génétique et amélioration des plantes, Musa acuminata, Musa balbisiana, génome, phylogénie, hybridation, http://aims.fao.org/aos/agrovoc/c_4994Test, http://aims.fao.org/aos/agrovoc/c_4995Test, http://aims.fao.org/aos/agrovoc/c_3224Test, http://aims.fao.org/aos/agrovoc/c_13325Test, http://aims.fao.org/aos/agrovoc/c_3706Test, http://aims.fao.org/aos/agrovoc/c_7260Test, http://aims.fao.org/aos/agrovoc/c_1556Test, http://aims.fao.org/aos/agrovoc/c_4533Test, http://aims.fao.org/aos/agrovoc/c_3840Test

جغرافية الموضوع: Asie du Sud-Est, Chine, Malaisie, Indonésie

الوصف: 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.

وصف الملف: text

العلاقة: http://agritrop.cirad.fr/589366Test/; Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana). Rouard Mathieu, Droc Gaëtan, Martin Guillaume, Sardos Julie, Hueber Yann, Guignon Valentin, Cenci Alberto, Geigle B., Hibbins M.S., Yahiaoui Nabila, Baurens Franc-Christophe, Berry Vinvent, Hahn M.W., D'Hont Angélique, Roux Nicolas. 2018. Genome Biology and Evolution, 10 (12) : 3129-3140.https://doi.org/10.1093/gbe/evy227Test; http://agritrop.cirad.fr/589366/7/589366.pdfTest

الإتاحة: https://doi.org/10.1093/gbe/evy227Test
http://agritrop.cirad.fr/589366Test/
http://agritrop.cirad.fr/589366/7/589366.pdfTest

المؤلفون: Martin, Guillaume, Carreel, Françoise, Coriton, Olivier, Hervouet, Catherine, Cardi, Céline, Derouault, Paco, Roques, Danièle, Salmon, Frédéric, Rouard, Mathieu, Sardos, Julie, Labadie, Karine, Baurens, Franc-Christophe, D'Hont, Angélique

المصدر: Molecular Biology and Evolution

مصطلحات موضوعية: F30 - Génétique et amélioration des plantes, F63 - Physiologie végétale - Reproduction, Musa acuminata, translocation chromosomique, génome, ségrégation, chromosome, séquence nucléotidique, génotype, génie génétique, http://aims.fao.org/aos/agrovoc/c_4994Test, http://aims.fao.org/aos/agrovoc/c_24003Test, http://aims.fao.org/aos/agrovoc/c_3224Test, http://aims.fao.org/aos/agrovoc/c_6947Test, http://aims.fao.org/aos/agrovoc/c_1598Test, http://aims.fao.org/aos/agrovoc/c_27583Test, http://aims.fao.org/aos/agrovoc/c_3225Test, http://aims.fao.org/aos/agrovoc/c_15974Test

الوصف: Most banana cultivars are triploid seedless parthenocarpic clones derived from hybridization between Musa acuminata subspecies and sometimes M. balbisiana. M. acuminata subspecies were suggested to differ by a few large chromosomal rearrangements based on chromosome pairing configurations in inter-subspecies hybrids. We searched for large chromosomal rearrangements in a seedy M. acuminata ssp. malaccensis banana accession through mate-pair sequencing, BAC-FISH, targeted PCR and marker (DArTseq) segregation in its progeny. We identified a heterozygous reciprocal translocation involving two distal 3 Mb and 10 Mb segments from chromosomes 01 and 04, respectively, and showed that it generated high segregation distortion, reduced recombination and linkage between chromosomes 01 and 04 in its progeny. The two chromosome structures were found to be mutually exclusive in gametes and the rearranged structure was preferentially transmitted to the progeny. The rearranged chromosome structure was frequently found in triploid cultivars but present only in wild malaccensis ssp. accessions, thus suggesting that this rearrangement occurred in M. acuminata ssp. malaccensis. We propose a mechanism for the spread of this rearrangement in Musa diversity and suggest that this rearrangement could have played a role in the emergence of triploid cultivars.

وصف الملف: text

العلاقة: http://agritrop.cirad.fr/584605Test/; Evolution of the banana genome (Musa acuminata) is impacted by large chromosomal translocations. Martin Guillaume, Carreel Françoise, Coriton Olivier, Hervouet Catherine, Cardi Céline, Derouault Paco, Roques Danièle, Salmon Frédéric, Rouard Mathieu, Sardos Julie, Labadie Karine, Baurens Franc-Christophe, D'Hont Angélique. 2017. Molecular Biology and Evolution, 34 (9), 28 p.https://doi.org/10.1093/molbev/msx164Test; http://agritrop.cirad.fr/584605/14/584605.pdfTest

الإتاحة: https://doi.org/10.1093/molbev/msx164Test
http://agritrop.cirad.fr/584605Test/
http://agritrop.cirad.fr/584605/14/584605.pdfTest

المؤلفون: Martin, Guillaume, Baurens, Franc-Christophe, Droc, Gaetan, Rouard, Mathieu, Cenci, Alberto, Kilian, Andrzej, Hastie, Alex, Doležel, Jaroslav, Aury, Jean-Marc, Alberti, Adriana, A., Carreel, Françoise, D'Hont, Angélique

المساهمون: Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Bioversity International Montpellier, Bioversity International Rome, Consultative Group on International Agricultural Research CGIAR (CGIAR)-Consultative Group on International Agricultural Research CGIAR (CGIAR), Diversity Arrays Technology Pty Ltd (DArT P/L), Bionano Genomics Inc, Centre of the Region Haná for Biotechnological and Agricultural Research Univ Palacký (CRH), Faculty of Science Univ Palacký, Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences Prague (CAS)-Czech Academy of Sciences Prague (CAS), Genoscope - Centre national de séquençage Evry (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), The authors thank the Diversity Arrays Technology Pty Ltd for DArTSeq genotyping, Jan Vrána and Hana Šimková for preparation of HMW DNA, and CGIAR Research Program on Roots, Tubers and Bananas (RTB) for financial support for sequencing data acquisition. We also thank the South Green Bioinformatics Platform (http://southgreen.cirad.frTest) for providing us with computational resources. We thank Christophe Jenny for providing the Pahang segregating population from the CIRAD research station in Guadeloupe, French West Indies.

المصدر: ISSN: 1471-2164 ; BMC Genomics ; https://cea.hal.science/cea-04541793Test ; BMC Genomics, 2016, 17, pp.243. ⟨10.1186/s12864-016-2579-4⟩ ; https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2579-4Test.

مصطلحات موضوعية: Musa acuminata, Genome assembly, Bioinformatics tool, Paired-end sequences GBS, Genome map, [SDV.GEN]Life Sciences [q-bio]/Genetics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]

الوصف: Datasets (contigs, scaffold assembly, Pseudo-molecules, makers matrix and raw data of the genome map) are available through the banana genome hub (http://banana-genome.cirad.frTest/) and the 5 kb library is deposited on the ENA read archive (ID number: ERP013665). ; International audience ; Background: 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). Results: 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 ...

العلاقة: info:eu-repo/semantics/altIdentifier/pmid/26984673; cea-04541793; https://cea.hal.science/cea-04541793Test; https://cea.hal.science/cea-04541793/documentTest; https://cea.hal.science/cea-04541793/file/s12864-016-2579-4.pdfTest; PUBMED: 26984673; WOS: 000372091000004

الإتاحة: https://doi.org/10.1186/s12864-016-2579-4Test
https://cea.hal.science/cea-04541793Test
https://cea.hal.science/cea-04541793/documentTest
https://cea.hal.science/cea-04541793/file/s12864-016-2579-4.pdfTest

المؤلفون: Martin, Guillaume, Baurens, Franc-Christophe, Cardi, Céline, Aury, Jean-Marc, D'Hont, Angélique

المصدر: PloS One

مصطلحات موضوعية: F30 - Génétique et amélioration des plantes, F60 - Physiologie et biochimie végétale, Musa acuminata, Monocotylédone, chloroplaste, évolution, génome, séquence nucléotidique, marqueur génétique, carte génétique, phylogénie, http://aims.fao.org/aos/agrovoc/c_4994Test, http://aims.fao.org/aos/agrovoc/c_4914Test, http://aims.fao.org/aos/agrovoc/c_9824Test, http://aims.fao.org/aos/agrovoc/c_2745Test, http://aims.fao.org/aos/agrovoc/c_3224Test, http://aims.fao.org/aos/agrovoc/c_27583Test, http://aims.fao.org/aos/agrovoc/c_24030Test, http://aims.fao.org/aos/agrovoc/c_24002Test, http://aims.fao.org/aos/agrovoc/c_13325Test

الوصف: Background: Banana (genus Musa) is a crop of major economic importance worldwide. It is a monocotyledonous member of the Zingiberales, a sister group of the widely studied Poales. Most cultivated bananas are natural Musa inter-(sub-)specific triploid hybrids. A Musa acuminata reference nuclear genome sequence was recently produced based on sequencing of genomic DNA enriched in nucleus. Methodology/Principal Findings: The Musa acuminata chloroplast genome was assembled with chloroplast reads extracted from whole-genome-shotgun sequence data. The Musa chloroplast genome is a circular molecule of 169,972 bp with a quadripartite structure containing two single copy regions, a Large Single Copy region (LSC, 88,338 bp) and a Small Single Copy region (SSC, 10,768 bp) separated by Inverted Repeat regions (IRs, 35,433 bp). Two forms of the chloroplast genome relative to the orientation of SSC versus LSC were found. The Musa chloroplast genome shows an extreme IR expansion at the IR/SSC boundary relative to the most common structures found in angiosperms. This expansion consists of the integration of three additional complete genes (rps15, ndhH and ycf1) and part of the ndhA gene. No such expansion has been observed in monocots so far. Simple Sequence Repeats were identified in the Musa chloroplast genome and a new set of Musa chloroplastic markers was designed. Conclusion: The complete sequence of M. acuminata ssp malaccensis chloroplast we reported here is the first one for the Zingiberales order. As such it provides new insight in the evolution of the chloroplast of monocotyledons. In particular, it reinforces that IR/SSC expansion has occurred independently several times within monocotyledons. The discovery of new polymorphic markers within Musa chloroplast opens new perspectives to better understand the origin of cultivated triploid bananas.

وصف الملف: application/pdf

العلاقة: http://agritrop.cirad.fr/570107Test/; The complete chloroplast genome of banana (Musa acuminata, Zingiberales): Insight into plastid monocotyledon evolution. Martin Guillaume, Baurens Franc-Christophe, Cardi Céline, Aury Jean-Marc, D'Hont Angélique. 2013. PloS One, 8 (6):e67350, 10 p.https://doi.org/10.1371/journal.pone.0067350Test; http://agritrop.cirad.fr/570107/1/document_570107.pdfTest

الإتاحة: https://doi.org/10.1371/journal.pone.0067350Test
http://agritrop.cirad.fr/570107Test/
http://agritrop.cirad.fr/570107/1/document_570107.pdfTest

المؤلفون: Martin, guillaume, Cardi, Céline, Sarah, Gautier, Ricci, Sébastien, Jenny, Christophe, Fondi, Emmanuel, PERRIER, Xavier, Glaszmann, Jean-Christophe, D'Hont, Angélique, Yahiaoui, Nabila

المساهمون: Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), African Center for Research on Bananas and Plantains = Centre Africain de Recherches sur Bananiers et Plantains (CARBAP), French National Research Agency (ANR) : 0900-001, ANR-10-LABX-0001-01, French National Research Agency (ANR) : ANR-10-LABX-0001-01, 1504-006, CGIAR Research Programme on Roots, Tubers, and Bananas (RTB), CIRAD - UMR AGAP HPC Data Center of the South Green Bioinfor-matics platform, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)

المصدر: Plant Journal (In press), 1-18. (2020)
Plant Journal
The Plant Journal
Plant Journal, Wiley, 2020, 102 (5), pp.1008-1025. ⟨10.1111/tpj.14683⟩

مصطلحات موضوعية: Crops, Agricultural, Hybridation intergénérique, Musa acuminata, Chromosomes, Plant, diversity, F30 - Génétique et amélioration des plantes, Variation génétique, admixture, genome ancestry, hybridization, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Variété, Génome, Vegetal Biology, Domestication des plantes, fungi, food and beverages, Musa, Original Articles, F70 - Taxonomie végétale et phytogéographie, Hybridization, Genetic, Original Article, Genome, Plant, Biologie végétale

الوصف: Summary Hybridizations between closely related species commonly occur in the domestication process of many crops. Banana cultivars are derived from such hybridizations between species and subspecies of the Musa genus that have diverged in various tropical Southeast Asian regions and archipelagos. Among the diploid and triploid hybrids generated, those with seedless parthenocarpic fruits were selected by humans and thereafter dispersed through vegetative propagation. Musa acuminata subspecies contribute to most of these cultivars. We analyzed sequence data from 14 M. acuminata wild accessions and 10 M. acuminata‐based cultivars, including diploids and one triploid, to characterize the ancestral origins along their chromosomes. We used multivariate analysis and single nucleotide polymorphism clustering and identified five ancestral groups as contributors to these cultivars. Four of these corresponded to known M. acuminata subspecies. A fifth group, found only in cultivars, was defined based on the ‘Pisang Madu’ cultivar and represented two uncharacterized genetic pools. Diverse ancestral contributions along cultivar chromosomes were found, resulting in mosaics with at least three and up to five ancestries. The commercially important triploid Cavendish banana cultivar had contributions from at least one of the uncharacterized genetic pools and three known M. acuminata subspecies. Our results highlighted that cultivated banana origins are more complex than expected – involving multiple hybridization steps – and also that major wild banana ancestors have yet to be identified. This study revealed the extent to which admixture has framed the evolution and domestication of a crop plant.
Significance Statement Hybridizations between subspecies of Musa acuminata are at the origin of a diversity of banana cultivars whose genomes remain to be fully characterized for their ancestry. We developed a bioinformatics approach to decipher the genome ancestry mosaic in a set of banana cultivars including the commercially important Cavendish banana. We revealed that the cultivars resulted from multiple hybridization events involving known M. acuminata subspecies but also unknown contributors still to be discovered. These results bring essential information for breeding strategies in this crop that is particularly threatened by disease.

وصف الملف: text; application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=pmid_dedup__::aa46beaf6a42581beeaeb2d30f4bc0c6Test
http://agritrop.cirad.fr/594210Test/