203,381 research outputs found

    Paleoploidization events in the Musa (banana) lineage

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    Bananas (Musa spp.) are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales. Cultivars are mainly triploid, from inter(sub)specific origin and clonally propagated. We sequenced the genome of a Musa acuminata doubled-haploid genotype (Pahang-HD) providing the first monocotyledon high-continuity whole-genome sequence reported outside Poales. The analysis of the genome revealed three rounds of whole genome duplications (WGD), denoted as alpha, beta and gamma (from the most recent event to the oldest). Based on Ks analyses and synteny relationships, twelve beta Musa ancestral blocks were constructed, representing the ancestral genome before alpha and beta duplications. Comparative genomics and phylogenetic approaches revealed that these three WGDs occurred in the Musa lineage independently of those described in the Poales lineage and the one that we detected in the Arecales lineage. Following WGDs, that are particularly frequent in the flowering plant lineages, most duplicated genes are deleted by intrachromosomal recombination, a process referred to as fractionation. We are currently analyzing the fractionation pattern following the Musa polyploidization events. Finally, this Musa reference sequence represents an invaluable reference for studying monocot evolution and associated genomic changes. (Résumé d'auteur

    Using genotyping-by-sequencing to understand Musa diversity : [P449]

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    This project is part of a larger effort to apply genomics technologies to assess genetic diversity and to advance genetic improvement efforts in Musa (banana and plantain), a major staple food crop in the developing world. Most cultivated varieties of bananas result from intra- or inter-specific crosses of the wild diploid species, Musa acuminata (A genome) and Musa balbisiana (B genome). Somaclonal mutation and human selection has resulted in current day bananas with a wide morphological diversity. The Cavendish (AAA) subgroups are believed to have derived from an individual unique initial genotype, and similarly for the subgroup plantain (AAB). However, little or no genetic diversity can be detected within these groups using conventional molecular markers such as RFLP, SSR, DArT. To assess genetic diversity with an improved resolution, we have selected 65 accessions with diploid and triploid combinations of the A and/or B genomes including AAB plantains and AAA Cavendish, and cultivated or wild Musa accessions from the core collection at the Global Musa Genomics Consortium (GMGC) (http://www.musagenomics.org). We have used a high-throughput reduced representation genome sequencing approach - genotyping-by-sequencing (GBS) to obtain high density sequence markers. Genotypes are determined for each diploid and triploid accession, and dissimilarity computed across all accessions. We will discuss the value of GBS markers to characterize the genetic diversity of individual Musa subgroups with high resolution. This work is funded by the USAID linkage funds. (Texte intégral

    The Musa Germplasm Information System enhances knowledge of banana diversity

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    Bananas (Musa spp.) are a staple food and vital source of income for millions of people. These livelihoods in developing countries depend on over 1000 traditional varieties that are mostly consumed locally. Because Musa cultivars are usually seedless, their genetic diversity must be conserved as full-size plants or plantlets, in field collections or in in vitro genebanks. More than 6000 accessions are conserved in about 60 Musa national collections. The Global Musa Germplasm Collection (ITC) in Belgium, managed by Bioversity International, stores more than 1400 Musa germplasm accessions in trust. The utilization of the germplasm in the collection depends on the availability of information relating to the characteristics of each germplasm accession. In 1997, the Musa Germplasm Information System (MGIS) was developed. It is a global exchange system and the most extensive source of data on Musa genetic resources. It contains information on 5522 accessions managed in 22 banana collections, including passport data (where and when the germplasm accession was collected, donated or developed), botanical classification, morpho-taxonomic descriptors, and evaluation data (characteristics such as agronomic traits, disease, and stress tolerance) as well as many different photographs. Each participating collection enters and manages its own accession data, which is centralized by Bioversity. Links have been created to external data sources such as the System-wide Information Network for Genetic Resources (SINGER), under which FAO in-trust accessions held by ITC are published. MGIS has been recognised by the Generation Challenge Programme as a model system for storing accession-level data. However, it represents an incomplete dataset due to either the lack of capacity or motivation by several collections to contribute to it. The database has undergone two upgrades (see new release http://www.crop-diversity.org/banana/) and new features should be made available in the coming months, such as links to a molecular database (TropGENE DB), Geographic Information System (GIS) information, data quality control and inter-collection data comparison. (Texte intégral

    Comparison of hom(oe)ologous regions containing clusters of duplicated RGAs within Musa species and with rice

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    Understanding structure and evolution of genomic regions coding for proteins of agronomical interest is an important objective for crop improvement. We compare hom(oe)ologous regions within monocot genomes through BAC annotation. Here, we present putative orthologous and paralogous relationships of a highly duplicated Resistance Gene Analog (RGA) locus within Musa species and between Musa and rice species. (Résumé d'auteur

    Investigating chromosomal structural variations in Musa acuminate using NGS approaches : [W077]

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    Structural heterozygosity is thought to be one of the main causes of sterility in banana (Musa spp.) hybrids. These structural variations impact chromosomal segregation and recombination, limiting crossing possibilities and complicating genetic analyses. It is thus important to better understand their nature and location in the genome. For the production of the Musa accuminata reference genome sequence (D'Hont et al., Nature, 2012), we generated a genetic map that allowed anchoring 70% of the genome assembly on the 11 Musa chromosomes. The genetic map was based on a self progeny of the wild diploid Musa acuminata 'Pahang', the parent of the sequenced doubled haploid DH-Pahang. Strongly distorted markers were found on linkage group 1 and part of linkage group 4 that might indicate a structural rearrangement affecting these two linkage groups. We have developed a bioinformatic pipeline to help characterize structural variation based on resequencing approaches. We are using this pipeline on resequencing data of DH-Pahang and its parent and are densifying the genetic map with DArTseq markers to better understand the causes of the strong markers distortions and their link with structural variation. (Résumé d'auteur

    Evolution of gene families involved in banana fruit development and ripening : W077

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    A reference genome sequence of banana was recently obtained from a Musa acuminata doubled-haploid accession (DH-Pahang, 523 Mb) and organized into eleven pseudomolecules. This genome opens brand new perspectives for the identification of genes underlying key physiological processes and agricultural traits in this economically important species. To identify genes involved in banana fruit development and ripening, we used a whole genome-scale approach combining phylogenomic analyses and gene expression profiling. Global analysis of gene expression in banana fruits in response to ethylenic treatment was performed using RNA-seq. In parallel, gene families involved in core ethylene biosynthesis/signaling pathways and starch/sucrose metabolism were identified in the Musa genome using comparative genomics and phylogenomic analyses with eleven plant species. Our results showed a progressive global reprogramming of banana fruits during ripening characterized by an inhibition of the downstream ethylene signaling pathway. In addition, we identified expansions of gene families encoding transcriptional regulation elements of the ethylene signaling pathway in Musa. These expansions are currently analyzed in relation to Musa whole genome duplications. Finally, the combined structural and gene expression analyses led to the identification of candidate genes and gene family members involved in banana fruit ripening. (Résumé d'auteur

    Towards a bioinformatics platform for the Musa research community : [Abstract W076]

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    Current experiments in genomics produce a large amount of data that needs to be organized into databases and broadly accessible. Like other species, the Musa genomics community would benefit from centralized and innovative ways to study its genome. Over the past years, genetic and genomic data (e.g. BAC, EST, Markers) have been generated and stored in databases. Several pipelines of analyses were implemented for gene, transposable element, and expression data analyses, and for comparative genomics such as ortholog predictions via a phylogenomic approach (GreenPhyl). Web tools have been developed or implemented to facilitate access to data, such as genetic makers (TropGeneDB), genetic maps (CMap), a physical Map (GBrowse), and Expressed sequence Tags (ESTtik) gene/TE predictions, and to allow online manual genome annotation (GnpAnnot). The number of tools may continue to grow, in particular with the near release of the Musa genome sequence, and the increase of Next-Generation Sequencing (NGS) facilities. The GMGC website (http://www.musagenomics.org) is a place where data can be shared, and where databases and tools can be listed in an homogeneous way to serve the Musa genomics community. It is intended to provide the researchers interested in Musa with a common set of resources in order to work more efficiently and effectively. (Texte intégral

    Banana and plantain (Musa spp.) cultivar preference, local processing techniques and consumption patterns in Eastern Democratic Republic of Congo

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    This cross-sectional study carried out in North Kivu (NK) and South Kivu (SK) of the Eastern Democratic Republic of Congo aimed to identify the most preferred Musa cultivars, their processing/cooking methods and Musa consumption patterns among rural households. Our results showed that the preferred cooking banana varieties included yellow-pulped AAA-East African Highland bananas [EAHB] 'Nshikazi' (SK) and 'Vulambya' (NK), which were valued for their cooking qualities, large bunches and suitability for production of banana beer. The preferred plantains were orange-pulped and included 'Musheba' (SK) and 'Musilongo' (NK) and were preferred for their short maturation period, large bunches and higher market prices. Over 60% of the households examined had consumed EAHB within 24 hours, whereas <10% had consumed plantains. The most common cooking method was simple boiling of bananas/plantains and main accompaniments include beans and amaranth leaves. Over 69% of surveyed households that had consumed Musa products had con-sumed them boiled. The majority of the households (90%) obtained banana/plantains from their farms, and >55% of households from SK and NK consumed banana products between 2 and 4 times/week. This information will be used to help direct researchers on the Musa cultivars that could be further sampled for carotenoid analysis and those found to be rich could be used in the fast-tracking approach to reduce Vitamin A deficiency. (Résumé d'auteur

    The Banana (Musa acuminata) genome and the evolution of monocotyledonous plants : W401

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    Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the Zingiberales order, a sister group to the well-studied Poales. We sequenced and assembled the 520 Mb genome of a doubled-haploid of the accession 'Pahang'. This accession belongs to the Musa acuminata species (AA genome) malaccensis subspecies. 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 sheds new light on the monocotyledon lineage, reveals Poaceae specific features and has led to the discovery of conserved noncoding sequences predating monocotyledon-eudicotyledon divergence. The complete list of authors involved in this work can be found in D'Hont et al. Nature. 2012 Aug 9; 488(7410):213-7 (Résumé d'auteur

    Sequencing the banana genome (W069)

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    Bananas (Musa) are the fourth most important crop in developing countries. They are important as an export crop but also play a major role in local food security. Crops of Musa are susceptible to an ever increasing range of diseases requiring massive use of pesticides that have dramatic environmental and health impacts and threaten the sustainability of the crop. There is thus an urgent need for a wider diversity of genetically improved banana cultivars with more robust disease resistance, increased productivity and better adaptability to a large range of growing conditions. The production of export dessert bananas relies on very few related genotypes of the Cavendish subgroup with an AAA genome constitution. However, numerous dessert and cooking types with an AAA, AAB (including plantain) or ABB genome constitution are grown for local consumption. The Musa accession selected for sequencing is a doubled haploid of the accession 'Pahang' (DH Pahang). This accession belongs to the Musa acuminata species (AA genome) malaccensis subspecies. We generated 20x coverage using paired and single 454 reads, complemented by Sanger BESs and ~50 x coverage of Illumina shotgun data. The assembly was performed with Newbler, and the scaffolds were anchored to a genetic map. Genes were predicted using a reconciliation approach taking ESTs, protein sequences and ab initio data as input. A genetic map of the parent accession 'Pahang' was developed with SSR and DArT markers to assemble the scaffolds in pseudo-molecules. (Texte intégral
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