Sequencing the banana genome (W069)

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

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

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

Fluorescence in situ hybridization in sugarcane or fish-ing in the genomic wilderness. [MO06]

Cytogenetics applied to sugarcane has brought our fundamental understanding of the sugarcane genome to a new level. In the mid-nineties, Genomic in situ Hybridisation (GISH) was first applied to sugarcane to determine the specific composition of the modern cultivar R570. GISH revealed the chromosomal composition of R570 was 80% Saccharum officinarum, 10% S. spontaneum and 10% of recombined chromosomes. The Australian counterpart Q165, revealed a slightly different species composition as 75%, 15% and 10%, respectively. Both R570 and Q165 genetic maps have portrayed a partial coverage of linkage groups (LG) despite the large number of molecular markers invested in the maps. It also shows that S. spontaneum chromosomes seem to have a better vertical coverage than S. officinarum chromosomes as the S. spontaneum genome is more polymorphic. To gain a better understanding of the genome composition in terms of LG number per homology group (HG) and species attribution of the LG, we applied BAC-FISH to sugarcane. Bacterial Artificial Chromosomes (BAC) consist of large chromosome segments (around 100kb). BAC from the Sorghum or Saccharum genomes were used as anchorage points on the sugarcane cultivars to identify homologous/homeologous chromosomes for each HG. We will present some examples of results of BAC-FISH applied to several cultivars for at least 4 different HG. The determination and comparison of the number of chromosomes per HG to the number of LG from the genetic maps will determine the saturation level of the genetic maps. This will help us to obtain critical knowledge of the horizontal chromosome distribution for a particular cultivar and compare its structure to another cultivar. Eventually we will have a better understanding of the distribution of the chromosomes during crossing and this will help breeders to make more informed and targeted choices in their selection programs. (Texte intégral

The Sequence of the Banana (Musa acuminata) Genome. W068

We produced a reference genome sequence of banana. 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 20.5X coverage of the 523 Mb genome of DH-Pahang (estimated by flow cytometry) using paired and single 454 reads, complemented by Sanger plasmid- and BAC- End Sequences. An additional ~50X coverage of Illumina shotgun data was produced in order to ensure a high quality sequence draft. The assembly, performed with Newbler software, covers 472.2 Mb which represent 90% of the genome of DH-Pahang. A high-density genetic map was produced using SSR and DArT markers that enabled anchoring 70% of the assembly in 11 pseudo-chromosomes. We identified 36,542 protein-coding gene models using a reconciliation approach taking ESTs, protein sequences and ab initio data as input. The general features of the Musa sequence and its comparison with other sequenced genomes, in particular from the Poaceae, will be presented. This project is carried out in the framework and with the participation of partners of the Global Musa Genomics Consortium. (Texte integral

Characterization of large chromosomal structural variations between Musa acuminata sub-species by NGS re-sequencing

M. acuminata has evolved in several sub-species that have been geographically isolated on various archipelagos, and have accumulated large structural variations. Domestication of banana involving hybridization between these subspecies has been made possible by human migration and selection of diploid and triploid inter-sub-specific hybrids with seedless parthenocarpic fruits. Large structural variations within M. acuminata have been hypothesized based on chromosome pairing analysis and genetic mapping. These structural variations are suspected to be at least partially responsible for M. acuminata hybrids sterility. This sterility allows the production of seedless fruits but complicates breeding programs by limiting crossing possibilities. These structural variations also impact chromosomal segregation and recombination, complicating the transmission of agronomical traits of interest and genetic analyses. There is thus a strong need to characterize these structural variations within the Musa acuminata sub-species. A re-sequencing approach to characterize these structural variations is currently being tested. lt is based on paired-end sequencing of genomic fragments of known sizes from banana accessions, and comparison to the Musa acuminata reference genome to detect discrepancies in paired-read mapping. A specific bioinformatics pipeline has been developed to detect different types of structural variations, and validated on simulated data. The pipeline is currently being tested on diploid banana accessions using various DNA fragment sizes (5kb to 15kb) in order to optimize the detection of large structural variations. (Résumé d'auteur

Molecular breeding of sugarcane using linkage disequilibrium maps and quantitative trait alleles : [Abstract W247]

Sugarcane breeding generally involves forms of recurrent selection using overlapping generations of parent genotypes, with the number of parents used in the order of 100 to 400, depending on the size of the breeding program. Genetic maps of one or a few genotypes are thus not very useful in routine breeding applications, as they provide no information on the allelic variation at important loci within the breeding population. In order to integrate mapping, marker discovery and conventional breeding we have developed methods (i) to create population-level maps of haplotypes in linkage disequilibrium within the breeding population, (ii) to identify potentially useful quantitative trait alleles (QTAs) through association analysis, and (iii) to predict to performance of progeny of bi-parental crosses from the marker (QTA) profile of the parents. The usefulness of the approach has been empirically verified in an experiment which demonstrated that the performance of progeny is better predicted by parental QTAs than by parent phenotype (h2 = 0.82, versus 0.57). By examining the population-level haplotype map, cryptic population structure caused by the complex linkage arrangements that can exist in polyploids could be detected, and accounting for this structure/linkage can further improve the effectiveness of molecular breeding. Additional uses of the map, such as identifying the ancestral origins of haplotypes, and detecting signatures of selection and recombination over several generations of breeding will be demonstrated. (Texte intégral

GNPAnnot community annotation system applied to sugarcane bac clone sequences (W572)

A large amount of data is being produced by current genome sequencing projects. Sequence annotations and analyses need to be organized into databases and widely accessible. Like other species, sugarcane would benefit from centralized and innovative systems to study its genome. The GNPAnnot community annotation system (CAS) could be particularly relevant to the SUGESI sequencing project. It consists in a system for structural and functional annotations supported by comparative genomics allowing both automatic predictions and manual curations of genes and transposable elements. The core of the GNPAnnot CAS dedicated to tropical plants is made of GMOD components.The Chado database can be browsed using the Generic Genome Browser (GBrowse) which provides links to genome editors (ie. Artemis and Apollo). We developed the Chado controller in order to manage public and private annotation projects. It also provides an annotation history page for each gene or transposable element and an annotation inspector that automates several tasks and reports annotation mistakes. GNPAnnot CAS has already been used to annotate sugarcane BAC clones sequences and could be useful to facilitate the annotation of novel sugarcane sequences. (Résumé d'auteur

Evolutionary dynamics of hom(oe)ologous chromosome segments within the highly polyploid sugarcane genome

Modern sugarcane (Saccharum spp.) is the leading sugar crop and a primary energy crop. It presents one the most complex crop genome studied to date, mainly due to the very high level of vertical redundancy (2n = ca 12x = ca 120 = 10 Gb), together with an interspecific origin. Modern cultivars are derived from hybridization, performed by breeders a century ago, between two autopolyploid species, namely S. officinarum (domesticated, 2n=8x=80) and S. spontaneum (wild species, 2n=5x=40 to 16x=128). To investigate genome dynamics in this highly polyploid context, we sequenced and analyzed the structural organization of hom(oe)ologous chromosome segments (bacterial artificial chromosome clones) from a few regions the sugarcane cultivar R570. For all regions, almost perfect gene colinearity and high gene structure and sequence conservation were observed. Moreover, the vast majority of the homoeologous genes were predicted, based on their structure, to be functional and showed signs of evolving under purifying selection. Compared to sorghum, the sugarcane haplotypes displayed a high gene colinearity. By contrast, transposable elements displayed a general absence of colinearity among hom(oe)ologous haplotypes Our data suggest the presence of broad sets of functional homologous alleles in its genome, which could explain its unique efficiency, particularly its high phenotypic plasticity and wide adaptation. (Résumé d'auteur