Musatract: Sequencing of the banana (Musa acuminata) whole genome : [Abstract W075]

Genoscope (French National Sequencing Center) and the CIRAD are engaged in the complete sequencing of the banana genome in the framework of the Global Musa Genomics Consortium. The banana accession chosen is a doubled haploid (Musa acuminata, subspecies malaccensis, accession Pahang DH). M acuminata represents the main species that enters into the composition of dessert and cooking bananas; its genome consists of 500 to 600 million base pairs, depending of the subspecies, spread over 11 different chromosomes. The sequencing strategy is a mixed approach combining the Sanger, 454 and Solexa technologies. A high-density map is currently being developed for scaffold anchoring. The sequencing phase will be completed in early 2010 and automatic annotation will take place during the first semester of 2010. An update on the progress will be presented. (Texte intégral

Advancements in breeding Fusarium resistant vanilla varieties using Next Generation Sequencing

Demand for natural vanilla flavor is increasing, but the cultivated Vanilla planifolia faces critical challenges in response to biotic and abiotic stresses. In particular, Root and Stem Rot (RSR) disease caused by Fusarium oxysporum f. sp. radicis-vanillae (Forv) is the most damaging disease of vanilla. What can we do to reduce the damage? Prophylactic measures and use of chemicals or biocontrol agents are not effective in controlling RSR in the field. In this context, the use of resistant varieties is the best option to reduce Fusarium impact. Low genetic diversity has been detected within V. planifolia in accordance with the vegetative mode of dispersion of the vine. However, among the V. planifolia cultivars conserved in the Biological Resources Center Vatel at CIRAD La Réunion, several showed Forv resistance in lab tests as well as in the field. The exploration and deciphering of vanilla genomes using Next Generation Sequencing (NGS) provides a real reservoir of knowledge in support to the vanilla breeding programs. In particular, it opens access to genes involved in RSR plant resistance, allowing the development of molecular markers genetically linked to resistance

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

Detailed analyses of 12 hom(oe)ologous chromosome segments in the highly polyploid sugarcane genome

Modern sugarcane cultivars (Saccharum spp.) are recognized as the crop with the most complex genome studied to date, mainly due to the very high level of vertical redundancy (2n = ca 12x = ca 120), together with an interspecific origin. They are derived from hybridization, performed by breeders a century ago, between two autopolyploid species, namely S. officinarum (domesticated) and S. spontaneum (wild species, 2n=5x=40 to 16x=128). To investigate the impact of polyploidization on its genome organization and more widely on its performance and plasticity, we finely analyzed the structural organization of hom(oe)ologous chromosomes. Thirty-three homoeologous BAC clones from four regions of the sugarcane R570 genome were identified, sequenced, finely annotated and compared, representing more than 3 Mb of sugarcane DNA sequence. For all four regions, almost perfect gene colinearity and high gene structure and sequence conservation were observed, confirming previous preliminary analyses on two of these regions. 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. For one of the region carrying the Adh1 gene, we extended the homoeologous series to 13 hom(oe)ologous chromosome segments. Gene similarity and patterns of transposable element insertions are currently being analyzed in order to determine the origin (S. officinarum vs S. spontaneum) and the evolutionary dynamics of these hom(oe)ologous regions. (Résumé d'auteur

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

Comparison of hom(oe)ologous chromosome segments in the highly polyploid interspecific genome of sugarcane

Modern sugarcane cultivars (Saccharum spp.) present one of the most complex crop genome studied to date, mainly due to a very high degree of polyploidy (2n = 12x = 120), and an interspecific origin from two autopolyploid species, namely S. officinarum and S. spontaneum. To investigate the impact of polyploidization on the sugarcane genome organization and more widely on its performance and plasticity, we finely analyzed the structural organization of hom(oe)ologous chromosome segments. Twenty-seven homoeologous BAC clones from three distinct regions, carrying the genes Adh1 (13 hom(oe)ologous chromosome segments), PST2a (10 hom(oe)ologous chromosome segments) and CAD2 (4 hom(oe)ologous chromosome segments), were identified, sequenced, finely annotated and compared, representing more than 2.5 Mb of sugarcane DNA sequence. A very high gene colinearity, gene structure and sequence conservation (98.1% of average nucleotide sequence identity for the coding sequence, and 93.3% for the aligned part of the introns) was observed among all hom(oe)ologous chromosome segments, confirming preliminary observations. Based on their structure, the homoeologous genes were predicted to be functional and the vast majority of them showed signs of evolving under purifying selection. Colinearity between hom(oe)ologous chromosomes was also extended to many intergenic regions and transposable elements. Divergence between hom(oe)ologous genes and patterns of transposable element insertions are currently being analyzed in order to infer the origin (S. officinarum vs S. spontaneum) of the chromosome segments. The high level of gene colinearity and structure conservation has implication regarding whole genome sequencing strategy of this complex genome, since it suggests that one chromosome segment could serve as reference for the other hom(oe)ologous chromosome segments regarding gene content. The maintenance of a broad set of functional alleles, that we described, may be involved in the high phenotypic plasticity and wide adaptation of sugarcane. (Résumé d'auteur

GNPAnnot: a community annotation system applied to sugarcane sequences : W745

A large amount of data is being produced by current genome sequencing projects. Sequence annotations need to be organized into databases and widely accessible. Like other species, sugarcane would benefit from centralized and innovative systems to study its genome. GNPAnnot is a community system performing structural and functional annotations of genes and allowing both automatic predictions and manual curations of genes and transposable elements (TEs). The system is currently being used for various plants, insect and fungus species. The GNPAnnot pipeline is made of a collection of programs that are connected together to automate genomic sequence annotations. Sequences and results are stored into the Chado GMOD database and can be visualized through a genome browser accessible from the Web portal of the SouthGreen bioinformatic platform (http://southgreen.cirad.fr/). Annotations can be manually edited using the Artemis genome editor. A database controller has been developed (Chado controller) in order to manage public and private annotation projects. It also provides an annotation history page for each gene or TE, and an annotation inspector that reports manual annotation mistakes. The GNPAnnot system is currently being used to annotate sugarcane BAC sequences in the framework of the SUGESI (Sugarcane Genome Sequencing Initiative) that aims at sequencing around 5,000 BACs, from cultivar R570, corresponding to the gene rich part of a monoploid genome of sugarcane. The GNPAnnot system has been developed by partners of CIRAD, INRA and Bioversity and has been supported by the French National Research Agency and the Genoplante joint program. (Résumé d'auteur

High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane

Modern sugarcane (Saccharum spp.) has been recognized as one of the world's most efficient crops in solar energy conversion and as havlng the mast favorable input: output ratios. Beside ils importance for sugar production, ilthus became recently aprimary energy crop. Sugarcane also presents 01)6 the most complex crop genome studied to date, rnainly due to avery high degree of polyploidy (2n=ca 12x=ca 120), together wiltl an inlerspecffic origin. In arder to invesligate genome dynamics in this highly polyploid context and 10 provide guidelines for future whole genome sequencing project, we sequenced and compared seven homoeologous haplotypes (BAC clones). Our analysis revealed ahigh conservation at the gene level (high colinearlty and high gene structure and sequence conservation). Remarkably, ail homoeo-alleles are predicted functional and no apparent general decrease of purilying selection was observed. Thus Ihe high polyploldy of sugarcane does not seem to have induced a major reshaping of ils genome, alleast at the gene levaI. By contras~ transposable elements displayed ageneral absence 01 colinearily among homoeologous haplotypes and appeared fo have uooergone dynamic expansion in Saccharum, compared Vlith sorghum, its clOse relative ln the Andropogonea tribe. Our data sugges! lt1e presence of broad sets of funcllonal homologous alleles in the sugarcane genome, which could explain ,. ils unique efficiency, ils hlgh phenolypic plaslicily and wide adaptation. (Texte intégral

Evolutionary dynamics of hom(oe)ologous haplotypes (bacs) within the highly polyploid sugarcane genome

Sugarcane (Saccharum spp.) has been recognized as one of the world's most efficient crops in converting solar energy into chemical energy and having the most favorable input/output ratio. Beside its importance for sugar production it is thus also a primary energy crop. Sugarcane also presents one the most complex crop genomes studied to date. Modern sugarcane cultivars derive from the combination of two polyploid species: S. officinarum, the domesticated sugar-producing species with x=10 and 2n=8x=80, and S. spontaneum, a vigorous wild species with x=8 and 2n=5x=40 to 16x=128 and many aneuploid forms. Both species are thought to have an autopolyploid origin. Modern sugarcanes are highly polyploid (more than decaploid) and aneuploid, with around 120 chromosomes and a genome size of around 10 Gb. They typically display 70 to 80% of chromosomes entirely derived from S. officinarum, 10 to 20% from S. spontaneum and a few chromosomes derived from interspecific recombination. Their meiosis mainly involves bivalent pairing and chromosome assortment results from a combination of polysomy and preferential pairing. We investigated genome dynamics in this highly polyploid context by analyzing the sequence of hom(oe)ologous haplotypes (BAC clones) from the sugarcane cultivar R570. We first analyzed two homoeologous haplotypes from a gene-rich region bearing the Adh1 gene (Jannoo et al 2007), knowing that this region has been thoroughly studied within the Poaceae family. We then analyzed seven hom(oe)ologous haplotypes from a second gene-rich region. Our results indicated that the two Saccharum species diverged 1.5-2 mya from one another and 8-9 mya from sorghum. The sugarcane hom(oe)ologous haplotypes showed a very high colinearity as well as very high gene structure and sequence conservation. A high homology was also observed along the non-transcribed regions to the exception of transposable elements (TEs). Conversely, TEs that represent in average 33% of the BAC clones studied, were not conserved between hom(oe)ologous haplotypes. Compared to sorghum, the sugarcane haplotypes displayed a high colinearity and a remarkable homology in most of the non-coding parts of the genome. On this basis, the high ploidy of sugarcane does not seem to have induced a major reshaping of its genome (at least at the gene level). In addition, the coexistence of potentially in average 12 hom(oe)ologous alleles at each locus does not seems to induce a decrease of conservative selection at the gene sequence level. (Texte intégral

Whole genome profiling to generate a core physical map of the gene rich part of the sugarcane genome : [W778]

The sugarcane genome poses challenges that have not been addressed in any prior genome sequencing project. The main difficulties reside in its high polyploidy (2n ~ 12x ~ 120), and its high level of heterozygosity which makes an assembly of the whole genome very challenging through classical shotgun approaches. Previous studies demonstrated that sugarcane hom(e)ologous chromosomes share a very high level of microcolinearity among themselves and show good micro-colinearity with sorghum. These findings suggested that sequencing a minimum tiling path (MTP) of BACs representing the gene-rich part of the monoploid genome could represent a very-useful sugarcane reference sequence. Sorghum could provide a good template to select this core set of sugarcane BACs. In the present study, we exploited the Whole Genome Profiling (WGP) technology of Keygene to analyze a set of 20,736 BACs from cultivar R570, representing an approximate 2=- fold coverage of the monoploid genome of sugarcane. The WGP technology generates short sequence tags from the terminal ends of restriction fragments from pooled BACs, allowing the development of highly accurate sequence-based physical maps. Sequence tags were obtained for 18,787 sugarcane BACs that were assembled into 3,903 contigs with an average of 3.4 BACs per contig. An average of 37.2 sequence tags per BAC was generated which allowed the anchoring of more than 11,000 of the profiled R570 BACs on the sorghum sequence. A core subset (MTP) of these BACs will now be selected and sequenced to generate a reference sequence of the gene-rich part of the sugarcane genome. (Texte intégral