A mosaic monoploid reference sequence for the highly complex genome of sugarcane

La canne à sucre (Saccharum spp.) est une graminée (Poaceae) tropicale majoritairement cultivée pour produire du sucre mais son imposante masse végétale est aussi convertible en bio-energie. Les cultivars modernes de canne à sucre sont issus de croisements interspécifiques entre deux espèces polyploïdes, Saccharum officinarum (2n = 8X = 80 chromosomes) et Saccharum spontaneum (2n= 5X à 12X = 40 à 128 chromosomes). Le génome de ces cultivars est donc hautement polyploide (~12X), aneuploïde (2n = 8x à 12x = 100 à 130 chromosomes) et hétérozygote. Ces caractéristiques en font un des génomes les plus complexes parmi les plantes cultivées et l'obtention d'une séquence de référence de l'ensemble du génome avec les méthodes d'assemblage actuels représente donc un véritable challenge. Dans des études précédentes, nous avions montré que les chromosomes hom(e)ologues du génome de la canne à sucre partagent entre eux un très haut niveau de micro-colinéarité et présentent également une très bonne synténie avec le génome du sorgho. Ces résultats nous ont permis de proposer que le séquençage d'un génome de base (génome monoploïde) représenterait une bonne séquence de référence et que le sorgho pourrait nous permettre d'identifier cette partie du génome. Notre stratégie basée sur la technique de Whole Génome Profiling nous a permis d'identifier 4660 clones BAC de canne à sucre (BAC = fragment de chromosome d'environ 100 kb) recouvrant la partie riche en gène du génome du sorgho. Ces clones BAC ont été séquencés et assemblés en 10 chromosomes et correspondent à la partie riche en gène d'un génome monoploide de canne à sucre représentant une séquence de 382 Mb. 25,316 modèles de gènes ont été prédit et 17% d'entre eux ne sont pas retrouvés en position colinéaires avec leur orthologue chez le sorgho. D'autre part, nous avons montré que les génomes des deux espèces à l'origine des cultivars modernes, S. officinarum et S. spontaneum ont un contenu en éléments transposables différent qui explique leur différente taille de génome de base. Ces deux espèces diffèrent également par quelques larges réarrangements chromosomiques qui expliquent leur nombre de chromosomes de base différents

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

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

Complexities of chromosome landing in a highly polyploid, aneuploid, interspecific genome: Towards map-based cloning of a resistance gene (bru1) in sugarcane (2n=ca 115)

The genom e of modern sugarcane cultivars is highly polyploid (~12x), aneuploid, of interspecific origin, and contains 10 Gb of DNA. Its size and complexity represent a major challenge for the isolation of agronomically important genes. We have undertaken the first attempt to isolate a gene from sugarcane by map-based cloning, targeting a durable major rust resistance gene (Bru1).To overcome constraints associated with high polyploidy, we developed stategies including diploid/polyploid syntenic shuttle mapping with model diploid species (sorghum and rice) and haplotype-specific chromosome walking. These strategies allowed us to develop a high-resolution genetic map including 17 markers in an interval of 0.42 cM comprising Bru1 and to build a physical map of the target haplotype that still includes two gaps at this stage due to the discovery of an insertion specific to this haplotype. BAC clones representing seven differents hom(oe)ologous haplotypes have been sequenced. These sequence s are being used to complete the physical map of the target haplotype. (Texte intégral

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

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

Paleoploidization events in the Musa (banana) lineage

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

Exploiting Erianthus diversity to enhance sugarcane cultivars.[W1024]

Introgression of Erianthus arundinaceus into the SRA sugarcane-breeding program has been a goal for researchers for many years. The Erianthus genome was finally accessible to sugarcane breeders with the identification in 2005 of the first Saccharum/Erianthus fertile hybrids, developed in China. Today, Saccharum/Erianthus BC3 and BC4 clones are available in Australia, and Erianthus-sugarcane hybrids have been characterised by cytogenetics and investigated for their potential resistance against pachymetra root rot, sugarcane smut and nematodes. Some clones have shown potential as new sources of resistance for incorporation into the SRA breeding program. These hybrids were created from Erianthus clones indigenous to China and their reaction to the above diseases is unknown in Australian conditions. In Meringa we also have access to many Erianthus clones of Indonesian origin. Some of these Erianthus clones have previously shown immunity to pachymetra root rot. In the late 1990s, these Indonesian Erianthus clones were used in crossing but no fertile hybrids were ever produced due to an incompatibility between the Saccharum and the Erianthus genomes. We revisited this untapped source of resistance by utilising the fertile Erianthus hybrids derived from China to cross with the Indonesian Erianthus of known resistance to pachymetra root rot. Here we report on the early stage results of introgressing Indonesian Erianthus into the SRA breeding program

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