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

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

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

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

A community annotation system for Musa genomes

Poster presented at ISHS/ProMusa Banana Symposium Global Perspectives on Asian Challenges. Guangzhou (China), 14-18 Sep 200

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

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

Molecular characterisation of integrated sequences of Banana streak virus in the banana plant genome

The genome of banana (Musa sp.) harbours multiple integrations of several species of Banana streak virus (BSV), certainly resulting from illegitimate recombination between host and viral DNA. Surprisingly, this pararetrovirus does not require integration for its replication. Some integrations, only existing in the Musa balbisiana genome (denoted B), are infectious by reconstituting a functional viral genome. To date, four widespread species of BSV (Goldfinger -BSGfV, Imové - BSImV, Mysore - BSMysV and Obino l'Ewai - BSOLV) have been reported as integrated into the B genome and as infectious, under stress conditions, resulting in viral infection of the banana plant. In order to study BSV expression from such viral integrants, a characterisation of infectious integrants (eBSV) was undergone by studying both a Musa BAC library obtained from the wild diploid M. balbisiana cv. Pisang Klutuk Wulung (PKW) containing the four BSV species described above and one interspecific genetic cross using carrier PKW. The organization of eBSGfV was fully characterized recently in our lab (Gayral et al., 2008). eBSGfV results from a single event of integration corresponding to an allelic insertion extensively rearranged, containing at least one full-length viral genome. Although the four BSV species present important differences with each other, the organisation of the three other eBSVs looks like eBSGFV. Indeed, preliminary data indicate that each of them is extensively rearranged in PKW and present as two insertions at the same locus. This suggests an allelic insertion resulting from a single even of integration. Experimental evidences to demonstrate BSV expression and to validate the infectious nature of every eBSV are on the way. (Texte intégral

Transposable elements in the robusta coffee genome (Coffea canephora) : [W187]

Coffee is one of the most important international trade commodities and is ranked as the second most valuable primary commodity exported by southern countries. Two species are mainly used in commercial production: Coffea arabica, known as Arabica and Coffea canephora, a perennial diploid species known as Robusta. Recently, 54.4 million of Roche 454 sequences, 131,412 Sanger BAC-end sequences and 60X Illumina coverage of the 710 Mb genome of a C. canephora Double Haploid accession (DH200-94) were generated, assembled and anchored to a genetic map. The C. canephora genome sequence represents a formidable resource to understand the chromosome structure and the genome evolution. It is now well established that plant genomes are dynamic structures submitted to a wide range of modifications via the activity of Transposable Elements (TEs). Transposable elements are mobile sequences that share several key properties such as the ability to move from one chromosome location to another, to amplify their copy number within the host genome and to contribute to the chromosome structure, organization and evolution. Particularly, TEs play a major role in creating structural variation and genetic diversity in plant genomes. Here we present the identification and classification of TEs in the 568 Mb genomic sequences of the C. canephora using a combination of ab initio, similarity and structure search approaches. We used mainly the REPET package V.2.1-RC (Flutre et al., 2011) to identify, classify and annotate TE. We found that 49% of the genomic sequences are composed of TEs similarly to other sequenced plant genomes such as banana, papaya, castor bean and soybean. Class I LTR retrotransposons represent the vast majority of identified elements, accounting to 42% of the genome assembly. Gypsy elements clearly outnumbering Copiaelements since Ty3-Gypsy family covers 24.1% of the genome. Interestingly active non-autonomous LTR retrotransposons elements were detected and classified into a new subgroup of non-autonomous elements containing a capsid domain but lacking the polyprotein region. Finally in an attempt to study conservation of LTR retrotransposons between coffee and reference plant genomes, we identified an outstanding conservation of several Copia groups across very distantly related plant species, suggesting that conservation of such elements or horizontal transfer events might be more frequent than recognized actually. (Texte intégral

Identification and characterization of genes involved in ABA perception and signal transduction in Coffea spp : S02P13

The Coffea genus represents a major agricultural commodity in world trade. Nowadays, drought and elevated temperatures are the major climatic limitations for coffee production. These variations also influence biochemical composition of beans, affecting directly the final cup quality. There is genetic variability within the Coffea genus that could be used to increase drought tolerance and generate coffee varieties better adapted to climatic variations. Abscisic acid (ABA) is a vital plant hormone acting as central regulator that protects plants against abiotic stresses such as drought. Recently, novel intracellular ABA receptors (PYL/RCARs) involved in ABA sensing and signaling have been identified in several species. A mechanism of ABA transduction has been proposed, involving PYR/PYL/RCARs receptors interacting with PP2Cs phosphatases and SnRK2 protein kinases. The goal of this study was to identify and characterize ortholog genes of this tripartite system in Coffea sp. For this purpose, protein sequences from Arabidopsis, citrus, rice, grape, and tomato were chosen as query to search ortholog genes in the coffee-sequence database. Using 51 PYR/PYL/RCAR sequences from those plant species, it was possible to identify 9 sequences for ABA receptors in coffee. Likewise, the 40 and 29 sequences query resulted in 6 and 9 similar sequences of PP2Cs and SnRK2 specific to ABA in Coffea sp. The 24 genes isolated, that belong to the tripartite system of the coffee's ABA pathway, showed in silico differential expression in tissues as leaves, seeds, roots and floral organs. Polymorphisms were found among the orthologs and homeologs genes. All analyses allowed the identification in C. arabica genome of sequences variations between the two ancestral diploid sub-genomes, C. canephora (CaCc) and C. eugenioides (CaCe). Further analyses will predict the functional effect of these polymorphisms in protein structure in different coffee species. All these evidences will also help us to identify the genetic determinism of drought tolerance essential to obtain molecular markers that could be used in coffeebreeding programs. Work supported by CAPES-COFECUB, Consórcio Pesquisa Café and INCT-Café (CNPq/FAPEMIG). (Texte intégral