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

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

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

Genome sequencing project has begun on two plant trypanosomatids (Phytomonas)

Some trypanosomatids are responsible for wilt in tropical crops, such as hartrot disease in the coconut palm. They have a major economic impact in Latin America and the Caribbean. In the latex vessels of some plants, other trypanosomatids appear to be "symbiont-like", without any negative effect on their host, and others multiply in fruits and seeds. The latter usually belong to the genera #Crithidia#, #Herpetomonas# and #Leptomonas#, formerly known as "lower trypanosomatids". Only one arbitrary genus name has been proposed as yet for all these trypanosomatids living in plants, in different tissues, with different consequences: #Phytomonas#. After the Trytrip project and the recent discovery of lower trypanosomatids in immuno-suppressed patients, it became increasingly interesting to compare genome sequences outside #Trypanosoma# and #Leishmania# in order to better understand the molecular evolutionary relationships within the protozoan order Kinetoplastida. In 2008, the French National Research Agency (ANR) decided to sponsor a project on the sequencing of two plant trypanosomatids, one -Hart 1, group H - responsible for a disease of coconut (hartrot) in Latin America, and non-pathogenic one -EM1, group D - from Euphorbia in France. Sequencing of the isolates was performed using data from three different technologies (454 Titanium, Illumina GAIIx and Sanger). Assemblies obtained by Newbler (Roche) showed high continuity. We also obtained cDNA sequences using 454 Titanium to help annotation. The assemblies were of sufficient continuity to start an automatic annotation phase, using procedures that involve cDNA, matches to protein data, and de novo gene finding. (Résumé d'auteur

Transcriptome analyses to investigate symbiotic relationships between marine protists

International audienceRhizaria are an important component of oceanic plankton communities worldwide. A number of species harbor eukaryotic microalgal symbionts, which are horizontally acquired in the environment at each generation. Although these photosymbioses are determinant for Rhizaria ability to thrive in oceanic ecosystems, the mechanisms for symbiotic interactions are unclear. Using high-throughput sequencing technology (i.e., 454), we generated large Expressed Sequence Tag (EST) datasets from four uncultured Rhizaria, an acantharian (Amphilonche elongata), two polycystines (Collozoum sp. and Spongosphaera streptacantha), and one phaeodarian (Aulacantha scolymantha). We assessed the main genetic features of the host/symbionts consortium (i.e., the holobiont) transcriptomes and found rRNA sequences affiliated to a wide range of bacteria and protists in all samples, suggesting that diverse microbial communities are associated with the holobionts. A particular focus was then carried out to search for genes potentially involved in symbiotic processes such as the presence of c-type lectins-coding genes, which are proteins that play a role in cell recognition among eukaryotes. Unigenes coding putative c-type lectin domains (CTLD) were found in the species bearing photosynthetic symbionts (A. elongata, Collozoum sp., and S. streptacantha) but not in the non-symbiotic one (A. scolymantha). More particularly, phylogenetic analyses group CTLDs from A. elongata and Collozoum sp. on a distinct branch from S. streptacantha CTLDs, which contained carbohydrate-binding motifs typically observed in other marine photosymbiosis. Our data suggest that similarly to other well-known marine photosymbiosis involving metazoans, the interactions of glycans with c-type lectins is likely involved in modulation of the host/symbiont specific recognition in Radiolaria

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

Le séquençage du génome de deux trypanosomatides de plantes - Phytomonas spp.- au secours d'une taxonomie dépassée

Plusieurs espèces de plantes laticifères sont parasitées au niveau des tubes laticifères, par des Trypanosomatidae. La question de leur pouvoir pathogène reste ouverte. Un nom de genre leur a été attribué arbitrairement: " Phytomonas", uniquement basée sur la nature de l'hôte. Or il a été montré que ces organismes se multipliaient dans les insectes qui les transmettaient. De plus, depuis les années 80, on sait que d'autres trypanosomatidés, jusque là considérés comme des " trypanosomatidés monoxéniques d'insectes "" (Crithidia, Herpetomonas, Leptomonas) peuvent être transmis par hétéroptères à des fruits de diverses familles, dont les solanacées (tomate). En Amérique latine et dans la Caraïbe, il existe des trypanosomatidés intraphlo èmiques spécifiquement associées à des dépérissements de palmiers (cocotier, palmier à huile, Arecaceae), de cultures horticoles (Alpinia purpurata, Zingiberaceae) et du caféier (Rubiaceae). Le genre arbitraire Phytomonas ne reflète donc pas la diversité des trypanosomatidés se multipliant dans des milieux aussi différents que le latex, la sève, la pulpe des fruits ou des graines, sur différents continents, et ne fait pas de différence entre les organismes pathogènes responsables de maladies aux graves conséquences économiques et ceux qui s'apparentent èa des symbiontes. Nous avons travaillée à la caractérisation de ces trypanosomatidés en utilisant divers marqueurs moléculaires comme le gène du Splice Leader RNA, l'ARN r 5S, les mini cercles d'ADN kinetoplastique et les ITS de l'opéron ribosomal. En tenant compte de ces résultats, en les associant aux données sérologiques et des iso enzymes et RAPD, nous pouvons conclure à l'existence de 10 "groupes" différents. Parmi ces groupes certains se démarquent très nettement. C'est le cas des trypanosomatidés intraphlo èmiques (" groupe H ""). Par leur localisation (tubes criblées du phloème), leur effet pathogène, leur endémisme en Amérique latine, leur culture in vitro, qui contrairement aux autres ne peut se réaliser qu'avec des cellules nourricières d'insectes, et les marqueurs moléculaires, ils sont uniques. Un autre groupe se distingue : " D "", comprenant des isolats du latex de l'Ancien Monde (Inde, Sénégal et France). L'étude des caryotypes moléculaires d'un isolat de chacun de ces deux groupes (EM1 d'Euphorbia pinea de France et Hart1 associée au dépérissement du cocotier en Guyane) révèle bien deux organismes différents avec respectivement 21 chromosomes et 7 chromosomes hétérologues. L'ensemble de ces résultats ainsi que d'autres données conduisent à dire qu'il serait nécessaire de réviser la taxonomie des trypanosomatidés de plantes/insectes. Pour étayer cette présomption, le génome de deux isolats, un isolat du latex (EM1) et un du phloème (Hart1), a été séquencé au Génoscope. Les premiers résultats montrant les différences entre ces deux groupes de trypanosomatidés seront présentées. Ils permettront de fournir des clés pour établir une nouvelle taxonomie, mais aussi d'identifier de possibles nouvelles méthodes de lutte. Projet ANR -08- GENM-020-001 SEQTRYPLANT. (Résumé d'auteur

AphanoDB: a genomic resource for Aphanomyces pathogens.

BACKGROUND: The Oomycete genus Aphanomyces comprises devastating plant and animal pathogens. However, little is known about the molecular mechanisms underlying pathogenicity of Aphanomyces species. In this study, we report on the development of a public database called AphanoDB which is dedicated to Aphanomyces genomic data. As a first step, a large collection of Expressed Sequence Tags was obtained from the legume pathogen A. euteiches, which was then processed and collected into AphanoDB. DESCRIPTION: Two cDNA libraries of A. euteiches were created: one from mycelium growing on synthetic medium and one from mycelium grown in contact to root tissues of the model legume Medicago truncatula. From these libraries, 18,684 expressed sequence tags were obtained and assembled into 7,977 unigenes which were compared to public databases for annotation. Queries on AphanoDB allow the users to retrieve information for each unigene including similarity to known protein sequences, protein domains and Gene Ontology classification. Statistical analysis of EST frequency from the two different growth conditions was also added to the database. CONCLUSION: AphanoDB is a public database with a user-friendly web interface. The sequence report pages are the main web interface which provides all annotation details for each unigene. These interactive sequence report pages are easily available through text, BLAST, Gene Ontology and expression profile search utilities. AphanoDB is available from URL: http://www.polebio.scsv.ups-tlse.fr/aphano/

Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell

International audienceBackground: Eukaryotes are classified as either haplontic, diplontic, or haplo-diplontic, depending on which ploidy levels undergo mitotic cell division in the life cycle. Emiliania huxleyi is one of the most abundant phytoplankton species in the ocean, playing an important role in global carbon fluxes, and represents haptophytes, an enigmatic group of unicellular organisms that diverged early in eukaryotic evolution. This species is haplo-diplontic. Little is known about the haploid cells, but they have been hypothesized to allow persistence of the species between the yearly blooms of diploid cells. We sequenced over 38,000 expressed sequence tags from haploid and diploid E. huxleyi normalized cDNA libraries to identify genes involved in important processes specific to each life phase (2N calcification or 1N motility), and to better understand the haploid phase of this prominent haplo-diplontic organism. Results: The haploid and diploid transcriptomes showed a dramatic differentiation, with approximately 20% greater transcriptome richness in diploid cells than in haploid cells and only <= 50% of transcripts estimated to be common between the two phases. The major functional category of transcripts differentiating haploids included signal transduction and motility genes. Diploid-specific transcripts included Ca(2+), H(+), and HCO(3)(-) pumps. Potential factors differentiating the transcriptomes included haploid-specific Myb transcription factor homologs and an unusual diploid-specific histone H4 homolog. Conclusions: This study permitted the identification of genes likely involved in diploid-specific biomineralization, haploid-specific motility, and transcriptional control. Greater transcriptome richness in diploid cells suggests they may be more versatile for exploiting a diversity of rich environments whereas haploid cells are intrinsically more streamlined

Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria

Background: The picocyanobacterial genus Synechococcus occurs over wide oceanic expanses, having colonized most available niches in the photic zone. Large scale distribution patterns of the different Synechococcus clades (based on 16S rRNA gene markers) suggest the occurrence of two major lifestyles ('opportunists'/'specialists'), corresponding to two distinct broad habitats ('coastal'/'open ocean'). Yet, the genetic basis of niche partitioning is still poorly understood in this ecologically important group. Results: Here, we compare the genomes of 11 marine Synechococcus isolates, representing 10 distinct lineages. Phylogenies inferred from the core genome allowed us to refine the taxonomic relationships between clades by revealing a clear dichotomy within the main subcluster, reminiscent of the two aforementioned lifestyles. Genome size is strongly correlated with the cumulative lengths of hypervariable regions (or 'islands'). One of these, encompassing most genes encoding the light-harvesting phycobilisome rod complexes, is involved in adaptation to changes in light quality and has clearly been transferred between members of different Synechococcus lineages. Furthermore, we observed that two strains (RS9917 and WH5701) that have similar pigmentation and physiology have an unusually high number of genes in common, given their phylogenetic distance. Conclusion: We propose that while members of a given marine Synechococcus lineage may have the same broad geographical distribution, local niche occupancy is facilitated by lateral gene transfers, a process in which genomic islands play a key role as a repository for transferred genes. Our work also highlights the need for developing picocyanobacterial systematics based on genome-derived parameters combined with ecological and physiological data