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International audience; In 2015, the South Green Bioinformatics Platform http://www.southgreen.fr/ is a network of 35 bioinformaticians from five biology research institutes working with two High - Performance Computing Data Centres to develop and use new tools for NGS/ Omic analytics of tropical and Mediterranean crops under projects studying relationsh ip between genetic diversity, agronomic performance and response to selection. South Green is affiliated to the South regional centre of the French Institute of Bioinformatics (the French node of the European research infrastructure, ELIXIR). This communit y and the HPC data centres are all located in Montpellier, which facilitates close collaboration and significant pooling to best meet the biologists' demands of our research units. Since 2004, we developed web - based applications with both generic and in - ho use components, for databases, analysis workflows and web interfaces, in order to: manage genetic and phenotypic information ( e.g. TropGeneDB), analyse molecular markers and genetic diversity ( e.g. SNiPlay), assemble transcriptomes ( e.g. ESTtik) map RNA - Se q ( e.g. ARCAD), annotate and compare genomes ( e.g. GNPAnnot), reconstruct evolutionary history of gene families by phylogenomics ( e.g. GreenPhyl). We also participate to the analysis of numerous crop species, that requires computing and storage facilities as well as interoperable information systems, such as rice ( e.g. OryGenesDB), wheat, sorghum, sugarcane, banana (Banana Genome Hub), palms, yam, coffee (CGH), rubber, cacao (CocoaGenDB), cotton, apple, grapevine, olive, eucalyptus, cassava. To face the dat a deluge, we must increase our analytics capabilities. We document our operation at both, administrator/ developer and user/ scientist level, to provide high quality services and reproducible research. We pool into working groups on key themes such as GBS, at both, developer (extreme pair programming) and user (interdisciplinary knowledge exchange) level. We provide training sessions each year. Finally, we implemented several instances of the Galaxy workflow manager and encapsulated our tools. These instanc es serve as a catalyst for massive NGS analyses but it remains to increase storage capacity and improve data management plans. (Résumé d'auteur)

Coffea arabica which accounts for 70% of world coffee production is an allotetraploid with a genome size of approximately 1.3 Gb and is derived from the hybridization of C. canephora (710 Mb) and C. eugenioides (670 Mb). To elucidate the evolutionary history of C. arabica, and generate critical information for breeding programs, a sequencing project is underway to finalize a reference genome using a dihaploid line and a set of 30 C. arabica accessions. For the reference genome, we have generated two assemblies, one from Illumina data (>150x coverage) and a second from PacBio sequences (>50x coverage). The present assemblies cover 1,031 and 1,042 Mb, respectively. After further refinement, using Illumina mate pairs and optical mapping, the genome assemblies will be annotated using RNA-Seq. Resequencing of C. eugenioides and C. canephora has been completed and is being used to better assess homeologs within the sub-genomes. Furthermore, 30 C. arabica accessions, representing wild and cultivated genotypes, are being resequenced (20x coverage) using Illumina. A C. arabica genetic map, currently including over 600 SSR markers, that differentiate between the two sub-genomes, is used to anchor the assemblies. Newly identified SNP markers are being added to the map. The final goals of the project are to produce a high quality reference genome, assess an eventual neo-diversification occurring in the cultivated varieties, have a better understanding of the species formation and evolution, and develop tools that will make the finished genome accessible and useful to breeders and researchers. (Texte intégral)

• Premise of the study: To complement existing sets of primarily dinucleotide microsatellite loci from noncoding sequences of date palm, we developed primers for tri- and hexanucleotide microsatellite loci identified within genes. Due to their conserved genomic locations, the primers should be useful in other palm taxa, and their utility was tested in seven other Phoenix species and in Chamaerops, Livistona, and Hyphaene. • Methods and Results: Tandem repeat motifs of 3–6 bp were searched using a simple sequence repeat (SSR)–pipeline package in coding portions of the date palm draft genome sequence. Fifteen loci produced highly consistent amplification, intraspecific polymorphisms, and stepwise mutation patterns. • Conclusions: These microsatellite loci showed sufficient levels of variability and transferability to make them useful for population genetic, selection signature, and interspecific gene flow studies in Phoenix and other Coryphoideae genera.

The GLASS project (GLAberrima ASSembly), jointly between IRD and AfricaRice, aims to sequence de novo the two African NERICA parents, CG14 and TOG5681, representing the two opposite of the glaberrima variability. For that purpose we choose an hybrid approach combining the Illumina high-quality short reads and the PacificBioscience Long Reads technology. Tests were performed using Illumina data on TOG 5307 and TOG5681, using AbySS short-reads assembler, with 19x and 25x total data respectively. For TOG5307, we obtained 153'774 contigs (minimum size of 200b), mean size of 1.5 kb (N50 = 2.4kb, N90 = 637b). On TOG5681, we obtained 97'196 contigs (minimum size 200b), with a mean size of 2.8kb (N50 = 5kb, N90 = 1.3 kb). The overall assembly for each genome is of 0.56x for TOG5307 and of 0.69x for TOG5681. Just adding +6x of Illumina data almost doubled the assembly efficiency. PacBio data test on C2 and XL kits were also perfomed for CG14 data, providing respectively 143'456 and 99'488 contigs (mean size of 3140b and 3184b), with a 1.12x and 0.79x coverage. The C2 10x sequencing in PacBio for CG14 and TOG5681, and the 60x sequencing in Illumina for each is on the way. The annotation will be transfered from the Nipponbare MSU7.0 reference genome using tools such as QOD (Mancheron et al, 2010) and BLAST/BLAT based scripts. These sequences will be immediatly available for the whole community without restriction. The IRIGIN project from France Genomique (International RIce Genomic INitiative, http://irigin.org) is headed by IRD and CIRAD, and aimed to provide valuable genetic stocks genomic data in the frame of GriSP. African rice (300 O. glaberrima and 100 O. barthii) will be deeply resequenced (25x) and aligned on their reference (from the GLASS project). In the same time , NAMs population (indica x tropical japonica) from AfricaRice and CIAT will be genotyped (using low-coverage sequencing), to provide to the rice community the best genetic map ever created in plants, with the highest level of coverage ever seen. Thousand of terabytes of raw data and billions of polymorphic data will be gathered within this project, and will be distributed to the whole rice community as soon as possible.

Because of their detrimental influence on plant genome structure and gene expression, Transposable Elements (TEs) are maintained in a transcriptionally inactive state through powerful and specific epigenetic mechanisms involving DNA methylation. However, these silencing processes can be alleviated under stress conditions, leading to the more or less transient reactivation of TEs and, in some cases, to the emergence of variant phenotypes. The mantled somaclonal variation resulting from the in vitro propagation of oil palm (Elaeis guineensis Jacq.) has been correlated with the occurrence of a genome-wide hypomethylation in both in vitro- cultivated and adult tissues, as well as with alterations in gene expression. The time-dependent increase of DNA methylation in long-term in vitro cultures retaining their embryogenic ability has also been demonstrated. In order to assess the contribution of TEs to a possible loss of genomic stability during long-term in vitro propagation of embryogenic suspensions, we evaluated the background genetic instability of the cultures using AFLP and used the retrotransposon-based S-SAP technique to detect evidence of retroelement mobility. Cultures derived from normal and mantled oil palms from two different genotypes were compared in the aim of identifying phenotype-associated TE insertions. (Texte intégral)

Premise of the study: Informative markers are required for assessing the diversity of Amborella trichopoda, the only species of its order, endemic to New Caledonia and considered to be the sister species to all flowering plants. Therefore, expressed sequence tag (EST)-based microsatellite markers were developed. Methods and Results: Fifty-five microsatellite loci were characterized in 14 896 putative unigenes, which were generated by assembling A. trichopoda ESTs from the public sequence database. Seventeen markers revealed polymorphism in 80 adult shrubs from three populations. The number of alleles per locus ranged from two to 12, with a total of 132 alleles scored. The mean expected heterozygosity per population ranged from 0.336 to 0.567. Conclusions: These markers offer an appropriate amount of variation to investigate genetic diversity structure, gene flow, and other conservation issues.

Several ethylene-response factor (ERF) transcription factors are believed to play a crucial role in the activation of plant defence responses, but little is known about the relationships between the diversity of this family and the functions of groups or individual ERFs in this process. In this study, 200 ERF genes from the unigene cotton database were identified. Conserved amino acid residues and phylogeny reconstruction using the AP2 conserved domain suggest that the classification into 10 major groups used for Arabidopsis and rice is applicable to the cotton ERF family. Based on in silico studies, we predict that group IX ERF genes in cotton are involved in jasmonate (JA), ethylene (ET) and pathogen responses. To test this hypothesis, we analysed the transcript profiles of the group IXa subfamily in the regulation of specific resistance to Xanthomonas campestris pathovar malvacearum. The expression of four members of group IXa was induced on challenge with X. campestris pv. malvacearum. Furthermore, the expression of several ERF genes of group IXa was induced synergistically by JA in combination with ET, suggesting that the encoded ERF proteins may play key roles in the integration of both signals to activate JA- and ET-dependent responses.

Additional file 6: Figure S3. Structure of the population. (a) evolution of the cross-entropy criterion with increasing K, (b) bar plot of ancestries membership considering K = 4 ancestral population.

Additional file 7: Figure S4. Geographic distribution of traits. We plotted the mean value of each trait for accessions having sampling location in their passport data.

High throughput sequencing (HTS) data analyses are done every day for biologist and bioinformatics in order to give biological sense of their data. These analyses must to be reproducible, robust and efficient. A generic tool TOGGLe (Toolbox for Generic NGS Analyses) was developed to allow running simple and complex pipelines without require any programming skills. This workflow manager is friendly to users and transparent for developers. User only need basic Linux commands and to specify freely their favorite software parameters through a simple text file given. TOGGLe manages, controls, verifies and concatenates every step in your favorite workflow. This workflow manager checks structure and compatibility of steps given in the software parameters file, it builds a workflow and launches it. TOGGLe reports parameters, commands executed, software versions as well as errors if they occur. These informations are kept in logs and reports files. Results are organized in a structured tree of directories. TOGGLe allows compressing or removing intermediate data and it uses scheduler machinery. TOGGLe integrates a large panel of tools for HTS analyses (demultiplexing, cleaning, trimming, calling, assembly, structural variation detection, transcriptomic ...) and post-analysis (haplotype detection, population structure ...). This workflow manager is highly flexible on the data type, working on sequencing raw data (Illumina, 454 or Pacific Biosciences), as well as on various other formats (e.g. SAM, BAM, VCF). This HTS workflow manager allows running parallel analysis or global, where several samples will be analysed together. TOGGLe was used on numerous sequencing projects with high number of samples, or/and high depth sequencing. It was shown to be highly adaptable to various biological questions as well as to a large array of computing architecture and data. In this poster, we are going to show how users can enjoy of TOGGLe in their data analysis.

Additional file 3: Figure S1. Histograms of trait distribution and quantile-quantile plots for each non-transformed and transformed variables.

Additional file 3: Figure S1. Histograms of trait distribution and quantile-quantile plots for each non-transformed and transformed variables.

South Green (www.southgreen.fr) est une plateforme de bio-informatique dédiée `a la génétique et la génomique des plantes tropicales et méditerranéennes d'intérêt agronomique et de leurs pathogènes. Elle fédère un réseau de bio informaticiens appartenant à différentes unités et instituts de Montpellier (Bioversity International, CIRAD, INRA et IRD) soit environ une vingtaine de personnes en interaction avec les équipes de recherches, avec une expertise multidisciplinaire allant de l'intégration de données et de connaissance au développement de logiciels en bio-informatique, à l'analyse de données de séquençage (détection de polymorphismes et variants structuraux, pangénomique, métagénomique, analyse différentielle de données RNAseq) et le calcul haute performance. Le plateforme South Green a pour objectifs de : Promouvoir des outils originaux issus de la recherche méthodologique. Promouvoir l'interopérabilité des applications développées au sein du réseau. Centraliser l'ensemble des logiciels et systèmes d'information développées au sein d'un portail Web unique (http://www.southgreen.fr) Promouvoir les échanges et les développements collaboratifs Proposer des formations en bio-informatique, bio analyse de données et `a l'utilisation de clusters de calcul Promouvoir la démarche qualité au sein du réseau. Proposer un support pour le calcul à haute performance La plateforme assure le développement de systèmes d'informations et d'outils innovants, nécessaires aux projets scientifiques, réalises au sein de la plateforme et en lien avec l'analyse des données produites par les technologies de séquençage à haut débit (annotation des génomes et de transcriptomes, phylogénie, génotypage) tels que GreenPhylDB, SNiPlay, Gigwa ou AgroLD. Elle propose également des pipelines d'analyses de données de séquençage au travers de deux gestionnaires de workflows : Galaxy et TOGGLe. Enfin, impliquée dans plusieurs projets de séquençage international, elle possède une forte expertise en développement de ”génome hub” qu'elle a déployé sur de nombreuses plantes (bananier, caféier, manioc, cacaoyer) au niveau duquel sont disponibles de nombreuses applications utiles pour l'étude de ces génomes. La plateforme assure aussi des formations spécialisées en bio-informatique au niveau national et international (analyse des données de séquençage haut débit, Galaxy) et informatique (logiciel R, Perl, Linux). Les ressources sont disponibles sur le site https://southgreenplatform.github.io/trainings/. South Green s'inscrit dans le réseau des plateformes de l'Institut Français de Bio-informatique (IFB) et fait partie du réseau Renabi (Réseau national des plates-formes bio-informatiques).

Additional file 7: Figure S4. Geographic distribution of traits. We plotted the mean value of each trait for accessions having sampling location in their passport data.

Coffee, tea, and chocolate converge Caffeine has evolved multiple times among plant species, but no one knows whether these events involved similar genes. Denoeud et al. sequenced the Coffea canephora (coffee) genome and identified a conserved gene order (see the Perspective by Zamir). Although this species underwent fewer genome duplications than related species, the relevant caffeine genes experienced tandem duplications that expanded their numbers within this species. Scientists have seen similar but independent expansions in distantly related species of tea and cacao, suggesting that caffeine might have played an adaptive role in coffee evolution. Science , this issue p. 1181 ; see also p. 1124