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The timing of floral budbreak in apple has a significant effect on fruit production and quality. Budbreak occurs as a result of a complex molecular mechanism that relies on accurate integration of external environmental cues, principally temperature. In the pursuit of understanding this mechanism, especially with respect to aiding adaptation to climate change, a QTL at the top of linkage group (LG) 9 has been identified by many studies on budbreak, but the genes underlying it remain elusive. Here, together with a dessert apple core collection of 239 cultivars, we used a targeted capture sequencing approach to increase SNP resolution in apple orthologues of known or suspected A. thaliana flowering time-related genes, as well as approximately 200 genes within the LG9 QTL interval. This increased the 275 223 SNP Axiom® Apple 480 K array dataset by an additional 40 857 markers. Robust GWAS analyses identified MdPRX10, a peroxidase superfamily gene, as a strong candidate that demonstrated a dormancy-related expression pattern and down-regulation in response to chilling. In-silico analyses also predicted the residue change resulting from the SNP allele associated with late budbreak could alter protein conformation and likely function. Late budbreak cultivars homozygous for this SNP allele also showed significantly up-regulated expression of C-REPEAT BINDING FACTOR (CBF) genes, which are involved in cold tolerance and perception, compared to reference cultivars, such as Gala. Taken together, these results indicate a role for MdPRX10 in budbreak, potentially via redox-mediated signaling and CBF gene regulation. Moving forward, this provides a focus for developing our understanding of the effects of temperature on flowering time and how redox processes may influence integration of external cues in dormancy pathways.

The timing of floral budbreak in apple has a significant effect on fruit production and quality. Budbreak occurs as a result of a complex molecular mechanism that relies on accurate integration of external environmental cues, principally temperature. In the pursuit of understanding this mechanism, especially with respect to aiding adaptation to climate change, a QTL at the top of linkage group (LG) 9 has been identified by many studies on budbreak, but the genes underlying it remain elusive. Here, together with a dessert apple core collection of 239 cultivars, we used a targeted capture sequencing approach to increase SNP resolution in apple orthologues of known or suspected A. thaliana flowering time-related genes, as well as approximately 200 genes within the LG9 QTL interval. This increased the 275 223 SNP Axiom® Apple 480 K array dataset by an additional 40 857 markers. Robust GWAS analyses identified MdPRX10, a peroxidase superfamily gene, as a strong candidate that demonstrated a dormancy-related expression pattern and down-regulation in response to chilling. In-silico analyses also predicted the residue change resulting from the SNP allele associated with late budbreak could alter protein conformation and likely function. Late budbreak cultivars homozygous for this SNP allele also showed significantly up-regulated expression of C-REPEAT BINDING FACTOR (CBF) genes, which are involved in cold tolerance and perception, compared to reference cultivars, such as Gala. Taken together, these results indicate a role for MdPRX10 in budbreak, potentially via redox-mediated signaling and CBF gene regulation. Moving forward, this provides a focus for developing our understanding of the effects of temperature on flowering time and how redox processes may influence integration of external cues in dormancy pathways.

Crop-to-wild gene flow is a mechanism process widely documented, both in plants and animals. This can have positive or negative impacts on the evolution of admixed populations in natural environments, yet the phenomenon is still misunderstood in long-lived woody species, contrary to short-lived crops. Wild olive Olea europaea L. occurs in the same eco-geographical range as domesticated olive, i.e. the Mediterranean Basin (MB). Moreover, it is an allogamous and anemophilous species whose seeds are disseminated by birds, i.e. factors that drive gene flow between crops and their wild relatives. Here we investigated the genetic structure of western MB wild olive populations in natural environments assuming a homogenous gene pool with limited impact of cultivated alleles, as previously suggested. We used a target sequencing method based on annotated genes from the Farga reference genome to analyze 27 western MB olive tree populations sampled in natural environments in France, Spain and Morocco. We also target sequenced cultivated olive tree accessions from the Worldwide Olive Germplasm Bank of Marrakech and Porquerolles and from an eastern MB wild olive tree population. We combined PCA, sNMF, pairwise FST and TreeMix and clearly identified genuine wild olive trees throughout their natural distribution range along a north-south gradient including, for the first time, in southern France. However, contrary to our assumption, we highlighted more admixed than genuine wild olive trees. Our results raise questions regarding the admixed population evolution pattern in this environment, which might be facilitated by crop-to-wild gene flow.

Sorghum is considered like a rainfed crop but it is also grown in the dry season: direct sowing in northern Senegal and transplanted after approximately 45 days of growth in the nursery in the Lake Chad Basin. The genetic diversity of these varieties of sorghum is not well known, the objective of this study is therefore to evaluate this diversity of rainfed sorghum and dry season sorghum collected in Senegal and in the Lake Chad Basin and to understand its organization. The plant material studied includes 153 accessions covering 4 eco-seasonal types of sorghum defined on the basis of seasonality (rainy season, dry season) and eco-geographical zone (Senegal and Lake Chad Basin). High-throughput sequencing data (GBS) made it possible, on the basis of approximately 120,000 SNPs covering the sorghum genome, to describe the genetic diversity of the collection studied in relation to the 4 eco-seasonal types. The genetic diversity of each population was estimated by evaluating its number of total alleles, its number of private alleles and its allelic richness. Principal component analysis was carried out to study the organization of the genetic diversity of the global population. The genomic analysis showed that the diversity of the 153 sorghum accessions is structured into 3 genetic groups. This organization of the diversity reflects the influence of seasonality and geographical origin of sorghum accessions. Two-thirds of dry season sorghum accessions in the Lake Chad Basin form a welldifferentiated group from rainfed sorghum accessions. These experimental results provide new directions for integrating dry season sorghum diversity into sorghum improvement programs.

Vanilla planifolia, the species cultivated to produce one of the world's most popular flavors, is highly prone to partial genome endoreplication, which leads to highly unbalanced DNA content in cells. We report here the first molecular evidence of partial endoreplication at the chromosome scale by the assembly and annotation of an accurate haplotype-phased genome of V. planifolia. Cytogenetic data demonstrated that the diploid genome size is 4.09 Gb, with 16 chromosome pairs, although aneuploid cells are frequently observed. Using PacBio HiFi and optical mapping, we assembled and phased a diploid genome of 3.4 Gb with a scaffold N50 of 1.2 Mb and 59 128 predicted protein-coding genes. The atypical k-mer frequencies and the uneven sequencing depth observed agreed with our expectation of unbalanced genome representation. Sixty-seven percent of the genes were scattered over only 30% of the genome, putatively linking gene-rich regions and the endoreplication phenomenon. By contrast, low-coverage regions (non-endoreplicated) were rich in repeated elements but also contained 33% of the annotated genes. Furthermore, this assembly showed distinct haplotype-specific sequencing depth variation patterns, suggesting complex molecular regulation of endoreplication along the chromosomes. This high-quality, anchored assembly represents 83% of the estimated V. planifolia genome. It provides a significant step toward the elucidation of this complex genome. To support post-genomics efforts, we developed the Vanilla Genome Hub, a user-friendly integrated web portal that enables centralized access to high-throughput genomic and other omics data and interoperable use of bioinformatics tools.

RapGreen is a modular software package targeted at scientists handling large datasets for phylogenetic analysis. Its primary function is the graphical visualization and exploration of large trees. In addition, RapGreen offers a tree pattern search function to seek evolutionary scenarios among large collections of phylogenetic trees. Other functionalities include tree reconciliation with a given species tree: the detection of duplication or loss events during evolution and tree rooting. Last but not least, RapGreen features the ability to integrate heterogeneous data while visualizing and otherwise analyzing phylogenetic trees.

The natural rubber biosynthetic pathway is well described in Hevea, although the final stages of rubber elongation are still poorly understood. Small Rubber Particle Proteins and Rubber Elongation Factors (SRPPs and REFs) are proteins with major function in rubber particle formation and stabilization. Their corresponding genes are clustered on a scaffold1222 of the reference genomic sequence of the Hevea brasiliensis genome. Apart from gene expression by transcriptomic analyses, to date, no deep analyses have been carried out for the genomic environment of SRPPs and REFs loci. By integrative analyses on transposable element annotation, small RNAs production and gene expression, we analysed their role in the control of the transcription of rubber biosynthetic genes. The first in-depth annotation of TEs (Transposable Elements) and their capacity to produce TE-derived siRNAs (small interfering RNAs) is presented, only possible in the Hevea brasiliensis clone PB 260 for which all data are available. We observed that 11% of genes are located near TEs and their presence may interfere in their transcription at both genetic and epigenetic level. We hypothesized that the genomic environment of rubber biosynthesis genes has been shaped by TE and TE-derived siRNAs with possible transcriptional interference on their gene expression. We discussed possible functionalization of TEs as enhancers and as donors of alternative transcription start sites in promoter sequences, possibly through the modelling of genetic and epigenetic landscapes.

Oil palm production is gaining importance in Central and South America. However, the main species Elaeis guineensis (Eg) is suffering severely from bud rod disease, restricting the potential cultivation areas. Therefore, breeding companies have started to work with interspecific Elaeis oleifera × Eg (Eo × Eg) hybrids which are tolerant to this disease. We performed association studies between candidate gene (CG) single nucleotide polymorphisms (SNP) and six production and 19 oil quality traits in 198 accessions of interspecific oil palm hybrids from five different origins. For this purpose, barcoded amplicons of initially 167 CG were produced from each genotype and sequenced with Ion Torrent. After sequence cleaning 115 SNP remained targeting 62 CG. The influence of the origins on the different traits was analyzed and a genetic diversity study was performed. Two generalized linear models (GLM) with principle component analysis (PCA) or structure (Q) matrixes as covariates and two mixed linear models (MLM) which included in addition a Kinship (K) matrix were applied for association mapping using GAPIT. False discovery rate (FDR) multiple testing corrections were applied in order to avoid Type I errors. However, with FDR adjusted p values no significant associations between SNP and traits were detected. If using unadjusted p values below 0.05, seven of the studied CG showed potential associations with production traits, while 23 CG may influence different quality traits. Under these conditions the current approach and the detected candidate genes could be exploited for selecting genotypes with superior CG alleles in Marker Assisted Selection systems.

The myrtle rust disease, caused by the fungus Austropuccinia psidii, infects a wide range of host species within the Myrtaceae family worldwide. Since its first report in 2013 in New Caledonia, it was found on various types of native environments where Myrtaceae are the dominant or codominant species, as well as in several commercial nurseries. It is now considered as a significant threat to ecosystems biodiversity and Myrtaceae-related economy. The use of predictive molecular markers for resistance against myrtle rust is currently the most cost-effective and ecological approach to control the disease. Such an approach for neo Caledonian endemic Myrtaceae species was not possible because of the lack of genomic resources. The recent advancement in new generation sequencing technologies accompanied with relevant bioinformatics tools now provide new research opportunity for work in non-model organism at the transcriptomic level. The present study focuses on transcriptome analysis on three Myrtaceae species endemic to New Caledonia (Arillastrum gummiferum, Syzygium longifolium and Tristaniopsis glauca) that display contrasting responses to the pathogen (non-infected vs infected). Differential gene expression (DGE) and variant calling analysis were conducted on each species. We combined a dual approach by using 1) the annotated reference genome of a related Myrtaceae species (Eucalyptus grandis) and 2) a de novo transcriptomes of each species.

To assess the genetic and environmental components of gene-expression variation among trees we used RNA-seq technology and Eucalyptus urophylla x grandis hybrid clones tested in field conditions. Leaf and xylem transcriptomes of three 20 month old clones differing in terms of growth, repeated in two blocks, were investigated. Transcriptomes were very similar between ramets. The number of expressed genes was significantly (P<0.05) higher in leaf (25,665±634) than in xylem (23,637±1,241). A pairwise clone comparisons approach showed that 4.5 to 14 % of the genes were diffe¬rentially expressed (false discovery rate [FDR]<0.05) in leaf and 7.1 to 16 % in xylem. An assessment of among clone variance components revealed significant results in leaf and xylem in 3431 (248) genes (at FDR<0.2) and 160 (3) (at FDR<0.05), respectively. These two complementary approa¬ches displayed correlated results. A focus on the phenylpro¬panoid, cellulose and xylan pathways revealed a large majo¬rity of low expressed genes and a few highly expressed ones, with RPKM values ranging from nearly 0 to 600 in leaf and 10,000 in xylem. Out of the 115 genes of these pathways, 45 showed differential expression for at least one pair of geno¬type, five of which displaying also clone variance compo¬nents. These preliminary results are promising in evaluating whether gene expression can serve as possible 'intermediate phenotypes' that could improve the accuracy of selection of grossly observable traits.

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 d

As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, intended to be stable over time, and cover all aspects from start to finish of a general assembly and annotation project. Intrinsic properties of genomes are discussed, as is the importance of using high quality DNA. Different sequencing technologies and generally applicable workflows for genome assembly are also detailed. We cover structural and functional annotation and encourage readers to also annotate transposable elements, something that is often omitted from annotation workflows. The importance of data management is stressed, and we give advice on where to submit data and how to make your results Findable, Accessible, Interoperable, and Reusable (FAIR).