Beyond COST Action INTEGRAPE: The Grapevine Genomics Encyclopedia Initiative

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Introgression reshapes recombination distribution in grapevine interspecific hybrids

In grapevine interspecific hybrids, meiotic recombination is suppressed in homeologous regions and enhanced in homologous regions of recombined chromosomes, whereas crossover rate remains unchanged when chromosome pairs are entirely homeologous

The Grape Gene Reference Catalogue as a Standard Resource for Gene Selection and Genetic Improvement

Effective crop improvement, whether through selective breeding or biotech strategies, is largely dependent on the cumulative knowledge of a species' pangenome and its containing genes. Acquiring this knowledge is specially challenging in grapevine, one of the oldest fruit crops grown worldwide, which is known to have more than 30,000 genes. Well-established research communities studying model organisms have created and maintained, through public and private funds, a diverse range of online tools and databases serving as repositories of genomes and gene function data. The lack of such resources for the non-model, but economically important, Vitis vinifera species has driven the need for a standardised collection of genes within the grapevine community. In an effort led by the Integrape COST Action CA17111, we have recently developed the first grape gene reference catalogue, where genes are ascribed to functional data, including their accession identifiers from different genome-annotation versions (https://integrape.eu/resources/genes-genomes/). We present and discuss this gene repository together with a validation-level scheme based on varied supporting evidence found in current literature. The catalogue structure and online submission form provided permits community curation. Finally, we present the Gene Cards tool, developed within the Vitis Visualization (VitViz) platform, to visualize the data collected in the catalogue and link gene function with tissue-specific expression derived from public transcriptomic data. This perspective article aims to present these resources to the community as well as highlight their potential use, in particular for plant-breeding applications

Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources

<p>Abstract</p> <p>Background</p> <p>Because of its size, allohexaploid nature and high repeat content, the wheat genome has always been perceived as too complex for efficient molecular studies. We recently constructed the first physical map of a wheat chromosome (3B). However gene mapping is still laborious in wheat because of high redundancy between the three homoeologous genomes. In contrast, in the closely related diploid species, barley, numerous gene-based markers have been developed. This study aims at combining the unique genomic resources developed in wheat and barley to decipher the organisation of gene space on wheat chromosome 3B.</p> <p>Results</p> <p>Three dimensional pools of the minimal tiling path of wheat chromosome 3B physical map were hybridised to a barley Agilent 15K expression microarray. This led to the fine mapping of 738 barley orthologous genes on wheat chromosome 3B. In addition, comparative analyses revealed that 68% of the genes identified were syntenic between the wheat chromosome 3B and barley chromosome 3 H and 59% between wheat chromosome 3B and rice chromosome 1, together with some wheat-specific rearrangements. Finally, it indicated an increasing gradient of gene density from the centromere to the telomeres positively correlated with the number of genes clustered in islands on wheat chromosome 3B.</p> <p>Conclusion</p> <p>Our study shows that novel structural genomics resources now available in wheat and barley can be combined efficiently to overcome specific problems of genetic anchoring of physical contigs in wheat and to perform high-resolution comparative analyses with rice for deciphering the organisation of the wheat gene space.</p

The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding

Grapevine is one of the most economically important crops worldwide. However, the previous versions of the grapevine reference genome consisted of thousands of fragments with missing centromeres and telomeres, which limited the accessibility of the repetitive sequences, the centromeric and telomeric regions, and the inheritance of important agronomic traits in these regions. Here, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the pinot noir cultivar (PN40024) using the PacBio HiFi long reads. The T2T reference genome (PN_T2T) was 69 Mb longer with 9026 more genes identified than the 12X.v2 version (Canaguier et al., 2017). We annotated 67% repetitive sequences, 19 centromeres and 36 telomeres, and incorporated gene annotations of previous versions into the PN_T2T. We detected a total of 377 gene clusters, which showed associations with complex traits, such as aroma and disease resistance. Even though the PN40024 sample had been selfed for nine generations, we still found nine genomic hotspots of heterozygous sites associated with biological processes, such as the oxidation-reduction process and protein phosphorylation. The fully annotated complete reference genome, therefore, provides important resources for grapevine genetics and breeding.This work was supported by the National Natural Science Fund for Excellent Young Scientists Fund Program (Overseas) to Yongfeng Zhou, the National Key Research and Development Program of China(grant2019YFA0906200), the Agricultural Science and Technology Innovation Program (CAAS-ZDRW202101), the Shenzhen Science and Technology Program (grant KQTD2016113010482651), the BMBF funded de.NBI Cloud within the German Network for Bioinformatics Infrastructure (de.NBI). We thank Bianca Frommer, Marie Lahaye, David Navarro-Payá, Marcela K. Tello-Ruiz and Kapeel Chougule for their help in analyzing the RNA-Seq data and in running the gene annotation pipeline. This study is also based upon work from COST Action CA17111 INTEGRAPE and form COST Innovators Grant IG17111 GRAPEDIA, supported by COST (European Cooperation in Science and Technology).ViticultureT2Tgap-fregene clustercentromeretelomerePublishe

Impact de la structure du génome sur l'organisation, la régulation et la fonction des gènes sur le chromosome 3B du blé hexaploïde (Triticum aestivum L.)

Because of its size (17 Gb), allohexaploid nature and high repeat content (>80%), the bread wheat genome has always been perceived as too complex for efficient molecular studies. As a consequence, our knowledge of the wheat genome structure is still limited. Following a chromosome-specific approach, the physical map of wheat chromosome 3B has recently been constructed and allowed the development of unique genomic resources. During my PhD the use of transcriptomic approaches based on these resources allowed me analysing the relationships between the structure of the genome, the evolution, the function and the regulation of the genes along wheat chromosome 3B. First macroarrays carrying the BACs of the chromosome 3B “Minimal Tiling Path” (MTP) were hybridised with 15 mRNA samples to identify the BACs carrying genes. Then barley Agilent 15K expression microarrays were hybridised with the MTP of chromosome 3B pooled in three-dimension (3D) to precisely locate the genes on the physical map. To build the first transcription map of a wheat chromosome, the 3D pools as well as the 15 mRNA samples were hybridised onto wheat NimbleGen 40K expression microarrays. The results from these experiments allowed drawing some conclusions about gene space organisation on chromosome 3B. Thus the genes are spread all along chromosome 3B with a gradient of the gene density from the centromere to the telomeres with a higher proportion of genes organised in islands at the telomeres. An evolutionary analysis demonstrated that the islands would essentially be composed of genes that have undergone rearrangements in the wheat genome. Furthermore the transcription map also showed that a significant fraction of the genes organised in islands display similar expression profiles and / or share the same function and / or play a role in the same biological process. Moreover, at the scale of the whole chromosome 3B, mechanisms of long distance regulation between gene islands were suspected. In conclusion this study allowed for the first time to find relationships between the genome structure, the evolution, the function and the regulation of the genes at a wheat chromosome scale. The sequencing and the annotation of chromosome 3B as well as the use of technologies like RNAseq will enable to analyse these relationships in an even more precise and exhaustive way.Du fait de sa taille (17 Gb), de sa nature allohexaploïde et de son fort taux de séquences répétées (>80%), le génome du blé tendre a toujours été considéré comme trop complexe pour des analyses moléculaires efficaces. En conséquence, la connaissance de la structure de son génome reste limitée. Utilisant une approche chromosome-spécifique, la carte physique du chromosome 3B du blé a récemment été établie et a permis le développement de ressources génomiques uniques. Pendant ma thèse, la mise en oeuvre d‟approches transcriptomiques utilisant ces ressources m‟a permis d‟analyser les relations entre la structure du génome, l‟évolution, la fonction et la régulation des gènes le long du chromosome 3B de blé. Tout d‟abord, des filtres portant les BAC du « Minimal Tiling Path » (MTP) du chromosome 3B ont été hybridés avec 15 échantillons d‟ARNm pour identifier les BAC portant des gènes. Ensuite, des puces Agilent 15K d‟expression d‟orge ont été hybridées avec les pools tridimensionnels (3D) du MTP du chromosome 3B pour localiser les gènes plus précisément sur la carte physique. Afin de construire la première carte transcriptionnelle d‟un chromosome de blé, ces mêmes pools 3D ainsi que les 15 échantillons d‟ARNm ont été hybridés sur des puces NimbleGen 40K d‟expression de blé. Les résultats obtenus à partir de ces expériences ont permis de tirer des conclusions quant à l‟organisation de l‟espace génique sur le chromosome 3B. Ainsi les gènes sont répartis tout le long du chromosome 3B selon un gradient de densité de gènes du centromère vers les télomères avec une plus forte proportion de gènes regroupés en îlots au niveau des télomères. Une analyse évolutive a montré que les îlots seraient essentiellement constitués de gènes ayant subi des réarrangements dans le génome du blé. De plus, la carte transcriptionnelle a également mis en évidence qu'une part significative des gènes organisés en îlot présentent des profils d‟expression similaires et / ou ont la même fonction et / ou interviennent dans le même processus biologique. De plus, à l‟échelle du chromosome 3B entier, des mécanismes de régulation à longue distance entre îlots de gènes ont été suspectés. En conclusion, cette étude a permis pour la première fois de mettre en évidence des relations entre la structure du génome, l‟évolution, la fonction et la régulation des gènes à l‟échelle d‟un chromosome de blé. Le séquençage et l‟annotation du chromosome 3B ainsi que l'utilisation de technologies telles que le RNAseq permettront d‟analyser ces relations de façon encore plus précise et exhaustive

Integrating “Omics” Data and Expression QTL to Understand Maize Heterosis

International audienc

Impact de la structure du génome sur l'organisation, la régulation et la fonction des gènes sur le chromosome 3B du blé hexaploïde (Triticum aestivum L.)

Du fait de sa taille (17 Gb), de sa nature allohexaploïde et de son fort taux de séquences répétées (>80%), le génome du blé tendre a toujours été considéré comme trop complexe pour des analyses moléculaires efficaces. En conséquence, la connaissance de la structure de son génome reste limitée. Utilisant une approche chromosome-spécifique, la carte physique du chromosome 3B du blé a récemment été établie et a permis le développement de ressources génomiques uniques. Pendant ma thèse, la mise en oeuvre d approches transcriptomiques utilisant ces ressources m a permis d analyser les relations entre la structure du génome, l évolution, la fonction et la régulation des gènes le long du chromosome 3B de blé. Tout d abord, des filtres portant les BAC du Minimal Tiling Path (MTP) du chromosome 3B ont été hybridés avec 15 échantillons d ARNm pour identifier les BAC portant des gènes. Ensuite, des puces Agilent 15K d expression d orge ont été hybridées avec les pools tridimensionnels (3D) du MTP du chromosome 3B pour localiser les gènes plus précisément sur la carte physique. Afin de construire la première carte transcriptionnelle d un chromosome de blé, ces mêmes pools 3D ainsi que les 15 échantillons d ARNm ont été hybridés sur des puces NimbleGen 40K d expression de blé. Les résultats obtenus à partir de ces expériences ont permis de tirer des conclusions quant à l organisation de l espace génique sur le chromosome 3B. Ainsi les gènes sont répartis tout le long du chromosome 3B selon un gradient de densité de gènes du centromère vers les télomères avec une plus forte proportion de gènes regroupés en îlots au niveau des télomères. Une analyse évolutive a montré que les îlots seraient essentiellement constitués de gènes ayant subi des réarrangements dans le génome du blé. De plus, la carte transcriptionnelle a également mis en évidence qu'une part significative des gènes organisés en îlot présentent des profils d expression similaires et / ou ont la même fonction et / ou interviennent dans le même processus biologique. De plus, à l échelle du chromosome 3B entier, des mécanismes de régulation à longue distance entre îlots de gènes ont été suspectés. En conclusion, cette étude a permis pour la première fois de mettre en évidence des relations entre la structure du génome, l évolution, la fonction et la régulation des gènes à l échelle d un chromosome de blé. Le séquençage et l annotation du chromosome 3B ainsi que l'utilisation de technologies telles que le RNAseq permettront d analyser ces relations de façon encore plus précise et exhaustive.Because of its size (17 Gb), allohexaploid nature and high repeat content (>80%), the bread wheat genome has always been perceived as too complex for efficient molecular studies. As a consequence, our knowledge of the wheat genome structure is still limited. Following a chromosome-specific approach, the physical map of wheat chromosome 3B has recently been constructed and allowed the development of unique genomic resources. During my PhD the use of transcriptomic approaches based on these resources allowed me analysing the relationships between the structure of the genome, the evolution, the function and the regulation of the genes along wheat chromosome 3B. First macroarrays carrying the BACs of the chromosome 3B Minimal Tiling Path (MTP) were hybridised with 15 mRNA samples to identify the BACs carrying genes. Then barley Agilent 15K expression microarrays were hybridised with the MTP of chromosome 3B pooled in three-dimension (3D) to precisely locate the genes on the physical map. To build the first transcription map of a wheat chromosome, the 3D pools as well as the 15 mRNA samples were hybridised onto wheat NimbleGen 40K expression microarrays. The results from these experiments allowed drawing some conclusions about gene space organisation on chromosome 3B. Thus the genes are spread all along chromosome 3B with a gradient of the gene density from the centromere to the telomeres with a higher proportion of genes organised in islands at the telomeres. An evolutionary analysis demonstrated that the islands would essentially be composed of genes that have undergone rearrangements in the wheat genome. Furthermore the transcription map also showed that a significant fraction of the genes organised in islands display similar expression profiles and / or share the same function and / or play a role in the same biological process. Moreover, at the scale of the whole chromosome 3B, mechanisms of long distance regulation between gene islands were suspected. In conclusion this study allowed for the first time to find relationships between the genome structure, the evolution, the function and the regulation of the genes at a wheat chromosome scale. The sequencing and the annotation of chromosome 3B as well as the use of technologies like RNAseq will enable to analyse these relationships in an even more precise and exhaustive way.CLERMONT FD-Bib.électronique (631139902) / SudocSudocFranceF

Towards the construction of an aphid densovirus-derived vector for gene functional validation

National audienc