Structure and expression analysis of rice paleo duplications

Having a well-known history of genome duplication, rice is a good model for studying structural and functional evolution of paleo duplications. Improved sequence alignment criteria were used to characterize 10 major chromosome-to-chromosome duplication relationships associated with 1440 paralogous pairs, covering 47.8% of the rice genome, with 12.6% of genes that are conserved within sister blocks. Using a micro-array experiment, a genome-wide expression map has been produced, in which 2382 genes show significant differences of expression in root, leaf and grain. By integrating both structural (1440 paralogous pairs) and functional information (2382 differentially expressed genes), we identified 115 paralogous gene pairs for which at least one copy is differentially expressed in one of the three tissues. A vast majority of the 115 paralogous gene pairs have been neofunctionalized or subfunctionalized as 88%, 89% and 96% of duplicates, respectively, expressed in grain, leaf and root show distinct expression patterns. On the basis of a Gene Ontology analysis, we have identified and characterized the gene families that have been structurally and functionally preferentially retained in the duplication showing that the vast majority (>85%) of duplicated have been either lost or have been subfunctionalized or neofunctionalized during 50–70 million years of evolution

Organ and Cell Type–Specific Complementary Expression Patterns and Regulatory Neofunctionalization between Duplicated Genes in Arabidopsis thaliana

Duplicated genes can contribute to the evolution of new functions and they are common in eukaryotic genomes. After duplication, genes can show divergence in their sequence and/or expression patterns. Qualitative complementary expression, or reciprocal expression, is when only one copy is expressed in some organ or tissue types and only the other copy is expressed in others, indicative of regulatory subfunctionalization or neofunctionalization. From analyses of two microarray data sets with 83 different organ types, developmental stages, and cell types in Arabidopsis thaliana, we determined that 30% of whole-genome duplicate pairs and 38% of tandem duplicate pairs show reciprocal expression patterns. We reconstructed the ancestral state of expression patterns to infer that considerably more cases of reciprocal expression resulted from gain of a new expression pattern (regulatory neofunctionalization) than from partitioning of ancestral expression patterns (regulatory subfunctionalization). Pollen was an especially common organ type for expression gain, resulting in contrasting expression of some duplicates in pollen. Many of the gene pairs with reciprocal expression showed asymmetric sequence rate evolution, consistent with neofunctionalization, and the more rapidly evolving copy often showed a more restricted expression pattern. A gene with reciprocal expression in pollen, involved in brassinosteroid signal transduction, has evolved more rapidly than its paralog, and it shows evidence for a new function in pollen. This study indicates the evolutionary importance of reciprocal expression patterns between gene duplicates, showing that they are common, often associated with regulatory neofunctionalization, and may be a factor allowing for retention and divergence of duplicated genes

Selection for Higher Gene Copy Number after Different Types of Plant Gene Duplications

The evolutionary origins of the multitude of duplicate genes in the plant genomes are still incompletely understood. To gain an appreciation of the potential selective forces acting on these duplicates, we phylogenetically inferred the set of metabolic gene families from 10 flowering plant (angiosperm) genomes. We then compared the metabolic fluxes for these families, predicted using the Arabidopsis thaliana and Sorghum bicolor metabolic networks, with the families' duplication propensities. For duplications produced by both small scale (small-scale duplications) and genome duplication (whole-genome duplications), there is a significant association between the flux and the tendency to duplicate. Following this global analysis, we made a more fine-scale study of the selective constraints observed on plant sodium and phosphate transporters. We find that the different duplication mechanisms give rise to differing selective constraints. However, the exact nature of this pattern varies between the gene families, and we argue that the duplication mechanism alone does not define a duplicated gene's subsequent evolutionary trajectory. Collectively, our results argue for the interplay of history, function, and selection in shaping the duplicate gene evolution in plants

Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia

International audienceBACKGROUND: The genome of Paramecium tetraurelia, a unicellular model that belongs to the ciliate phylum, has been shaped by at least 3 successive whole genome duplications (WGD). These dramatic events, which have also been documented in plants, animals and fungi, are resolved over evolutionary time by the loss of one duplicate for the majority of genes. Thanks to a low rate of large scale genome rearrangement in Paramecium, an unprecedented large number of gene duplicates of different ages have been identified, making this organism an outstanding model to investigate the evolutionary consequences of polyploidization. The most recent WGD, with 51% of pre-duplication genes still in 2 copies, provides a snapshot of a phase of rapid gene loss that is not accessible in more ancient polyploids such as yeast. RESULTS: We designed a custom oligonucleotide microarray platform for P. tetraurelia genome-wide expression profiling and used the platform to measure gene expression during 1) the sexual cycle of autogamy, 2) growth of new cilia in response to deciliation and 3) biogenesis of secretory granules after massive exocytosis. Genes that are differentially expressed during these time course experiments have expression patterns consistent with a very low rate of subfunctionalization (partition of ancestral functions between duplicated genes) in particular since the most recent polyploidization event. CONCLUSIONS: A public transcriptome resource is now available for Paramecium tetraurelia. The resource has been integrated into the ParameciumDB model organism database, providing searchable access to the data. The microarray platform, freely available through NimbleGen Systems, provides a robust, cost-effective approach for genome-wide expression profiling in P. tetraurelia. The expression data support previous studies showing that at short evolutionary times after a whole genome duplication, gene dosage balance constraints and not functional change are the major determinants of gene retention

CAP’2ER® “équins”: an environmental footprint calculator tested on 39 French equine systems

International audienceThe agricultural sector is developing new tools to enhance knowledge about livestock activities consequences on climate change. The first environmental impact calculator for equine structures in France, CAP’2ER ‘équins’, has been created to help farmers better evaluate and manage environmental impacts of their activities. CAP’2ER has already existed for ruminant farming. It measures four impacts: climate change, air acidification, eutrophication and fossil energy consumption. Moreover, it quantifies three positive contributions: carbon storage, maintenance of biodiversity and nutritional performance. The tool requires 55 technical data collected on the farm and emission factors for each source of greenhouse gas pollution (housing, storage, spreading, grazing and inputs) found in the scientific literature and specific to the equine species. The CAP’2ER is based on algorithms based on IPCC (2019) for animal and farm emissions and the boundaries of the analysis were from cradle to farm gate, according to LCA analysis. In 2021, the tool was tested on a sample of 39 equine structures (30 riding centres and 9 breeding farms), as varied as possible. The estimated emissions were at 1,544 kg CO 2 eq/head on average (57% due to CO 2 , 31% to CH 4 and 12% to N 2 O). The calculated carbon storage was at 1,429 kg CO 2 eq/head on average. Thus, the sample offset its emissions by 93%, with variations depending on the production system. The main emission source is the purchase of cereal grains or processed feeds, fodder and bedding (38% of total emissions) by equestrian establishments, explained by their low food autonomy. A better optimisation of diets by limiting cereals and extending grazing time (thus decreasing the quantity of fodder and bedding), or even by increasing the surfaces in meadows would be some ways to decrease indirect CO 2 emissions. These first estimates depend on parameters that are not widely available in the literature and that require further studies. Research should develop consolidated emission factors that are more adapted to the various equine systems found in France and Europe

CAP’2ER® équin – Outil de diagnostic environnemental quantitatif des structures équines françaises

National audienceLe secteur agricole se positionne comme le deuxième secteur le plus émetteur de gaz à effet de serre (GES), après le transport et ex-aequo avec l’industrie (CITEPA, inventaire Secten, éd. 2021). Pour estimer ces émissions, connaître avec précision les postes les plus émetteurs et déployer des actions concrètes pour les diminuer, des outils ont été créés, comme CAP’2ER ® (Calcul Automatisé des Performances Environnementales pour des Exploitations Responsables). La version adaptée à la filière équine permet de chiffrer les différents impacts sur l’environnement d’une structure équine, mais aussi les contributions positives de celle-ci. Cet article vise à présenter le fonctionnement de l’outil et les résultats des tests réalisés sur le terrain en 2021

CAP’2ER® équins : bilan carbone de 39 structures en France

National audienceLa version équine de CAP’2ER® (Calcul Automatisé des Performances Environnementales pour des Exploitations Responsables) a été développée par l’IFCE, l’IDELE et l’INRAE en 2020. Basé sur la méthodologie de l’Analyse de Cycle de Vie, cet outil vise à : (1) sensibiliser à la prise en compte des impacts environnementaux d’une structure équine (positifs et négatifs), (2) évaluer l’empreinte environnementale (émissions de gaz à effet de serre, consommation d’énergie fossile…), (3) situer les structures par rapport à un groupe d’exploitations, et mettre en place un plan d’action personnalisé.Des tests sur le terrain, réalisés en 2021 sur 39 structures équines, permettent d’esquisser des premières tendances : un équidé émet en moyenne 1 482 kg eq. CO2 en un an, dont 62 % est dû au CO2 émis indirectement via l’achat d’intrants (fourrages, céréales, paille). Des leviers d’action peuvent être utilisés pour réduire ce poste d’émission, comme réaliser un bilan de la ration pour s’assurer qu’elle est équilibrée

CAP’2ER® équins : bilan carbone de 39 structures en France

National audienceLa version équine de CAP’2ER® (Calcul Automatisé des Performances Environnementales pour des Exploitations Responsables) a été développée par l’IFCE, l’IDELE et l’INRAE en 2020. Basé sur la méthodologie de l’Analyse de Cycle de Vie, cet outil vise à : (1) sensibiliser à la prise en compte des impacts environnementaux d’une structure équine (positifs et négatifs), (2) évaluer l’empreinte environnementale (émissions de gaz à effet de serre, consommation d’énergie fossile…), (3) situer les structures par rapport à un groupe d’exploitations, et mettre en place un plan d’action personnalisé.Des tests sur le terrain, réalisés en 2021 sur 39 structures équines, permettent d’esquisser des premières tendances : un équidé émet en moyenne 1 482 kg eq. CO2 en un an, dont 62 % est dû au CO2 émis indirectement via l’achat d’intrants (fourrages, céréales, paille). Des leviers d’action peuvent être utilisés pour réduire ce poste d’émission, comme réaliser un bilan de la ration pour s’assurer qu’elle est équilibrée

CAP’2ER® “équins”: an environmental footprint calculator tested on 39 French equine systems

International audienceThe agricultural sector is developing new tools to enhance knowledge about livestock activities consequences on climate change. The first environmental impact calculator for equine structures in France, CAP’2ER ‘équins’, has been created to help farmers better evaluate and manage environmental impacts of their activities. CAP’2ER has already existed for ruminant farming. It measures four impacts: climate change, air acidification, eutrophication and fossil energy consumption. Moreover, it quantifies three positive contributions: carbon storage, maintenance of biodiversity and nutritional performance. The tool requires 55 technical data collected on the farm and emission factors for each source of greenhouse gas pollution (housing, storage, spreading, grazing and inputs) found in the scientific literature and specific to the equine species. The CAP’2ER is based on algorithms based on IPCC (2019) for animal and farm emissions and the boundaries of the analysis were from cradle to farm gate, according to LCA analysis. In 2021, the tool was tested on a sample of 39 equine structures (30 riding centres and 9 breeding farms), as varied as possible. The estimated emissions were at 1,544 kg CO 2 eq/head on average (57% due to CO 2 , 31% to CH 4 and 12% to N 2 O). The calculated carbon storage was at 1,429 kg CO 2 eq/head on average. Thus, the sample offset its emissions by 93%, with variations depending on the production system. The main emission source is the purchase of cereal grains or processed feeds, fodder and bedding (38% of total emissions) by equestrian establishments, explained by their low food autonomy. A better optimisation of diets by limiting cereals and extending grazing time (thus decreasing the quantity of fodder and bedding), or even by increasing the surfaces in meadows would be some ways to decrease indirect CO 2 emissions. These first estimates depend on parameters that are not widely available in the literature and that require further studies. Research should develop consolidated emission factors that are more adapted to the various equine systems found in France and Europe

CAP’2ER® “équins”: an environmental footprint calculator tested on 39 French equine systems

International audienceThe agricultural sector is developing new tools to enhance knowledge about livestock activities consequences on climate change. The first environmental impact calculator for equine structures in France, CAP’2ER ‘équins’, has been created to help farmers better evaluate and manage environmental impacts of their activities. CAP’2ER has already existed for ruminant farming. It measures four impacts: climate change, air acidification, eutrophication and fossil energy consumption. Moreover, it quantifies three positive contributions: carbon storage, maintenance of biodiversity and nutritional performance. The tool requires 55 technical data collected on the farm and emission factors for each source of greenhouse gas pollution (housing, storage, spreading, grazing and inputs) found in the scientific literature and specific to the equine species. The CAP’2ER is based on algorithms based on IPCC (2019) for animal and farm emissions and the boundaries of the analysis were from cradle to farm gate, according to LCA analysis. In 2021, the tool was tested on a sample of 39 equine structures (30 riding centres and 9 breeding farms), as varied as possible. The estimated emissions were at 1,544 kg CO 2 eq/head on average (57% due to CO 2 , 31% to CH 4 and 12% to N 2 O). The calculated carbon storage was at 1,429 kg CO 2 eq/head on average. Thus, the sample offset its emissions by 93%, with variations depending on the production system. The main emission source is the purchase of cereal grains or processed feeds, fodder and bedding (38% of total emissions) by equestrian establishments, explained by their low food autonomy. A better optimisation of diets by limiting cereals and extending grazing time (thus decreasing the quantity of fodder and bedding), or even by increasing the surfaces in meadows would be some ways to decrease indirect CO 2 emissions. These first estimates depend on parameters that are not widely available in the literature and that require further studies. Research should develop consolidated emission factors that are more adapted to the various equine systems found in France and Europe