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1. Evolutionary history of glucose-6-phosphatase encoding genes in vertebrate lineages: towards a better understanding of the functions of multiple duplicates

Author

Elisabeth Plagnes-Juan, Eva Arbenoits, Stéphane Panserat, Lucie Marandel, José L. Soengas, Julien Bobe, Nutrition, Métabolisme, Aquaculture (NuMéA), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Departamento de Bioloxia Funcional e Ciencias da Saude, Laboratorio de Fisioloxia Animal, Facultade de Bioloxia, Universidate de Vigo, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), This study was supported by research grants from the INRA PHASE Department (France) to LM and from the Ministerio de Economía y Competitividad (Spain) and European Fund for Regional Development to JLS (AGL2016-74857-C3-1-R and FEDER)., Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), and Universidade de Vigo

Subjects
0301 basic medicine, Sarcopterygii, glucose 6 phosphate, Duplicated genes, Proteomics, Teleosts, chemistry.chemical_compound, 0302 clinical medicine, poisson, duplication de gènes, Gene duplication, Glucose homeostasis, glucose, duplication des génomes, Phylogeny, ComputingMilieux_MISCELLANEOUS, Animal biology, Genetics, trout, teleost, [SDV.BA]Life Sciences [q-bio]/Animal biology, Vertebrate, Heart, duplicated gene, Phenotype, Vertebrates, Glucose-6-Phosphatase, teleosteen, DNA microarray, duplicate genes, expression des gènes, Research Article, Biotechnology, lcsh:QH426-470, brain, lcsh:Biotechnology, truite, Biology, analyse phylogénétique, Synteny, Gene Expression Regulation, Enzymologic, Evolution, Molecular, 03 medical and health sciences, biology.animal, lcsh:TP248.13-248.65, Biologie animale, Dietary Carbohydrates, Animals, Humans, gène dupliqué, Gene, Actinopterygii, Myocardium, sarcopterygii, actinopterygii, vertébré, lcsh:Genetics, 030104 developmental biology, Glucose 6-phosphate, chemistry, Evolutionary biology, 030217 neurology & neurosurgery, homéostasie glucidique
Abstract

Background Glucose-6-phosphate (G6pc) is a key enzyme involved in the regulation of the glucose homeostasis. The present study aims at revisiting and clarifying the evolutionary history of g6pc genes in vertebrates. Results g6pc duplications happened by successive rounds of whole genome duplication that occurred during vertebrate evolution. g6pc duplicated before or around Osteichthyes/Chondrichthyes radiation, giving rise to g6pca and g6pcb as a consequence of the second vertebrate whole genome duplication. g6pca was lost after this duplication in Sarcopterygii whereas both g6pca and g6pcb then duplicated as a consequence of the teleost-specific whole genome duplication. One g6pca duplicate was lost after this duplication in teleosts. Similarly one g6pcb2 duplicate was lost at least in the ancestor of percomorpha. The analysis of the evolution of spatial expression patterns of g6pc genes in vertebrates showed that all g6pc were mainly expressed in intestine and liver whereas teleost-specific g6pcb2 genes were mainly and surprisingly expressed in brain and heart. g6pcb2b, one gene previously hypothesised to be involved in the glucose intolerant phenotype in trout, was unexpectedly up-regulated (as it was in liver) by carbohydrates in trout telencephalon without showing significant changes in other brain regions. This up-regulation is in striking contrast with expected glucosensing mechanisms suggesting that its positive response to glucose relates to specific unknown processes in this brain area. Conclusions Our results suggested that the fixation and the divergence of g6pc duplicated genes during vertebrates’ evolution may lead to adaptive novelty and probably to the emergence of novel phenotypes related to glucose homeostasis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3727-1) contains supplementary material, which is available to authorized users.

Published
2017
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2. Duplicate chlorophyll-deficient loci in soybean.

Author

Kato, K. K. and Palmer, R. G.

Subjects
*GENETICS, *SOYBEAN, *GENOMICS, *GENOMES, *ALLELES, *CHROMOSOMES
Abstract

Three lethal-yellow mutants have been identified in soybean (Glycine max (L.) Merr.), and assigned genetic type collection numbers T218H, T225H, and T362H. Previous genetic evaluation of T362H indicated allelism with T218H and T225H and duplicate-factor inheritance. Our objectives were to confirm the inheritance and allelism of T218H and T225H and to molecularly map the locus and (or) loci conditioning the lethal-yellow phenotype. The inheritance of T218H and T225H was 3 green : 1 lethal yellow in their original parental source germplasm of Glycine max 'Illini' and Glycine max 'Lincoln', respectively. In crosses to unrelated germplasm, a 15 green : 1 lethal yellow was observed. Allelism tests indicated that T218H and T225H were allelic. The molecular mapping population was Glycine max 'Minsoy' x T225H and simple sequence repeat (SSR) markers were used. The first locus, designated y18_1, was located on soybean molecular linkage group B2, between SSR markers Satt474 and Satt534, and linked to each by 4.4 and 13.4 cM, respectively. The second locus, designated y18_2, was located on soybean molecular linkage group D2, between SSR markers Satt543 and Sat_001, and linked to each by 2.2 and 4.4 cM, respectively. [ABSTRACT FROM AUTHOR]

Published
2004
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3. Pck-ing up steam: widening the salmonid gluconeogenic gene duplication trail

Author

Jan A. Mennigen, Lucie Marandel, Stéphane Panserat, Jingwei Liu, Johnathon L. I. Forbes, Carol Best, Daniel J. Kostyniuk, Nutrition, Métabolisme, Aquaculture (NuMéA), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Department of Biology, University of Memphis, This work benefited from the financial support of the INRA PHASE Department. This research was carried out under the E2S UPPA supported by the 'Investissements d'Avenir' managed by ANR (ANR-16- IDEX-0002). LM received EU support under the FP7 People: Marie- Curie Actions through an AgreenSkills+ fellowship (#609398). DJK gratefully acknowledges funding through a Mitacs Globalink grant, and JAM support from the Canada Foundation for Innovation (148035) and a NSERC Discovery grant (2114456-2017)., European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), University of Ottawa, University of Ottawa [Ottawa], and ANR-16-IDEX-0002,E2S,E2S(2016)

Subjects
0301 basic medicine, Low protein, animal diseases, phosphoenolpyruvate carboxykinase, Genome, 0302 clinical medicine, poisson, duplication de gènes, PCK1, Sequence Analysis, Protein, PCK2, Gene Duplication, Gene duplication, Phylogeny, Genetics, trout, teleost, [SDV.BA]Life Sciences [q-bio]/Animal biology, Intracellular Signaling Peptides and Proteins, Chromosome Mapping, General Medicine, rainbow trout, Trout, 030220 oncology & carcinogenesis, Oncorhynchus mykiss, duplicate genes, endocrine system, animal structures, Biology, digestive system, Evolution, Molecular, 03 medical and health sciences, gluconeogenesis glucose intolerance, rainbow, Animals, gène dupliqué, 14. Life underwater, Gene, gluconeogénèse, fish, urogenital system, génome, Gluconeogenesis, duplicated genes, biology.organism_classification, 030104 developmental biology, Glucose, Gene Expression Regulation, Rainbow trout, glyconeogenesis, Phosphoenolpyruvate Carboxykinase (ATP), truite arc en ciel
Abstract

Rainbow trout have, as salmonid fish species, undergone sequential genome duplication events in their evolutionary history. In addition to a teleost-specific whole genome duplication approximately 320–350 million years ago, rainbow trout and salmonids in general underwent an additional salmonid lineage-specific genome duplication event approximately 80 million years ago. Through the recent sequencing of salmonid genome sequences, including the rainbow trout, the identification and study of duplicated genes has become available. A particular focus of interest has been the evolution and regulation of rainbow trout gluconeogenic genes, as recent molecular and gene expression evidence points to a possible contribution of previously uncharacterized gluconeogenic gene paralogues to the rainbow trout long-studied glucose intolerant phenotype. Since the publication of the initial rainbow trout genome draft, resequencing and annotation have further improved genome coverage. Taking advantage of these recent improvements, we here identify a salmonid-specific genome duplication of ancestral mitochondrial phosphoenolpyruvate carboxykinase 2 isoenzyme, we termed pck2a and pck2b. Cytosolic phosphoenolpyruvate carboxykinase (Pck1) and, more recently mitochondrial Pck2, are considered to be the rate-limiting enzymes in de novo gluconeogenesis. Following in silico confirmation of salmonid pck2a and pck2b evolutionary history, we simultaneously profiled cytosolic pck1 and mitochondrial pck2a and pck2b expression in rainbow trout liver under several experimental conditions known to regulate hepatic gluconeogenesis. Cytosolic pck1 abundance was increased by nutritional (diets with a high protein to carbohydrate ratio compared to diets with a low carbohydrate to protein ratio) and glucoregulatory endocrine factors (glucagon and cortisol), revealing that the well-described transcriptional regulation of pck1 in mammals is present in rainbow trout. Conversely, and in contrast to mammals, we here describe endocrine regulation of pck2a (decrease in abundance in response to glucagon infusion), and nutritional, social-status-dependent and hypoxia-dependent regulation of pck2b. Specifically, pck2b transcript abundance increased in trout fed a diet with a low protein to carbohydrate ratio compared to a diet with a high protein to carbohydrate ratio, in dominant fish compared to subordinate fish as well as hypoxia. This specific and differential expression of rainbow trout pck2 ohnologues is indicative of functional diversification, and possible functional consequences are discussed in light of the recently highlighted gluconeogenic roles of mitochondrial pck2 in mammalian models.

Published
2019
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4. Première approche épigénétique en nutrition des poissons : étude de la régulation épigénétique de la néogluconéogénèse hépatique chez la truite arc-en-ciel (Oncorhynchus mykiss) - conséquences d'un régime hyperglucidique

Author

Marandel, Lucie, Panserat, Stephane, Nutrition, Aquaculture et Génomique (NUAGE), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), and ProdInra, Archive Ouverte

Subjects
fish, trout, oncorhynchus mykiss, [SDV.BA] Life Sciences [q-bio]/Animal biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, néoglucogenèse, régulation epigénétique, rainbow trout, glucide, épigénétique, poisson, rainbow, animal nutrition, gène dupliqué, nutrition animale, duplicate genes, truite arc en ciel
Abstract

Crédit Incitatif 2014. Champ thématique : Ressources, Adaptation; Première approche épigénétique en nutrition des poissons : étude de la régulation épigénétique de la néogluconéogénèse hépatique chez la truite arc-en-ciel (Oncorhynchus mykiss) - conséquences d'un régime hyperglucidique. Journées d’Animation des Crédits Incitatifs du Département de Physiologie Animale et Systèmes d’Elevage (JACI Phase 2016)

Published
2016

5. The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes

Author

Anthony Bretaudeau, Olivier Sallou, Olivier Demeure, Christian Diot, Charles Bettembourg, Frédéric Lecerf, Marion Ouedraogo, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Plateforme bioinformatique GenOuest [Rennes], GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), This work was funded by INRA, Agrocampus Ouest and the Brittany Region., Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Université de Rennes (UR)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)

Subjects
lcsh:Medicine, Value (computer science), BIOLOGY, Sequence alignment, Biology, computer.software_genre, Genome, genome structure, Molecular Genetics, 03 medical and health sciences, Databases, 0302 clinical medicine, Semantic similarity, Genes, Duplicate, Gene Duplication, Gene expression, Ontology and Logics, Databases, Genetic, gène dupliqué, chromosome, lcsh:Science, Gene, 030304 developmental biology, base de données, 0303 health sciences, Internet, Multidisciplinary, Database, génome, lcsh:R, Chromosome, Computational Biology, Genomics, Functional Genomics, [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, Computer Science, gene expression, lcsh:Q, Structural Genomics, Genome Expression Analysis, Information Technology, computer, Sequence Analysis, 030217 neurology & neurosurgery, Function (biology), expression des gènes, Research Article
Abstract

Chantier qualité GA; BACKGROUND: There has been a surge in studies linking genome structure and gene expression, with special focus on duplicated genes. Although initially duplicated from the same sequence, duplicated genes can diverge strongly over evolution and take on different functions or regulated expression. However, information on the function and expression of duplicated genes remains sparse. Identifying groups of duplicated genes in different genomes and characterizing their expression and function would therefore be of great interest to the research community. The 'Duplicated Genes Database' (DGD) was developed for this purpose. METHODOLOGY: Nine species were included in the DGD. For each species, BLAST analyses were conducted on peptide sequences corresponding to the genes mapped on a same chromosome. Groups of duplicated genes were defined based on these pairwise BLAST comparisons and the genomic location of the genes. For each group, Pearson correlations between gene expression data and semantic similarities between functional GO annotations were also computed when the relevant information was available. CONCLUSIONS: The Duplicated Gene Database provides a list of co-localised and duplicated genes for several species with the available gene co-expression level and semantic similarity value of functional annotation. Adding these data to the groups of duplicated genes provides biological information that can prove useful to gene expression analyses. The Duplicated Gene Database can be freely accessed through the DGD website at http://dgd.genouest.org.

Published
2012
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6. Duplication and partitioning in evolution and function of homoeologous Q loci governing domestication characters in polyploid wheat

Author

Piotr Gornicki, Valérie Barbe, Cecile Huneau, Sylvie Samain, Bikram S. Gill, Ghislaine Magdelenat, Boulos Chalhoub, Justin D. Faris, Harry Belcram, Jack B. Rasmussen, Arnaud Couloux, Zengcui Zhang, Jérémy Just, Mathieu Charles, North Dakota State University (NDSU), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Department of Molecular Genetics and Cell Biology, University of Chicago, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Kansas State University, and We thank Joseph Jahier (Institut National de la Recherche Agronomique) and Moshe Feldman (Weizmann Institute of Science) for valuable discussions and for providing some of the wheat samples. This project was supported by US Department of Agriculture (USDA), Agricultural Research Service, Current Research Information Systems Project 5442-22000-033-00D and the National Center for Sequencing (Centre National de Sequencage-Genoscope)/APCNS2003 Project: Triticum Species Comparative Genome Sequencing in Wheat. PCR-based tracing of retrotransposon insertions was funded by the Agence Nationale pour la Recherche (ANR) Biodiversitee Project (ANR-05-BDIV-015) and the ANR-05-Blanc Project impact of transposable elements on gene regulation.

Subjects
0106 biological sciences, multidisciplinary sciences, science and technology, Pseudogene, [SDV]Life Sciences [q-bio], Locus (genetics), subfunctionilization, Biology, 01 natural sciences, Chromosomes, Evolution, Molecular, Polyploidy, 03 medical and health sciences, fate of duplicated genes, blé, Polyploid, Gene Duplication, polyploïdie, Gene duplication, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, gène dupliqué, RNA, Messenger, 3' Untranslated Regions, Gene, Alleles, Triticum, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, hyperfunctionilization, Ploidies, Multidisciplinary, Models, Genetic, Chromosome, food and beverages, Exons, Biological Sciences, Introns, Phenotype, Mutation, Subfunctionalization, Ploidy, Genome, Plant, 010606 plant biology & botany
Abstract

The Q gene encodes an AP2 -like transcription factor that played an important role in domestication of polyploid wheat. The chromosome 5A Q alleles ( 5AQ and 5Aq ) have been well studied, but much less is known about the q alleles on wheat homoeologous chromosomes 5B ( 5Bq ) and 5D ( 5Dq ). We investigated the organization, evolution, and function of the Q/q homoeoalleles in hexaploid wheat ( Triticum aestivum L.). Q/q gene sequences are highly conserved within and among the A, B, and D genomes of hexaploid wheat, the A and B genomes of tetraploid wheat, and the A, S, and D genomes of the diploid progenitors, but the intergenic regions of the Q/q locus are highly divergent among homoeologous genomes. Duplication of the q gene 5.8 Mya was likely followed by selective loss of one of the copies from the A genome progenitor and the other copy from the B, D, and S genomes. A recent V 329 -to-I mutation in the A lineage is correlated with the Q phenotype. The 5Bq homoeoalleles became a pseudogene after allotetraploidization. Expression analysis indicated that the homoeoalleles are coregulated in a complex manner. Combined phenotypic and expression analysis indicated that, whereas 5AQ plays a major role in conferring domestication-related traits, 5Dq contributes directly and 5Bq indirectly to suppression of the speltoid phenotype. The evolution of the Q/q loci in polyploid wheat resulted in the hyperfunctionalization of 5AQ , pseudogenization of 5Bq , and subfunctionalization of 5Dq , all contributing to the domestication traits.

Published
2011
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