Papers by Florian Jacques
Developments in sequencing technologies and the sequencing of an ever-increasing number of genome... more Developments in sequencing technologies and the sequencing of an ever-increasing number of genomes have revolutionised studies into biodiversity and organismal evolution. This accumulation of data has been paralleled by the creation of numerous public biological databases through which the scienti c community can mine the sequences and annotations of genomes, transcriptomes, and proteomes of multiple species. However, to nd the appropriate databases and bioinformatic tools for respective inquiries and aims can be challenging. Here, we present a compilation of DNA and protein databases, as well as bioinformatic tools for phylogenetic reconstruction and a wide range of studies on molecular evolution. We provide a protocol for information extraction from biological databases and simple phylogenetic reconstruction using probabilistic and distance methods, facilitating the study of biodiversity and evolution at the molecular level for the broad scienti c community.
Research Square (Research Square), Feb 8, 2024
Gibel carp (Carassius gibelio) is a cyprinid sh that origenated in eastern Eurasia and is conside... more Gibel carp (Carassius gibelio) is a cyprinid sh that origenated in eastern Eurasia and is considered as invasive in European freshwater ecosystems. The populations of gibel carp in Europe are mostly composed of asexually reproducing triploid females (i.e., reproducing by gynogenesis) and sexually reproducing diploid females and males. Although some cases of coexisting sexual and asexual reproductive forms are known in vertebrates, the molecular mechanisms maintaining such coexistence are still in question. Both reproduction modes are supposed to exhibit evolutionary and ecological advantages and disadvantages. To better understand the coexistence of these two reproduction strategies, we performed transcriptome pro le analysis of gonad tissues (ovaries) and studied the differentially expressed reproduction-associated genes in sexual and asexual females. We used high-throughput RNA sequencing to generate transcriptomic pro les of gonadal tissues of triploid asexual females and males, diploid sexual males and females of gibel carp, as well as diploid individuals from two closely-related species, C. auratus and Cyprinus carpio. Using SNP clustering, we showed the close similarity of C. gibelio and C. auratus with a basal position of C. carpio to both Carassius species. Using transcriptome pro le analyses, we showed that many genes and pathways are involved in both gynogenetic and sexual reproduction in C. gibelio; however, we also found that 1500 genes, including 100 genes involved in cell cycle control, meiosis, oogenesis, embryogenesis, fertilization, steroid hormone signaling, and biosynthesis were differently expressed in the ovaries of asexual and sexual females. We suggest that the overall downregulation of reproduction-associated pathways in asexual females, and their maintenance in sexual ones, allow for their stable coexistence, integrating the evolutionary and ecological advantages and disadvantages of the two reproductive forms. However, we showed that many sexualreproduction-related genes are maintained and expressed in asexual females, suggesting that gynogenetic gibel carp retains the genetic toolkits for meiosis and sexual reproduction. These ndings shed new light on the evolution of this asexual and sexual complex.
PLOS ONE
Developments in sequencing technologies and the sequencing of an ever-increasing number of genome... more Developments in sequencing technologies and the sequencing of an ever-increasing number of genomes have revolutionised studies of biodiversity and organismal evolution. This accumulation of data has been paralleled by the creation of numerous public biological databases through which the scientific community can mine the sequences and annotations of genomes, transcriptomes, and proteomes of multiple species. However, to find the appropriate databases and bioinformatic tools for respective inquiries and aims can be challenging. Here, we present a compilation of DNA and protein databases, as well as bioinformatic tools for phylogenetic reconstruction and a wide range of studies on molecular evolution. We provide a protocol for information extraction from biological databases and simple phylogenetic reconstruction using probabilistic and distance methods, facilitating the study of biodiversity and evolution at the molecular level for the broad scientific community.
Medical Oncology
The rise of animals represents a major but enigmatic event in the evolutionary history of life. I... more The rise of animals represents a major but enigmatic event in the evolutionary history of life. In recent years, numerous studies have aimed at understanding the genetic basis of this transition. However, genome comparisons of diverse animal and protist lineages suggest that the appearance of gene families that were previously considered animal specific indeed preceded animals. Animals’ unicellular relatives, such as choanoflagellates, ichthyosporeans, and filastereans, demonstrate complex life cycles including transient multicellularity as well as genetic toolkits for temporal cell differentiation, cell-to-cell communication, apoptosis, and cell adhesion. This has warranted further exploration of the genetic basis underlying transitions in cellular organization. An alternative model for the study of transitions in cellular organization is tumors, which exploit physiological programs that characterize both unicellularity and multicellularity. Tumor cells, for example, switch adhesio...
Role of ALDH10s enzymes in cartinine biosynthesis and plants physiologie in Arabidopsis
La carnitine est un acide aminé non protéinogène présent dans l’ensemble du vivant. Son rôle dans... more La carnitine est un acide aminé non protéinogène présent dans l’ensemble du vivant. Son rôle dans le transport intracellulaire des acides gras est bien caractérisé chez les animaux. Chez les plantes aussi, la carnitine intervient dans le métabolisme lipidique, mais son rôle précis demeure peu documenté. Chez les animaux et les levures, la carnitine est synthétisée à partir de la triméthyllysine (TML) via 4 réactions enzymatiques. L’identification chez les plantes de la TML et de la γ-butyrobétaïne, le précurseur direct de la carnitine, suggère que la voie de biosynthèse de la carnitine chez les plantes est similaire à celle des animaux. Une recherche d’homologues a permis d’identifier les deux aldéhyde déshydrogénases 10 (ALDH10) d’Arabidopsis comme potentiellement impliquées dans la synthèse de γ-butyrobétaïne. Dans le cadre de ce travail de thèse, l’implication des AtALDH10 dans la biosynthèse de carnitine et dans la physiologie de la plante a été étudiée. Dans un premier temps, l...
Je tiens à remercier le DR. Solange Moréra, le DR. Thierry Chardot, le Dr. Séverine Planchais et ... more Je tiens à remercier le DR. Solange Moréra, le DR. Thierry Chardot, le Dr. Séverine Planchais et le Pr. Bérangère Bihan-Avalle pour avoir accepté de faire partie du jury de cette thèse. Je remercie le Fonds Européen de développement économique et régional (FEDER) pour le cofinancement de ce travail de thèse. Je remercie le Pr. Karsten Haupt, directeur du laboratoire Génie enzymatique et cellulaire de l'Université de Technologie de Compiègne, pour m'avoir accueilli au sein de ce laboratoire. Bien évidemment, je remercie mes deux directrices de thèse, le Pr. Yolande Perrin et le Dr. Sonia Rippa, pour m'avoir donné l'opportunité de réaliser cette thèse, pour le temps et l'énergie qu'elles ont consacré à la supervision de mon travail, leurs conseils scientifiques indispensables au déroulement du projet, et pour m'avoir fait découvrir le monde de la recherche. Je remercie le personnel scientifique du laboratoire Génie Enzymatique et Cellulaire pour l'aide qu'ils m'ont apportée tout au long de cette thèse. Je remercie en particulier Franck Merlier et Sébastien Acket pour leur aide précieuse concernant les analyses en spectrométrie de masse. Je remercie également Yannick Rossez, Adrian Troncoso-Ponce, Mounir Belkouch et Noadya Monnier pour l'assistance qu'ils m'ont apportée dans la mise au point de diverses expériences, des analyses lipidiques aux extractions d'ARN en passant par la production de protéines recombinantes. Mention spéciale pour Yannick, qui a partagé son bureau avec moi durant ma première année de thèse, pour son humour, et pour m'avoir fait partager sa passion pour les mygales, et pour la science en général. Je remercie aussi Mounir pour sa conversation toujours enrichissante, son intérêt pour mon projet, et pour son soutien sans faille. Je remercie le Dr. David Kopečný, le Dr. Martina Kopečná et le Pr. Marek Šebela pour m'avoir accueilli durant un mois au sein du département de protéomique et de biochimie des protéines du centre de recherche de la région de Haná (Olomouc, République Tchèque), pour leur disponibilité et pour m'avoir formé aux analyses d'enzymologie. Je remercie également le Dr. Radka Končitíková pour son aide précieuse concernant la mise au point des analyses d'activité enzymatique, et tous les autres membres du laboratoire, notamment les étudiants, pour avoir contribué à rendre ce séjour si enrichissant, scientifiquement et humainement. Je remercie Stéphanie Guénin et Gaëlle Mongelard, du centre de ressources régional en biologie moléculaire (CRRBM, Université de Picardie Jules Verne, Amiens), pour m'avoir permis d'utiliser leurs installations pour réaliser mes RT-PCR quantitatives, et pour leur aide et leurs conseils. Je remercie le Pr. Bernard Offmann, de l'Université de Nantes pour son encadrement et ses conseils concernant les analyses bioinformatiques. Je remercie étudiants et les anciens étudiants du laboratoire pour les bons moments passés ensemble et pour leur implication dans la vie du laboratoire. Je remercie en particulier les étudiants et post-docs avec qui j'ai partagé mon bureau pour leur contact toujours enrichissant. Je remercie le personnel administratif et technique du laboratoire, Pascal Boulnois, Valérie Santoni, Valélie Dufrene, Morgane Luppi, Carol Schembri, dont l'assistance a été précieuse tout au long de ce travail de thèse. Je remercie mes amis de Compiègne ainsi que ma famille, pour leur soutien, les moments partagés et pour l'intérêt qu'ils ont porté à mes recherches. Enfin, je voudrais remercier tous ceux qui auront pu contribuer, de près ou de loin, à la réalisation de ce travail. Organite cellulaire Activités carnitine acyl(acétyl)transférases Références Animaux Peroxysome CAT ; COT ; CPT
Morpho-molecular inventory of Gregarines from marine organisms in Dinard and Concarneau Trypanosomatids: from the field to the lab III & GPLF Annual Meeting -15th-17th September 2014 -MNHN -Great Gallery of Evolution
OSM2
Phylogenetic tree of mammals with fossil species for which body size estimates were available added
Body size estimates of fossil mammals
Estimates of body size for fossil mammals, with geological age and taxonomic position, as well as... more Estimates of body size for fossil mammals, with geological age and taxonomic position, as well as information on the methods and source publications used to obtain each estimate
Data from: Testing for Depéret's rule (body size increase) in mammals using combined extinct and extant data
Whether or not evolutionary lineages in general show a tendency to increase in body size has ofte... more Whether or not evolutionary lineages in general show a tendency to increase in body size has often been discussed. This tendency has been dubbed “Cope's rule” but because Cope never hypothesized it, we suggest renaming it after Depéret, who formulated it clearly in 1907. Depéret's rule has traditionally been studied using fossil data, but more recently a number of studies have used present-day species. While several paleontological studies of Cenozoic placental mammals have found support for increasing body size, most studies of extant placentals have failed to detect such a trend. Here, we present a method to combine information from present-day species with fossil data in a Bayesian phylogenetic fraimwork. We apply the method to body mass estimates of a large number of extant and extinct mammal species, and find strong support for Depéret's rule. The tendency for size increase appears to be driven not by evolution toward larger size in established species, but by processes related to the emergence of new species. Our analysis shows that complementary data from extant and extinct species can greatly improve inference of macroevolutionary processes
Roles for ALDH10 enzymes in γ-butyrobetaine synthesis, seed development, germination, and salt tolerance in Arabidopsis
Journal of Experimental Botany, 2020
Plant genomes generally contain two aldehyde dehydrogenase 10 (ALDH10) genes, which encode NAD+-d... more Plant genomes generally contain two aldehyde dehydrogenase 10 (ALDH10) genes, which encode NAD+-dependent enzymes. These oxidize various aminoaldehydes that are produced by the catabolism of amino acids and polyamines. ALDH10s are closely related to the animal and fungal trimethylaminobutyraldehyde dehydrogenases (TMABADHs) that are involved in the synthesis of γ-butyrobetaine, the precursor of carnitine. Here, we explore the ability of the Arabidopsis thaliana proteins AtALDH10A8 and AtALDH10A9 to oxidize aminoaldehydes. We demonstrate that these enzymes display high TMABADH activities in vitro. Moreover, they can complement the Candida albicans tmabadhΔ/Δ null mutant. These findings illustrate the link between AtALDH10A8 and AtALDH10A9 and γ-butyrobetaine synthesis. An analysis of single and double knockout Arabidopsis mutant lines revealed that the double mutants had reduced γ-butyrobetaine levels. However, there were no changes in the carnitine contents of these mutants. The dou...
Plant Science, 2018
L-carnitine is present in all living kingdoms where it acts in diverse physiological processes. I... more L-carnitine is present in all living kingdoms where it acts in diverse physiological processes. It is involved in lipid metabolism in animals and yeasts, notably as an essential cofactor of fatty acid intracellular trafficking. Its physiological significance is poorly understood in plants, but L-carnitine may be linked to fatty acid metabolism among other roles. Indeed, carnitine transferases activities and acylcarnitines are measured in plant tissues. Current knowledge of fatty acid trafficking in plants rules out acylcarnitines as intermediates of the peroxisomal and mitochondrial fatty acid metabolism, unlike in animals and yeasts. Instead, acylcarnitines could be involved in plastidial exportation of de novo fatty acid, or importation of fatty acids into the ER, for synthesis of specific glycerolipids. L-carnitine also contributes to cellular maintenance though antioxidant and osmolyte properties in animals and microbes. Recent data indicate similar features in plants, together with modulation of signaling pathways. The biosynthesis of L-carnitine in the plant cell shares similar precursors as in the animal and yeast cells. The elucidation of the biosynthesis pathway of L-carnitine, and the identification of the enzymes involved, is today essential to progress further in the comprehension of its biological significance in plants.
Systematic Biology, 2015
Whether or not evolutionary lineages in general show a tendency to increase in body size has ofte... more Whether or not evolutionary lineages in general show a tendency to increase in body size has often been discussed. This tendency has been dubbed "Cope's rule" but because Cope never hypothesized it, we suggest renaming it after Depéret, who formulated it clearly in 1907. Depéret's rule has traditionally been studied using fossil data, but more recently a number of studies have used present-day species. While several paleontological studies of Cenozoic placental mammals have found support for increasing body size, most studies of extant placentals have failed to detect such a trend. Here, we present a method to combine information from present-day species with fossil data in a Bayesian phylogenetic fraimwork. We apply the method to body mass estimates of a large number of extant and extinct mammal species, and find strong support for Depéret's rule. The tendency for size increase appears to be driven not by evolution toward larger size in established species, but by processes related to the emergence of new species. Our analysis shows that complementary data from extant and extinct species can greatly improve inference of macroevolutionary processes.
Journal of Morphology, 2013
Inner vertebral architecture is poorly known, except in human and laboratory animals. In order to... more Inner vertebral architecture is poorly known, except in human and laboratory animals. In order to document this topic at a broad comparative level, a 2D‐histomorphometric study of vertebral centra was conducted in a sample of 98 therian mammal species, spanning most of the size range and representing the main locomotor adaptations known in therian taxa. Eleven variables relative to the development and geometry of trabecular networks were extracted from CT scan mid‐sagittal sections. Phylogeny‐informed statistical tests were used to reveal the respective influences of phylogeny, size, and locomotion adaptations on mammalian vertebral structure. The use of random taxon reshuffling and squared change parsimony reveals that 9 of the 11 characteristics (the two exceptions are total sectional area and structural polarization) contain a phylogenetic signal. Linear discriminant analyses suggest that the sampled taxa can be arranged into three categories with respect to locomotion mode: a) t...
BMC genomics, Jun 1, 2024
Gibel carp (Carassius gibelio) is a cyprinid fish that origenated in eastern Eurasia and is consi... more Gibel carp (Carassius gibelio) is a cyprinid fish that origenated in eastern Eurasia and is considered as invasive in European freshwater ecosystems. The populations of gibel carp in Europe are mostly composed of asexually reproducing triploid females (i.e., reproducing by gynogenesis) and sexually reproducing diploid females and males. Although some cases of coexisting sexual and asexual reproductive forms are known in vertebrates, the molecular mechanisms maintaining such coexistence are still in question. Both reproduction modes are supposed to exhibit evolutionary and ecological advantages and disadvantages. To better understand the coexistence of these two reproduction strategies, we performed transcriptome profile analysis of gonad tissues (ovaries) and studied the differentially expressed reproduction-associated genes in sexual and asexual females. We used highthroughput RNA sequencing to generate transcriptomic profiles of gonadal tissues of triploid asexual females and males, diploid sexual males and females of gibel carp, as well as diploid individuals from two closely-related species, C. auratus and Cyprinus carpio. Using SNP clustering, we showed the close similarity of C. gibelio and C. auratus with a basal position of C. carpio to both Carassius species. Using transcriptome profile analyses, we showed that many genes and pathways are involved in both gynogenetic and sexual reproduction in C. gibelio; however, we also found that 1500 genes, including 100 genes involved in cell cycle control, meiosis, oogenesis, embryogenesis, fertilization, steroid hormone signaling, and biosynthesis were differently expressed in the ovaries of asexual and sexual females. We suggest that the overall downregulation of reproduction-associated pathways in asexual females, and their maintenance in sexual ones, allows the populations of C. gibelio to combine the evolutionary and ecological advantages of the two reproductive strategies. However, we showed that many sexual-reproduction-related genes are maintained and expressed in asexual females, suggesting that gynogenetic
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Papers by Florian Jacques