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Eric Ghigo - One of the best experts on this subject based on the ideXlab platform.

  • Chryseobacterium Schmidteae sp. nov. a novel bacterial species isolated from planarian Schmidtea mediterranea
    Springer Science and Business Media LLC, 2021
    Co-Authors: Luis Johnson Kangale, Eric Ghigo, Didier Raoult, Pierre-edouard Fournier
    Abstract:

    AbstractMarseille-P9602T is a Chryseobacterium-like strain that we isolated from planarian Schmidtea mediterranea and characterized by taxono-genomic approach. We found that Marseille-P9602T strain exhibits a 16S rRNA gene sequence similarity of 98.76% with Chryseobacterium scophthalmum LMG 13028T strain, the closest phylogenetic neighbor. Marseille-P9602T strain was observed to be a yellowish-pigmented, Gram-negative, rod-shaped bacterium, growing in aerobic conditions and belonging to the Flavobacteriaceae family. The major fatty acids detected are 13-methyl-tetradecanoic acid (57%), 15-methylhexadecenoic acid (18%) and 12-methyl-tetradecanoic acid (8%). Marseille-P9602 strain size was found from genome assembly to be of 4,271,905 bp, with a 35.5% G + C content. The highest values obtained for Ortho-ANI and dDDH were 91.67% and 44.60%, respectively. Thus, hereby we unravel that Marseille-P9602 strain is sufficiently different from other closed related species and can be classified as a novel bacterial species, for which we propose the name of Chryseobacterium Schmidteae sp. nov. Type strain is Marseille-P9602T (= CSUR P9602T = CECT 30295T).

  • metabacillus Schmidteae sp nov cultivated from planarian Schmidtea mediterranea microbiota
    Microbiological Research, 2021
    Co-Authors: Luis Johnson Kangale, Didier Raoult, Eric Ghigo
    Abstract:

    Taxonogenomics combines phenotypic assays and genomic analysis as a means of characterizing novel strains. We used this strategy to study Marseille-P9898T strain, an aerobic, motile, Gram-negative, spore-forming, and rod-shaped bacterium isolated from planarian Schmidtea mediterranea. Marseille-P9898T is catalase-positive and oxidase-negative. The major fatty acids detected are 12-methyl-tetradecanoic acid, 13-methyl-tetradecanoic acid, and hexadecanoic acid. Marseille-P9898T strain shared more than 98% sequence similarity with the Metabacillus niabensis strain 4T19T (98.99%), Metabacillus halosaccharovorans strain E33T (98.75%), Metabacillus malikii strain NCCP-662T (98.19%), and Metabacillus litoralis strain SW-211T (97.15%). Marseille-P9898 strain belongs to Metabacillus genus. Genomic analysis revealed the highest similarities with Ortho-ANI and dDDH, 85.76% with Metabacillus halosaccharovorans, and 34.20% with Bacillus acidicola, respectively. These results show that the Marseille-P9898T strain is a novel bacterial species from Metabacillus genus, for which we propose the name of Metabacillus Schmidteae sp. nov. (Type strain Marseille-P9898T = CSUR P9898T = DSM 111480T).

  • draft genome sequence of comamonas aquatilis strain lk csur p6418 cect 9772 isolated from the planarian Schmidtea mediterranea
    Microbiology Resource Announcements, 2021
    Co-Authors: Luis Johnson Kangale, Didier Raoult, Eric Ghigo
    Abstract:

    ABSTRACT Comamonas aquatilis was defined as a new Comamonas species based on its 16S rRNA sequence, but the genome from the type strain SB30-Cr27-3T (= CIP 111491T = CCM 8815T) is not available. We have cultivated from the planarian Schmidtea mediterranea a Comamonas aquatilis strain, LK (= CSUR P6418 = CECT 9772), that exhibits 100% 16S rRNA sequence similarity to strain SB30-Cr27-3T. We have sequenced the genome of strain LK and obtained a chromosome of 4,899,818 bp, with a G+C content of 61.75%, assembled into two contigs.

  • pedobacter Schmidteae sp nov a new bacterium isolated from the microbiota of the planarian Schmidtea mediterranea
    Scientific Reports, 2020
    Co-Authors: Luis Johnson Kangale, Eric Ghigo, Pierre-edouard Fournier
    Abstract:

    : Pedobacter Schmidteae sp. nov. strain EGT (Collection de Souches de l'Unite des Rickettsie CSUR P6417 = Coleccion Espanola de Cultivos Tipo CECT 9771) is a new Pedobacter species isolated from the planarian Schmidtea mediterranea. Schmidtea mediterranea are flatworms living in freshwater and exhibiting an unusual ability to regenerate amputated parts. To date, the gut microbiota of Schmidtea mediterranea remains poorly studied. Here, via the culturomics strategy that consists in using diversified culture conditions, we isolated a new bacterium, strain EG, that we characterized using the taxono-genomics approach that combines phenotypic assays and genome sequencing and analysis. Strain EG exhibits a 16S rRNA sequence similarity of 98.29% with Pedobacter nyackensis strain NWG-II14T, its closest neighbour with standing in nomenclature. It is an aerobic bacterium belonging to the family Sphingobacteriaceae. Colonies are small, round, smooth and transparent. Bacterial cells are Gram-negative, rod-shaped, motile and non-spore-forming bacilli with positive catalase and oxidase activities. The genome sequence is 6,198,518 bp-long with a G + C content of 41.13%, and the Ortho-ANI and dDDH values when compared to P. nyackensis are 77.34% and 21.50%, respectively. Strain EGT exhibits unique characteristics that classify it as the type strain of new bacterial species for which we propose the name Pedobacter Schmidteae sp. nov.

  • Temperature affects the biology of Schmidtea mediterranea
    Nature Publishing Group, 2018
    Co-Authors: Nassim Hammoudi, Eric Ghigo, Cédric Torre, Michel Drancourt
    Abstract:

    Abstract Studies of tissue regeneration and host-pathogen interactions using the model planarian Schmidtea mediterranea have been performed at an experimental temperature of 19 °C. S. mediterranea planarians exposed to 19 °C–32 °C were observed for survival, mobility, feeding and regeneration for three months and elimination of the Staphylococcus aureus pathogen over six days. S. mediterranea planarians died at 30 °C–32 °C after 18 days of observation but tolerated temperatures of 19 °C up to 28 °C with non-significant differences in mobility and feeding behavior. Genetic malleability tested by RNAi feeding was still efficient at 26 °C and 28 °C. Concerning the immune capacity of planarians, we reported an exacerbation of the immune response in worms infected by S. aureus at 26 °C and 28 °C. These observations suggest a temperature modulation of planarian stem cells and illustrate the importance of modulating experimental temperature when using planarians as model organisms to study regeneration and immune response

Luis Johnson Kangale - One of the best experts on this subject based on the ideXlab platform.

  • Chryseobacterium Schmidteae sp. nov. a novel bacterial species isolated from planarian Schmidtea mediterranea
    Springer Science and Business Media LLC, 2021
    Co-Authors: Luis Johnson Kangale, Eric Ghigo, Didier Raoult, Pierre-edouard Fournier
    Abstract:

    AbstractMarseille-P9602T is a Chryseobacterium-like strain that we isolated from planarian Schmidtea mediterranea and characterized by taxono-genomic approach. We found that Marseille-P9602T strain exhibits a 16S rRNA gene sequence similarity of 98.76% with Chryseobacterium scophthalmum LMG 13028T strain, the closest phylogenetic neighbor. Marseille-P9602T strain was observed to be a yellowish-pigmented, Gram-negative, rod-shaped bacterium, growing in aerobic conditions and belonging to the Flavobacteriaceae family. The major fatty acids detected are 13-methyl-tetradecanoic acid (57%), 15-methylhexadecenoic acid (18%) and 12-methyl-tetradecanoic acid (8%). Marseille-P9602 strain size was found from genome assembly to be of 4,271,905 bp, with a 35.5% G + C content. The highest values obtained for Ortho-ANI and dDDH were 91.67% and 44.60%, respectively. Thus, hereby we unravel that Marseille-P9602 strain is sufficiently different from other closed related species and can be classified as a novel bacterial species, for which we propose the name of Chryseobacterium Schmidteae sp. nov. Type strain is Marseille-P9602T (= CSUR P9602T = CECT 30295T).

  • metabacillus Schmidteae sp nov cultivated from planarian Schmidtea mediterranea microbiota
    Microbiological Research, 2021
    Co-Authors: Luis Johnson Kangale, Didier Raoult, Eric Ghigo
    Abstract:

    Taxonogenomics combines phenotypic assays and genomic analysis as a means of characterizing novel strains. We used this strategy to study Marseille-P9898T strain, an aerobic, motile, Gram-negative, spore-forming, and rod-shaped bacterium isolated from planarian Schmidtea mediterranea. Marseille-P9898T is catalase-positive and oxidase-negative. The major fatty acids detected are 12-methyl-tetradecanoic acid, 13-methyl-tetradecanoic acid, and hexadecanoic acid. Marseille-P9898T strain shared more than 98% sequence similarity with the Metabacillus niabensis strain 4T19T (98.99%), Metabacillus halosaccharovorans strain E33T (98.75%), Metabacillus malikii strain NCCP-662T (98.19%), and Metabacillus litoralis strain SW-211T (97.15%). Marseille-P9898 strain belongs to Metabacillus genus. Genomic analysis revealed the highest similarities with Ortho-ANI and dDDH, 85.76% with Metabacillus halosaccharovorans, and 34.20% with Bacillus acidicola, respectively. These results show that the Marseille-P9898T strain is a novel bacterial species from Metabacillus genus, for which we propose the name of Metabacillus Schmidteae sp. nov. (Type strain Marseille-P9898T = CSUR P9898T = DSM 111480T).

  • draft genome sequence of comamonas aquatilis strain lk csur p6418 cect 9772 isolated from the planarian Schmidtea mediterranea
    Microbiology Resource Announcements, 2021
    Co-Authors: Luis Johnson Kangale, Didier Raoult, Eric Ghigo
    Abstract:

    ABSTRACT Comamonas aquatilis was defined as a new Comamonas species based on its 16S rRNA sequence, but the genome from the type strain SB30-Cr27-3T (= CIP 111491T = CCM 8815T) is not available. We have cultivated from the planarian Schmidtea mediterranea a Comamonas aquatilis strain, LK (= CSUR P6418 = CECT 9772), that exhibits 100% 16S rRNA sequence similarity to strain SB30-Cr27-3T. We have sequenced the genome of strain LK and obtained a chromosome of 4,899,818 bp, with a G+C content of 61.75%, assembled into two contigs.

  • pedobacter Schmidteae sp nov a new bacterium isolated from the microbiota of the planarian Schmidtea mediterranea
    Scientific Reports, 2020
    Co-Authors: Luis Johnson Kangale, Eric Ghigo, Pierre-edouard Fournier
    Abstract:

    : Pedobacter Schmidteae sp. nov. strain EGT (Collection de Souches de l'Unite des Rickettsie CSUR P6417 = Coleccion Espanola de Cultivos Tipo CECT 9771) is a new Pedobacter species isolated from the planarian Schmidtea mediterranea. Schmidtea mediterranea are flatworms living in freshwater and exhibiting an unusual ability to regenerate amputated parts. To date, the gut microbiota of Schmidtea mediterranea remains poorly studied. Here, via the culturomics strategy that consists in using diversified culture conditions, we isolated a new bacterium, strain EG, that we characterized using the taxono-genomics approach that combines phenotypic assays and genome sequencing and analysis. Strain EG exhibits a 16S rRNA sequence similarity of 98.29% with Pedobacter nyackensis strain NWG-II14T, its closest neighbour with standing in nomenclature. It is an aerobic bacterium belonging to the family Sphingobacteriaceae. Colonies are small, round, smooth and transparent. Bacterial cells are Gram-negative, rod-shaped, motile and non-spore-forming bacilli with positive catalase and oxidase activities. The genome sequence is 6,198,518 bp-long with a G + C content of 41.13%, and the Ortho-ANI and dDDH values when compared to P. nyackensis are 77.34% and 21.50%, respectively. Strain EGT exhibits unique characteristics that classify it as the type strain of new bacterial species for which we propose the name Pedobacter Schmidteae sp. nov.

Didier Raoult - One of the best experts on this subject based on the ideXlab platform.

  • Chryseobacterium Schmidteae sp. nov. a novel bacterial species isolated from planarian Schmidtea mediterranea
    Springer Science and Business Media LLC, 2021
    Co-Authors: Luis Johnson Kangale, Eric Ghigo, Didier Raoult, Pierre-edouard Fournier
    Abstract:

    AbstractMarseille-P9602T is a Chryseobacterium-like strain that we isolated from planarian Schmidtea mediterranea and characterized by taxono-genomic approach. We found that Marseille-P9602T strain exhibits a 16S rRNA gene sequence similarity of 98.76% with Chryseobacterium scophthalmum LMG 13028T strain, the closest phylogenetic neighbor. Marseille-P9602T strain was observed to be a yellowish-pigmented, Gram-negative, rod-shaped bacterium, growing in aerobic conditions and belonging to the Flavobacteriaceae family. The major fatty acids detected are 13-methyl-tetradecanoic acid (57%), 15-methylhexadecenoic acid (18%) and 12-methyl-tetradecanoic acid (8%). Marseille-P9602 strain size was found from genome assembly to be of 4,271,905 bp, with a 35.5% G + C content. The highest values obtained for Ortho-ANI and dDDH were 91.67% and 44.60%, respectively. Thus, hereby we unravel that Marseille-P9602 strain is sufficiently different from other closed related species and can be classified as a novel bacterial species, for which we propose the name of Chryseobacterium Schmidteae sp. nov. Type strain is Marseille-P9602T (= CSUR P9602T = CECT 30295T).

  • metabacillus Schmidteae sp nov cultivated from planarian Schmidtea mediterranea microbiota
    Microbiological Research, 2021
    Co-Authors: Luis Johnson Kangale, Didier Raoult, Eric Ghigo
    Abstract:

    Taxonogenomics combines phenotypic assays and genomic analysis as a means of characterizing novel strains. We used this strategy to study Marseille-P9898T strain, an aerobic, motile, Gram-negative, spore-forming, and rod-shaped bacterium isolated from planarian Schmidtea mediterranea. Marseille-P9898T is catalase-positive and oxidase-negative. The major fatty acids detected are 12-methyl-tetradecanoic acid, 13-methyl-tetradecanoic acid, and hexadecanoic acid. Marseille-P9898T strain shared more than 98% sequence similarity with the Metabacillus niabensis strain 4T19T (98.99%), Metabacillus halosaccharovorans strain E33T (98.75%), Metabacillus malikii strain NCCP-662T (98.19%), and Metabacillus litoralis strain SW-211T (97.15%). Marseille-P9898 strain belongs to Metabacillus genus. Genomic analysis revealed the highest similarities with Ortho-ANI and dDDH, 85.76% with Metabacillus halosaccharovorans, and 34.20% with Bacillus acidicola, respectively. These results show that the Marseille-P9898T strain is a novel bacterial species from Metabacillus genus, for which we propose the name of Metabacillus Schmidteae sp. nov. (Type strain Marseille-P9898T = CSUR P9898T = DSM 111480T).

  • draft genome sequence of comamonas aquatilis strain lk csur p6418 cect 9772 isolated from the planarian Schmidtea mediterranea
    Microbiology Resource Announcements, 2021
    Co-Authors: Luis Johnson Kangale, Didier Raoult, Eric Ghigo
    Abstract:

    ABSTRACT Comamonas aquatilis was defined as a new Comamonas species based on its 16S rRNA sequence, but the genome from the type strain SB30-Cr27-3T (= CIP 111491T = CCM 8815T) is not available. We have cultivated from the planarian Schmidtea mediterranea a Comamonas aquatilis strain, LK (= CSUR P6418 = CECT 9772), that exhibits 100% 16S rRNA sequence similarity to strain SB30-Cr27-3T. We have sequenced the genome of strain LK and obtained a chromosome of 4,899,818 bp, with a G+C content of 61.75%, assembled into two contigs.

Barberán Martín Sara - One of the best experts on this subject based on the ideXlab platform.

  • The evolution of the EGFR pathway in Metazoa and its diversification in the planarian Schmidtea mediterranea
    'Springer Science and Business Media LLC', 2017
    Co-Authors: Barberán Martín Sara, Martín Durán, José M., Cebrià Sánchez Francesc
    Abstract:

    The EGFR pathway is an essential signaling system in animals, whose core components are the epidermal growth factors (EGF ligands) and their trans-membrane tyrosine kinase receptors (EGFRs). Despite extensive knowledge in classical model organisms, little is known of the composition and function of the EGFR pathway in most animal lineages. Here, we have performed an extensive search for the presence of EGFRs and EGF ligands in representative species of most major animal clades, with special focus on the planarian Schmidtea mediterranea. With the exception of placozoans and cnidarians, we found that the EGFR pathway is potentially present in all other analyzed animal groups, and has experienced frequent independent expansions. We further characterized the expression domains of the EGFR/EGF identified in S. mediterranea, revealing a wide variety of patterns and localization in almost all planarian tissues. Finally, functional experiments suggest an interaction between one of the previously described receptors, Smed-egfr-5, and the newly found ligand Smed-egf-6. Our findings provide the most comprehensive overview to date of the EGFR pathway, and indicate that the last common metazoan ancestor had an initial complement of one EGFR and one putative EGF ligand, which was often expanded or lost during animal evolution

  • Caracterización de la vía EGFR en la planaria Schmidtea mediterranea y su papel en la diferenciación de las células madre
    'Edicions de la Universitat de Barcelona', 2017
    Co-Authors: Barberán Martín Sara
    Abstract:

    [spa] Esta tesis doctoral estudia la evolución de la vía de señalización de los receptores de los factores de crecimiento epidérmicos (EGFR) en animales, y la identificación y caracterización de sus componentes principales –los receptores EGFR y los ligandos EGF—en la planaria Schmidtea mediterranea. Los resultados obtenidos sugieren que esta vía de señalización apareció muy temprano durante la evolución animal, ya que el ancestro común a todos los metazoos probablemente presentaba un receptor EGFR y un ligando EGF. Posteriormente, este complemento básico ha experimentando modificaciones independientes –pérdida o ganancia de elementos— en algunos grupos y/o especies. La planaria S. mediterranea es un claro ejemplo de expansión de la vía EGFR, puesto que tiene seis receptores EGFR y nueve ligandos EGF, uno de los cuales es de tipo neuregulina, subclase presente exclusivamente en Bilaterales. El estudio detallado de cada uno de estos elementos nos ha permitido demostrar que tanto los receptores como los ligandos se encuentran expresados en una gran variedad de tejidos en planarias y realizan una gran diversidad de funciones, tales como el mantenimiento y regeneración de la faringe, del sistema digestivo, del sistema excretor y de las células pigmentarias de los ojos. La activación del receptor EGFR, Smed-egfr-1, a través de la unión de su posible ligando Smed-nrg-1 es esencial para la diferenciación de las células madre de estos animales –los neoblastos—a células gastrodérmicas maduras. Nuestros resultados apoyan que la función de la vía EGFR en el mantenimiento y diferenciación de las células madre de animales está conservada en planarias. En conclusión, esta tesis doctoral avanza el conocimiento que tenemos de la vía EGFR en la evolución animal y en un modelo regenerativo como la planaria S. mediterranea, así como de los mecanismos que regulan las células madre adultas de estos organismos.[eng] This thesis studies the evolution of the epidermal growth factor receptor signaling pathway (EGFR) in animals, and the identification and characterization of its main components –the EGFR receptors and the EGF ligands– in the planarian Schmidtea mediterranea. The results obtained suggest that this signaling pathway appeared very early in animal evolution, since the common ancestor of all metazoans probably had one EGFR and one EGF ligand. Subsequently, this basic complement has undergone independent modifications -–gain or loss of elements– in some groups and / or species. The planarian S. mediterranea is a clear example of expansion of the EGFR pathway, since it has six EGFR and nine EGF ligands, one of which is a neuregulin type, subclass present exclusively in Bilateria. The detailed study of each of these elements has allowed us to demonstrate that both, receptors and ligands, are expressed in a wide variety of tissues in these animals and perform multiple functions, such as the maintenance and regeneration of the pharynx, the digestive system, the excretory system and the eye pigment cells. Specifically, the activation of the receptor Smed-egfr-1 through the binding of its possible ligand Smed-nrg-1, is essential for the differentiation of the stem cells of these animals –the neoblasts– to mature gastrodermal cells. Our results support that the known function of the EGFR signaling pathway in the maintenance and differentiation of the stem cells of other animals, is conserved in planarians. In conclusion, this thesis advances the knowledge we have of the EGFR pathway in animal evolution and in a regenerative model such as the planarian S. mediterranea, as well as in the mechanisms that regulate the adult stem cells of these organisms

  • Caracterización de la vía EGFR en la planaria Schmidtea mediterranea y su papel en la diferenciación de las células madre
    'Edicions de la Universitat de Barcelona', 2016
    Co-Authors: Barberán Martín Sara
    Abstract:

    Esta tesis doctoral estudia la evolución de la vía de señalización de los receptores de los factores de crecimiento epidérmicos (EGFR) en animales, y la identificación y caracterización de sus componentes principales –los receptores EGFR y los ligandos EGF—en la planaria Schmidtea mediterranea. Los resultados obtenidos sugieren que esta vía de señalización apareció muy temprano durante la evolución animal, ya que el ancestro común a todos los metazoos probablemente presentaba un receptor EGFR y un ligando EGF. Posteriormente, este complemento básico ha experimentando modificaciones independientes –pérdida o ganancia de elementos— en algunos grupos y/o especies. La planaria S. mediterranea es un claro ejemplo de expansión de la vía EGFR, puesto que tiene seis receptores EGFR y nueve ligandos EGF, uno de los cuales es de tipo neuregulina, subclase presente exclusivamente en Bilaterales. El estudio detallado de cada uno de estos elementos nos ha permitido demostrar que tanto los receptores como los ligandos se encuentran expresados en una gran variedad de tejidos en planarias y realizan una gran diversidad de funciones, tales como el mantenimiento y regeneración de la faringe, del sistema digestivo, del sistema excretor y de las células pigmentarias de los ojos. La activación del receptor EGFR, Smed-egfr-1, a través de la unión de su posible ligando Smed-nrg-1 es esencial para la diferenciación de las células madre de estos animales –los neoblastos—a células gastrodérmicas maduras. Nuestros resultados apoyan que la función de la vía EGFR en el mantenimiento y diferenciación de las células madre de animales está conservada en planarias. En conclusión, esta tesis doctoral avanza el conocimiento que tenemos de la vía EGFR en la evolución animal y en un modelo regenerativo como la planaria S. mediterranea, así como de los mecanismos que regulan las células madre adultas de estos organismos.This thesis studies the evolution of the epidermal growth factor receptor signaling pathway (EGFR) in animals, and the identification and characterization of its main components –the EGFR receptors and the EGF ligands– in the planarian Schmidtea mediterranea. The results obtained suggest that this signaling pathway appeared very early in animal evolution, since the common ancestor of all metazoans probably had one EGFR and one EGF ligand. Subsequently, this basic complement has undergone independent modifications -–gain or loss of elements– in some groups and / or species. The planarian S. mediterranea is a clear example of expansion of the EGFR pathway, since it has six EGFR and nine EGF ligands, one of which is a neuregulin type, subclass present exclusively in Bilateria. The detailed study of each of these elements has allowed us to demonstrate that both, receptors and ligands, are expressed in a wide variety of tissues in these animals and perform multiple functions, such as the maintenance and regeneration of the pharynx, the digestive system, the excretory system and the eye pigment cells. Specifically, the activation of the receptor Smed-egfr-1 through the binding of its possible ligand Smed-nrg-1, is essential for the differentiation of the stem cells of these animals –the neoblasts– to mature gastrodermal cells. Our results support that the known function of the EGFR signaling pathway in the maintenance and differentiation of the stem cells of other animals, is conserved in planarians. In conclusion, this thesis advances the knowledge we have of the EGFR pathway in animal evolution and in a regenerative model such as the planarian S. mediterranea, as well as in the mechanisms that regulate the adult stem cells of these organisms

Bret J Pearson - One of the best experts on this subject based on the ideXlab platform.

  • comparative transcriptomic analyses and single cell rna sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation
    Genome Biology, 2018
    Co-Authors: Lakshmipuram S Swapna, Bret J Pearson, Alyssa M Molinaro, Nicole Lindsaymosher, John Parkinson
    Abstract:

    In the Lophotrochozoa/Spiralia superphylum, few organisms have as high a capacity for rapid testing of gene function and single-cell transcriptomics as the freshwater planaria. The species Schmidtea mediterranea in particular has become a powerful model to use in studying adult stem cell biology and mechanisms of regeneration. Despite this, systematic attempts to define gene complements and their annotations are lacking, restricting comparative analyses that detail the conservation of biochemical pathways and identify lineage-specific innovations. In this study we compare several transcriptomes and define a robust set of 35,232 transcripts. From this, we perform systematic functional annotations and undertake a genome-scale metabolic reconstruction for S. mediterranea. Cross-species comparisons of gene content identify conserved, lineage-specific, and expanded gene families, which may contribute to the regenerative properties of planarians. In particular, we find that the TRAF gene family has been greatly expanded in planarians. We further provide a single-cell RNA sequencing analysis of 2000 cells, revealing both known and novel cell types defined by unique signatures of gene expression. Among these are a novel mesenchymal cell population as well as a cell type involved in eye regeneration. Integration of our metabolic reconstruction further reveals the extent to which given cell types have adapted energy and nucleotide biosynthetic pathways to support their specialized roles. In general, S. mediterranea displays a high level of gene and pathway conservation compared with other model systems, rendering it a viable model to study the roles of these pathways in stem cell biology and regeneration.

  • hox gene complement and expression in the planarian Schmidtea mediterranea
    Evodevo, 2016
    Co-Authors: Ko W Currie, David D R Brown, Shujun Zhu, Veronique Voisin, Gary D Bader, Bret J Pearson
    Abstract:

    Freshwater planarians are well known for their regenerative abilities. Less well known is how planarians maintain spatial patterning in long-lived adult animals or how they re-pattern tissues during regeneration. HOX genes are good candidates to regulate planarian spatial patterning, yet the full complement or genomic clustering of planarian HOX genes has not yet been described, primarily because only a few have been detectable by in situ hybridization, and none have given morphological phenotypes when knocked down by RNAi. Because the planarian Schmidtea mediterranea (S. mediterranea) is unsegmented, appendage less, and morphologically simple, it has been proposed that it may have a simplified HOX gene complement. Here, we argue against this hypothesis and show that S. mediterranea has a total of 13 HOX genes, which represent homologs to all major axial categories, and can be detected by whole-mount in situ hybridization using a highly sensitive method. In addition, we show that planarian HOX genes do not cluster in the genome, yet 5/13 have retained aspects of axially restricted expression. Finally, we confirm HOX gene axial expression by RNA deep-sequencing 6 anterior–posterior “zones” of the animal, which we provide as a dataset to the community to discover other axially restricted transcripts. Freshwater planarians have an unappreciated HOX gene complexity, with all major axial categories represented. However, we conclude based on adult expression patterns that planarians have a derived body plan and their asexual lifestyle may have allowed for large changes in HOX expression from the last common ancestor between arthropods, flatworms, and vertebrates. Using our in situ method and axial zone RNAseq data, it should be possible to further understand the pathways that pattern the anterior–posterior axis of adult planarians.

  • HOX gene complement and expression in the planarian Schmidtea mediterranea
    EvoDevo, 2016
    Co-Authors: Ko W Currie, David D R Brown, Shujun Zhu, Veronique Voisin, Gary D Bader, Bret J Pearson
    Abstract:

    Background Freshwater planarians are well known for their regenerative abilities. Less well known is how planarians maintain spatial patterning in long-lived adult animals or how they re-pattern tissues during regeneration. HOX genes are good candidates to regulate planarian spatial patterning, yet the full complement or genomic clustering of planarian HOX genes has not yet been described, primarily because only a few have been detectable by in situ hybridization, and none have given morphological phenotypes when knocked down by RNAi. Results Because the planarian Schmidtea mediterranea ( S. mediterranea ) is unsegmented, appendage less, and morphologically simple, it has been proposed that it may have a simplified HOX gene complement. Here, we argue against this hypothesis and show that S. mediterranea has a total of 13 HOX genes, which represent homologs to all major axial categories, and can be detected by whole-mount in situ hybridization using a highly sensitive method. In addition, we show that planarian HOX genes do not cluster in the genome, yet 5/13 have retained aspects of axially restricted expression. Finally, we confirm HOX gene axial expression by RNA deep-sequencing 6 anterior–posterior “zones” of the animal, which we provide as a dataset to the community to discover other axially restricted transcripts. Conclusions Freshwater planarians have an unappreciated HOX gene complexity, with all major axial categories represented. However, we conclude based on adult expression patterns that planarians have a derived body plan and their asexual lifestyle may have allowed for large changes in HOX expression from the last common ancestor between arthropods, flatworms, and vertebrates. Using our in situ method and axial zone RNAseq data, it should be possible to further understand the pathways that pattern the anterior–posterior axis of adult planarians.