Caroline Rocher
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View article: Why Homoscleromorph Sponges Have Ciliated Epithelia: Evidence for an Ancestral Role in Mucociliary Driven Particle Flux
Why Homoscleromorph Sponges Have Ciliated Epithelia: Evidence for an Ancestral Role in Mucociliary Driven Particle Flux Open
Cilia are found on the epithelia of almost all metazoans, so their absence from the epithelia of all but one class of Porifera is puzzling. Homoscleromorph sponges possess ciliated epithelia, but their function and evolutionary history wit…
View article: The Buds of <i>Oscarella lobularis</i> (Porifera, Homoscleromorpha): A New Convenient Model for Sponge Cell and Evolutionary Developmental Biology
The Buds of <i>Oscarella lobularis</i> (Porifera, Homoscleromorpha): A New Convenient Model for Sponge Cell and Evolutionary Developmental Biology Open
The comparative study of the four non‐bilaterian phyla (Cnidaria, Placozoa, Ctenophora, and Porifera) provides insights into the origin of bilaterian traits. To complete our knowledge of the cell biology and development of these animals, a…
View article: L’éponge marine Oscarella lobularis un modèle pour comprendre l’origine et l’évolution des épithéliums
L’éponge marine Oscarella lobularis un modèle pour comprendre l’origine et l’évolution des épithéliums Open
Afin d’émettre des hypothèses sur l’origine et l’évolution des épithéliums, nous développons un modèle d’éponge appartenant à la classe des homoscléromorphes. Les éponges sont l’une des lignées ayant émergé le plus précocement au cours de …
View article: The compact genome of the sponge Oopsacas minuta (Hexactinellida) is lacking key metazoan core genes
The compact genome of the sponge Oopsacas minuta (Hexactinellida) is lacking key metazoan core genes Open
View article: Methylmercury Exposure of the Sponge O. Lobularis Induces Strong Tissue and Cell Defects
Methylmercury Exposure of the Sponge O. Lobularis Induces Strong Tissue and Cell Defects Open
View article: The compact genome of the sponge<i>Oopsacas minuta</i>(Hexactinellida) is lacking key metazoan core genes
The compact genome of the sponge<i>Oopsacas minuta</i>(Hexactinellida) is lacking key metazoan core genes Open
Background Bilaterian animals today represent 99% of animal biodiversity. Elucidating how bilaterian hallmarks emerged is a central question of animal evo-devo and evolutionary genomics. Studies of non-bilaterian genomes have suggested tha…
View article: The Homoscleromorph Sponge, Oscarella lobularis
The Homoscleromorph Sponge, Oscarella lobularis Open
The last 20 years have shown a growing interest in developing non-conventional models for evo-devo purposes. In particular, the study of non-bilaterian metazoans offers the invaluable possibility to explore the origin of key bilaterian mor…
View article: Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis
Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis Open
Background The ancestral presence of epithelia in Metazoa is no longer debated. Porifera seem to be one of the best candidates to be the sister group to all other Metazoa. This makes them a key taxon to explore cell-adhesion evolution on a…
View article: Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation - reaggregation experiments in the sponge Oscarella lobularis
Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation - reaggregation experiments in the sponge Oscarella lobularis Open
Background: The ancestral presence of epithelia in Metazoa is no longer debated. Even though Porifera seem to be the best candidates to be the sister group to all other Metazoa, hardly anything is known about the proteins involved in the c…
View article: Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation - reaggregation experiments in the sponge Oscarella lobularis.
Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation - reaggregation experiments in the sponge Oscarella lobularis. Open
Background: The ancestral presence of epithelia in Metazoa is no longer debated. Even though Porifera seem to be the best candidates to be the sister group to all other Metazoa, hardly anything is known about the proteins involved in the c…
View article: Additional file 7 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis
Additional file 7 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis Open
Additional file 7: Table S4. General information about available sponge transcriptomes (according to Riesgo et. al, 2014; [47, 134], This study).
View article: Additional file 17 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis
Additional file 17 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis Open
Additional file 17: Table S12. Domain predictions for putative group 3 Aggregation Factors (AFs) using InterproScan Website ( https://www.ebi.ac.uk/interpro/ ). Related to Additional file 16: Figure S5.
View article: Additional file 21 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis
Additional file 21 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis Open
Additional file 21: Table S14. Mfuzz clusters stability. For each cluster the Jaccard index was calculated to evaluate the similarity of each cluster between each run (10 runs, Run 1 was taken as reference). Related to Fig. 8.
View article: Additional file 9 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis
Additional file 9 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis Open
Additional file 9: Table S6. Differential Expressed Genes (DEG) during (A) Dissociation process (B) dissociation and reaggregation processes and (C) reaggregation process. DEG extracted from DeSeq2 analysis with a threshold of pvalue ≤ 0.0…
View article: Additional file 15 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis
Additional file 15 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis Open
Additional file 15: Table S11: Transcripts Per Million (TPM) standardized and Log2 Fold Change values for (A) epithelial genes (see Fig. 1A) and (B) Aggregation factors (AFs). Related to Fig. 8 and 9.
View article: Additional file 11 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis
Additional file 11 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis Open
Additional file 11: Table S8. GO term enrichment analysis. (A) Enriched categories in Differential Expressed Genes (DEG) during dissociation only, reaggregation only and both (combined). (B) Enriched categories in the first 100 DEGs. (C) E…
View article: Additional file 13 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis
Additional file 13 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis Open
Additional file 13: Table S10. List of genes included in the core clusters (1 to 15) with orthologs (eggNOG) and gene ontology terms (GO). Related to Fig. 8.
View article: Additional file 19 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis
Additional file 19 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis Open
Additional file 19: Table S13. Raw file including mRNA-Seq Transcript Per Million count table using Kallisto.
View article: Additional file 12 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis
Additional file 12 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis Open
Additional file 12: Table S9. Identification of orthologous groups with eggNOG and BlastP searches (A) for significantly deregulated transcripts associated with GO biological processes of interest (complete list of GO terms in Additional f…
View article: Additional file 8 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis
Additional file 8 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis Open
Additional file 8: Table S5. Completeness of conserved domain arrangements (CDAs) estimated by the proportion of the CDAs found among the expected conserved CDAs in different metazoan species using DOGMA. Related to Fig. 6E.
View article: Additional file 3 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis
Additional file 3 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis Open
Additional file 3: Table S1. Estimated percentage of perturbations of the choanoderm after (A) 1 h of dissociation (1hD) regarding the aspect of the microvilli collar, (B) 4 h of dissociation (4hD) and (C) 24 h of reaggregation (24hR) conc…
View article: Additional file 10 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis
Additional file 10 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis Open
Additional file 10: Table S7. Phylostratigraphy analysis. (A) Transcriptomes and Proteomes used in Phylostratigraphy analyses. Each phylostratum represents a node. (B) Accession numbers and links of the different transcriptomes and proteom…
View article: Additional file 5 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis
Additional file 5 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis Open
Additional file 5: Table S2. Functional transcriptome annotation using groups of orthologs (eggNOG), gene ontology terms (GO), conserved domains (CDs) and analyses of gene expression with DeSeq2. Differentially Expressed Genes (DEG) were i…
View article: Additional file 22 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis
Additional file 22 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis Open
Additional file 22: File S1. Translated version of the Transcriptome obtain with Transdecoder (available at https://github.com/TransDecoder ).
View article: Additional file 6 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis
Additional file 6 of Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis Open
Additional file 6: Table S3. Number of orthologs shared between species estimated with Orthofinder and Percentage of orthologs between each species and O. lobularis Related to Fig. 6.
View article: The buds of<i>Oscarella lobularis</i>(Porifera): a new convenient model for sponge cell and developmental biology
The buds of<i>Oscarella lobularis</i>(Porifera): a new convenient model for sponge cell and developmental biology Open
The comparative study of the four non-bilaterian phyla (Cnidaria, Placozoa, Ctenophora, Porifera) should provide insights into the origin of bilaterian traits. Except for Cnidaria, present knowledge on the cell biology and development of t…
View article: From seascape ecology to population genomics and back. Spatial and ecological differentiation among cryptic species of the red algae Lithophyllum stictiforme/L. cabiochiae, main bioconstructors of coralligenous habitats
From seascape ecology to population genomics and back. Spatial and ecological differentiation among cryptic species of the red algae Lithophyllum stictiforme/L. cabiochiae, main bioconstructors of coralligenous habitats Open
View article: From seascape genomics to community ecology: comparing the physical factors structuring genetic diversity within a bioengineer species of the coralligenous habitats with those structuring the species composition of the coralligenous community
From seascape genomics to community ecology: comparing the physical factors structuring genetic diversity within a bioengineer species of the coralligenous habitats with those structuring the species composition of the coralligenous community Open
View article: The Conservation of the Germline Multipotency Program, from Sponges to Vertebrates: A Stepping Stone to Understanding the Somatic and Germline Origins
The Conservation of the Germline Multipotency Program, from Sponges to Vertebrates: A Stepping Stone to Understanding the Somatic and Germline Origins Open
The germline definition in metazoans was first based on few bilaterian models. As a result, gene function interpretations were often based on phenotypes observed in those models and led to the definition of a set of genes, considered as sp…
View article: Nucleotide diversity (π) of <i>Oscarella lobularis</i>, <i>O. tuberculata</i> and D3 members compared to Demospongiae species for the <i>atp6</i> marker.
Nucleotide diversity (π) of <i>Oscarella lobularis</i>, <i>O. tuberculata</i> and D3 members compared to Demospongiae species for the <i>atp6</i> marker. Open
For each species (or cluster), the number of sequences as well as of populations/localities is indicated.