The Experts below are selected from a list of 1392 Experts worldwide ranked by ideXlab platform
Paola Oliveri - One of the best experts on this subject based on the ideXlab platform.
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Extracellular matrix gene expression during arm regeneration in Amphiura filiformis
Cell and Tissue Research, 2020Co-Authors: Cinzia Ferrario, David V. Dylus, Anna Czarkwiani, M. Sugni, Laura Piovani, Maria Daniela Candia Carnevali, Paola OliveriAbstract:Extracellular matrix (ECM) plays a dynamic role during tissue development and re-growth. Body part regeneration efficiency relies also on effective ECM remodelling and deposition. Among invertebrates, echinoderms are well known for their striking regenerative abilities since they can rapidly regenerate functioning complex structures. To gather insights on the involvement of ECM during arm regeneration, the Brittle Star Amphiura filiformis was chosen as experimental model. Eight ECM genes were identified and cloned, and their spatio-temporal and quantitative expression patterns were analysed by means of whole mount in situ hybridisation and quantitative PCR on early and advanced regenerative stages. Our results show that almost none of the selected ECM genes are expressed at early stages of regeneration, suggesting a delay in their activation that may be responsible for the high regeneration efficiency of these animals, as described for other echinoderms and in contrast to most vertebrates. Moreover, at advanced stages, these genes are spatially and temporally differentially expressed, suggesting that the molecular regulation of ECM deposition/remodelling varies throughout the regenerative process. Phylogenetic analyses of the identified collagen-like genes reveal complex evolutionary dynamics with many rounds of duplications and losses and pinpointed their homologues in selected vertebrates. The study of other ECM genes will allow a better understanding of ECM contribution to Brittle Star arm regeneration.
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developmental transcriptomics of the Brittle Star amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution
Genome Biology, 2018Co-Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R Elphick, Paola OliveriAbstract:Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue, we have generated and assembled a large RNAseq data set of four key stages of development in the Brittle Star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm—the sea urchin Strongylocentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/ . We have identified highly conserved genes associated with the development of a biomineralised skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between Brittle Stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, rather than when cells initiate differentiation. Our findings indicate that there has been a high degree of gene regulatory network rewiring and clade-specific gene duplication, supporting the hypothesis of a convergent evolution of larval skeleton development in echinoderms.
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developmental transcriptomics of the Brittle Star amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution
bioRxiv, 2017Co-Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R Elphick, Paola OliveriAbstract:Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance, developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue we have generated and assembled a large RNAseq data set of four key stages of development in the Brittle Star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm - the sea urchin Strongyloncentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/. With a focus on skeleton development, we have identified highly conserved genes associated with the development of a biomineralized skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between Brittle Stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, than when cells initiate differentiation. Our findings indicate that there has been a high degree of gene regulatory network rewiring in the evolution of echinoderm larval development.
David V. Dylus - One of the best experts on this subject based on the ideXlab platform.
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Extracellular matrix gene expression during arm regeneration in Amphiura filiformis
Cell and Tissue Research, 2020Co-Authors: Cinzia Ferrario, David V. Dylus, Anna Czarkwiani, M. Sugni, Laura Piovani, Maria Daniela Candia Carnevali, Paola OliveriAbstract:Extracellular matrix (ECM) plays a dynamic role during tissue development and re-growth. Body part regeneration efficiency relies also on effective ECM remodelling and deposition. Among invertebrates, echinoderms are well known for their striking regenerative abilities since they can rapidly regenerate functioning complex structures. To gather insights on the involvement of ECM during arm regeneration, the Brittle Star Amphiura filiformis was chosen as experimental model. Eight ECM genes were identified and cloned, and their spatio-temporal and quantitative expression patterns were analysed by means of whole mount in situ hybridisation and quantitative PCR on early and advanced regenerative stages. Our results show that almost none of the selected ECM genes are expressed at early stages of regeneration, suggesting a delay in their activation that may be responsible for the high regeneration efficiency of these animals, as described for other echinoderms and in contrast to most vertebrates. Moreover, at advanced stages, these genes are spatially and temporally differentially expressed, suggesting that the molecular regulation of ECM deposition/remodelling varies throughout the regenerative process. Phylogenetic analyses of the identified collagen-like genes reveal complex evolutionary dynamics with many rounds of duplications and losses and pinpointed their homologues in selected vertebrates. The study of other ECM genes will allow a better understanding of ECM contribution to Brittle Star arm regeneration.
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Developmental transcriptomics of the Brittle Star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution
Genome Biology, 2018Co-Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R Elphick, Paolo OliveriAbstract:BackgroundAmongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue, we have generated and assembled a large RNAseq data set of four key stages of development in the Brittle Star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm—the sea urchin Strongylocentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/.ResultsWe have identified highly conserved genes associated with the development of a biomineralised skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between Brittle Stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, rather than when cells initiate differentiation.ConclusionsOur findings indicate that there has been a high degree of gene regulatory network rewiring and clade-specific gene duplication, supporting the hypothesis of a convergent evolution of larval skeleton development in echinoderms.
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developmental transcriptomics of the Brittle Star amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution
Genome Biology, 2018Co-Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R Elphick, Paola OliveriAbstract:Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue, we have generated and assembled a large RNAseq data set of four key stages of development in the Brittle Star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm—the sea urchin Strongylocentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/ . We have identified highly conserved genes associated with the development of a biomineralised skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between Brittle Stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, rather than when cells initiate differentiation. Our findings indicate that there has been a high degree of gene regulatory network rewiring and clade-specific gene duplication, supporting the hypothesis of a convergent evolution of larval skeleton development in echinoderms.
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developmental transcriptomics of the Brittle Star amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution
bioRxiv, 2017Co-Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R Elphick, Paola OliveriAbstract:Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance, developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue we have generated and assembled a large RNAseq data set of four key stages of development in the Brittle Star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm - the sea urchin Strongyloncentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/. With a focus on skeleton development, we have identified highly conserved genes associated with the development of a biomineralized skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between Brittle Stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, than when cells initiate differentiation. Our findings indicate that there has been a high degree of gene regulatory network rewiring in the evolution of echinoderm larval development.
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Molecular characterization of skeletal regeneration in the Brittle Star amphiura filiformis
2016Co-Authors: Anna Czarkwiani, David V. Dylus, C. Ferrario, P. OliveriAbstract:Echinoderms are well known for their extensive regenerative abilities, but have been neglected in the field due to the lack of available molecular tools and resources [1]. Recently, developmental [2] and adult transcriptomes [3, 4] of the Brittle Star Amphiura filiformis have been sequenced, which opened up this species for molecular investigations of its rapid arm regeneration process. We use this Brittle Star as a model to understand the cellular and molecular aspects of skeletogenesis during adult arm regeneration and the potential role of the FGF signalling pathway in this process. Ultimately, we compare the molecular network driving regeneration of the skeleton to that underlying embryonic skeleton development [5]. Following a characterization of the anatomy and development of the skeleton during arm regeneration in A. filiformis [6], we established methods for spatio-temporal expression analysis [7] and pharmacological treatments to characterise genes involved in adult arm regeneration. We found that 18 embryonic skeletogenic mesoderm genes (transcription factors, signaling receptors and downstream differentiation genes) are also expressed in the dermal layer of the adult regenerating arm, where skeletal spicules form. FGF signalling perturbation using the SU5402 inhibitor interferes with skeleton formation during both embryonic development and adult regeneration of this Brittle Star. A large-scale comparison of genes affected by SU5402 in adult arm regeneration and during embryonic development revealed a conservation of network components downstream of FGF signalling between those two developmental modes. Acknowledgements: We thank the staff at the Sven Lov\ue9n Centre for Marine Sciences in Kristineberg, especially Olga Ortega-Martinez and Sam Dupont, for assistance during animal and sample collection. References: 1. Dupont S, Thorndyke M (2007) Bridging the regeneration gap: insights from echinoderm models. Nat Rev Genet 8:8\u201310 2. Delroisse J, Ortega-Martinez O, Dupont S, Mallefet J, Flammang P (2015) De novo transcriptome of the European Brittle Star Amphiura filiformis pluteus larvae. Mar Genomics. doi: 10.1016/j.margen.2015.05.014 3. Purushothaman S, Saxena S, Meghah V, Swamy CVB, Ortega-Martinez O, Dupont S, Idris M (2014) Transcriptomic and proteomic analyses of Amphiura filiformis arm tissue-undergoing regeneration. J Proteomics 1\u201312 4. Delroisse J, Mallefet J, Flammang P (2016) De Novo Adult Transcriptomes of Two European Brittle Stars: Spotlight on Opsin-Based Photoreception. PLoS One 11:e0152988 5. Dylus DV, Czarkwiani A, St\ue5ngberg J, Ortega-Martinez O, Dupont S, Oliveri P (2016) Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks. Evodevo 7:2 6. Czarkwiani A, Ferrario C, Dylus D V., Sugni M, Oliveri P (2016) Skeletal regeneration in the Brittle Star Amphiura filiformis. Front Zool 13:18 7. Czarkwiani A, Dylus D V., Oliveri P (2013) Expression of skeletogenic genes during arm regeneration in the Brittle Star Amphiura filiformis. Gene Expr Patterns 13:464\u201347
Anna Czarkwiani - One of the best experts on this subject based on the ideXlab platform.
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Extracellular matrix gene expression during arm regeneration in Amphiura filiformis
Cell and Tissue Research, 2020Co-Authors: Cinzia Ferrario, David V. Dylus, Anna Czarkwiani, M. Sugni, Laura Piovani, Maria Daniela Candia Carnevali, Paola OliveriAbstract:Extracellular matrix (ECM) plays a dynamic role during tissue development and re-growth. Body part regeneration efficiency relies also on effective ECM remodelling and deposition. Among invertebrates, echinoderms are well known for their striking regenerative abilities since they can rapidly regenerate functioning complex structures. To gather insights on the involvement of ECM during arm regeneration, the Brittle Star Amphiura filiformis was chosen as experimental model. Eight ECM genes were identified and cloned, and their spatio-temporal and quantitative expression patterns were analysed by means of whole mount in situ hybridisation and quantitative PCR on early and advanced regenerative stages. Our results show that almost none of the selected ECM genes are expressed at early stages of regeneration, suggesting a delay in their activation that may be responsible for the high regeneration efficiency of these animals, as described for other echinoderms and in contrast to most vertebrates. Moreover, at advanced stages, these genes are spatially and temporally differentially expressed, suggesting that the molecular regulation of ECM deposition/remodelling varies throughout the regenerative process. Phylogenetic analyses of the identified collagen-like genes reveal complex evolutionary dynamics with many rounds of duplications and losses and pinpointed their homologues in selected vertebrates. The study of other ECM genes will allow a better understanding of ECM contribution to Brittle Star arm regeneration.
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When immunity and extracellular matrix matter: repair and regenerative events after echinoderm arm injury
2019Co-Authors: C. Ferrario, Anna Czarkwiani, P. Oliveri, M.d. Candia Carnevali, F. Bonasoro, M. SugniAbstract:Arm amputation in echinoderms is a traumatic event that removes differentiated body parts and damages all tissue types. Immediately after injury the repair phase begins. If phenomena typical of this phase, such as emergency reaction, inflammatory/immune response, wound closure and extracellular matrix (ECM) remodelling and deposition, do not properly occur, the following regenerative process may be prevented or ineffective. In this study, the Brittle Star Amphiura filiformis (Afi) was used as model to investigate the main repair and regenerative events after arm injury, with a specific focus on the involvement of immune and ECM genes and proteins. In this perspective, both microscopy and molecular analyses were performed to highlight similarities and differences between regeneration-competent (i.e. echinoderms) and non-competent (i.e. mammals) animals. Our microscopy results showed that both emergency reaction and re-epithelialisation are faster in Brittle Stars than in mammals. Fibrosis, i.e. over-deposition of ECM due to an exaggerated inflammatory reaction, is not detectable in echinoderms as, instead, described for mammals, suggesting that immunity modulation may facilitate subsequent regeneration. Our molecular analyses showed that Afi-ficolin (an important gene in the immune response) is expressed in the first phase after injury, whereas almost all the selected ECM genes are not expressed at early stage of regeneration, suggesting an activation delay that may be directly connected to their regeneration efficiency, as proposed for other echinoderms and in contrast to most vertebrates. Moreover, at advanced regenerative stages these same genes are differentially expressed, suggesting that the molecular regulation of ECM deposition/remodelling is different throughout re-growth. Overall, our Brittle Star model shows similarities in terms of repair and regenerative events and timing with other echinoderm species already studied. However, differences emerge between echinoderms and mammals: indeed, all phenomena should occur following specific signals and timing to ensure effective regeneration after severe wounds. Further quantitative analyses will allow a better understanding of immune system and ECM contribution to Brittle Star arm regeneration and of the evolutionary implications on the regeneration competence widespread in the animal kingdom
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Developmental transcriptomics of the Brittle Star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution
Genome Biology, 2018Co-Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R Elphick, Paolo OliveriAbstract:BackgroundAmongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue, we have generated and assembled a large RNAseq data set of four key stages of development in the Brittle Star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm—the sea urchin Strongylocentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/.ResultsWe have identified highly conserved genes associated with the development of a biomineralised skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between Brittle Stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, rather than when cells initiate differentiation.ConclusionsOur findings indicate that there has been a high degree of gene regulatory network rewiring and clade-specific gene duplication, supporting the hypothesis of a convergent evolution of larval skeleton development in echinoderms.
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developmental transcriptomics of the Brittle Star amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution
Genome Biology, 2018Co-Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R Elphick, Paola OliveriAbstract:Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue, we have generated and assembled a large RNAseq data set of four key stages of development in the Brittle Star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm—the sea urchin Strongylocentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/ . We have identified highly conserved genes associated with the development of a biomineralised skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between Brittle Stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, rather than when cells initiate differentiation. Our findings indicate that there has been a high degree of gene regulatory network rewiring and clade-specific gene duplication, supporting the hypothesis of a convergent evolution of larval skeleton development in echinoderms.
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developmental transcriptomics of the Brittle Star amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution
bioRxiv, 2017Co-Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R Elphick, Paola OliveriAbstract:Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance, developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue we have generated and assembled a large RNAseq data set of four key stages of development in the Brittle Star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm - the sea urchin Strongyloncentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/. With a focus on skeleton development, we have identified highly conserved genes associated with the development of a biomineralized skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between Brittle Stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, than when cells initiate differentiation. Our findings indicate that there has been a high degree of gene regulatory network rewiring in the evolution of echinoderm larval development.
Anne Chenuil - One of the best experts on this subject based on the ideXlab platform.
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positive selection on sperm ion channels in a brooding Brittle Star consequence of life history traits evolution
Molecular Ecology, 2017Co-Authors: Laurent Abirached, Juan I Montoyaburgos, Alexandra Anhthu Weber, Nicolas Galtier, Aurélien Bernard, Anne ChenuilAbstract:Closely related species are key models to investigate mechanisms leading to reproductive isolation and early stages of diversification, also at the genomic level. The Brittle Star cryptic species complex Ophioderma longicauda encompasses the sympatric broadcast-spawning species C3 and the internal brooding species C5. Here, we used de novo transcriptome sequencing and assembly in two closely related species displaying contrasting reproductive modes to compare their genetic diversity and to investigate the role of natural selection in reproductive isolation. We reconstructed 20 146 and 22 123 genes for C3 and C5, respectively, and characterized a set of 12 229 orthologs. Genetic diversity was 1.5-2 times higher in C3 compared to C5, confirming that species with low parental investment display higher levels of genetic diversity. Forty-eight genes were the targets of positive diversifying selection during the evolution of the two species. Notably, two genes (NHE and TetraKCNG) are sperm-specific ion channels involved in sperm motility. Ancestral sequence reconstructions show that natural selection targeted the two genes in the brooding species. This may result from an adaptation to the novel environmental conditions surrounding sperm in the brooding species, either directly affecting sperm or via an increase in male/female conflict. This phenomenon could have promoted prezygotic reproductive isolation between C3 and C5. Finally, the sperm receptors to egg chemoattractants differed between C3 and C5 in the ligand-binding region. We propose that mechanisms of species-specific gamete recognition in Brittle Stars occur during sperm chemotaxis (sperm attraction towards the eggs), contrary to other marine invertebrates where prezygotic barriers to interspecific hybridization typically occur before sperm-egg fusion.
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defining reproductively isolated units in a cryptic and syntopic species complex using mitochondrial and nuclear markers the brooding Brittle Star amphipholis squamata ophiuroidea
Molecular Ecology, 2008Co-Authors: E Boissin, Jeanpierre Feral, Anne ChenuilAbstract:At a time when biodiversity is threatened, we are still discovering new species, and particularly in the marine realm. Delimiting species boundaries is the first step to get a precise idea of diversity. For sympatric species which are morphologically undistinguishable, using a combination of independent molecular markers is a necessary step to define separate species. Amphipholis squamata, a cosmopolitan Brittle Star, includes several very divergent mitochondrial lineages. These lineages appear totally intermixed in the field and studies on morphology and colour polymorphism failed to find any diagnostic character. Therefore, these mitochondrial lineages may be totally interbreeding presently. To test this hypothesis, we characterized the genetic structure of the complex in the French Mediterranean coast using sequences of mitochondrial DNA (16S) and for the first time, several nuclear DNA markers (introns and microsatellites). The data revealed six phylogenetic lineages corresponding to at least four biological species. These sibling species seem to live in syntopy. However, they seem to display contrasted levels of genetic diversity, suggesting they have distinct demographic histories and/or life-history traits. Genetic differentiation and isolation-by-distance within the French Mediterranean coasts are revealed in three lineages, as expected for a species without a free larval phase. Finally, although recombinant nuclear genotypes are common within mitochondrial lineages, the data set displays a total lack of heterozygotes, suggesting a very high selfing rate, a feature likely to have favoured the formation of the species complex.
Liisa M. Blowes - One of the best experts on this subject based on the ideXlab platform.
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Developmental transcriptomics of the Brittle Star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution
Genome Biology, 2018Co-Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R Elphick, Paolo OliveriAbstract:BackgroundAmongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue, we have generated and assembled a large RNAseq data set of four key stages of development in the Brittle Star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm—the sea urchin Strongylocentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/.ResultsWe have identified highly conserved genes associated with the development of a biomineralised skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between Brittle Stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, rather than when cells initiate differentiation.ConclusionsOur findings indicate that there has been a high degree of gene regulatory network rewiring and clade-specific gene duplication, supporting the hypothesis of a convergent evolution of larval skeleton development in echinoderms.
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developmental transcriptomics of the Brittle Star amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution
Genome Biology, 2018Co-Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R Elphick, Paola OliveriAbstract:Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue, we have generated and assembled a large RNAseq data set of four key stages of development in the Brittle Star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm—the sea urchin Strongylocentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/ . We have identified highly conserved genes associated with the development of a biomineralised skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between Brittle Stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, rather than when cells initiate differentiation. Our findings indicate that there has been a high degree of gene regulatory network rewiring and clade-specific gene duplication, supporting the hypothesis of a convergent evolution of larval skeleton development in echinoderms.
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developmental transcriptomics of the Brittle Star amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution
bioRxiv, 2017Co-Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R Elphick, Paola OliveriAbstract:Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance, developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue we have generated and assembled a large RNAseq data set of four key stages of development in the Brittle Star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm - the sea urchin Strongyloncentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/. With a focus on skeleton development, we have identified highly conserved genes associated with the development of a biomineralized skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between Brittle Stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, than when cells initiate differentiation. Our findings indicate that there has been a high degree of gene regulatory network rewiring in the evolution of echinoderm larval development.