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Guo H, Rischer M, Westermann M, Beemelmanns C. Two Distinct Bacterial Biofilm Components Trigger Metamorphosis in the Colonial Hydrozoan Hydractinia echinata. mBio 2021; 12:e0040121. [PMID: 34154406 PMCID: PMC8262903 DOI: 10.1128/mbio.00401-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/13/2021] [Indexed: 12/28/2022] Open
Abstract
In marine environments, the bacterially induced metamorphosis of larvae is a widespread cross-kingdom communication phenomenon that is critical for the persistence of many marine invertebrates. However, the majority of inducing bacterial signals and underlying cellular mechanisms remain enigmatic. The marine hydroid Hydractinia echinata is a well-known model system for investigating bacterially stimulated larval metamorphosis, as larvae transform into the colonial adult stage within 24 h of signal detection. Although H. echinata has served as a cell biological model system for decades, the identity and influence of bacterial signals on the morphogenic transition remained largely unexplored. Using a bioassay-guided analysis, we first determined that specific bacterial (lyso)phospholipids, naturally present in bacterial membranes and vesicles, elicit metamorphosis in Hydractinia larvae in a dose-response manner. Lysophospholipids, as single compounds or in combination (50 μM), induced metamorphosis in up to 50% of all larvae within 48 h. Using fluorescence-labeled bacterial phospholipids, we demonstrated that phospholipids are incorporated into the larval membranes, where interactions with internal signaling cascades are proposed to occur. Second, we identified two structurally distinct exopolysaccharides of bacterial biofilms, the new Rha-Man polysaccharide from Pseudoalteromonas sp. strain P1-9 and curdlan from Alcaligenes faecalis, to induce metamorphosis in up to 75% of tested larvae. We also found that combinations of (lyso)phospholipids and curdlan induced transformation within 24 h, thereby exceeding the morphogenic activity observed for single compounds and bacterial biofilms. Our results demonstrate that two structurally distinct, bacterium-derived metabolites converge to induce high transformation rates of Hydractinia larvae and thus may help ensure optimal habitat selection. IMPORTANCE Bacterial biofilms profoundly influence the recruitment and settlement of marine invertebrates, critical steps for diverse marine processes such as the formation of coral reefs, the maintenance of marine fisheries, and the fouling of submerged surfaces. However, the complex composition of biofilms often makes the characterization of individual signals and regulatory mechanisms challenging. Developing tractable model systems to characterize these coevolved interactions is the key to understanding fundamental processes in evolutionary biology. Here, we characterized two types of bacterial signaling molecules, phospholipids and polysaccharides, that induce the morphogenic transition. We then analyzed their abundance and combinatorial activity. This study highlights the general importance of multiple bacterial signal converging activity in development-related cross-kingdom signaling and poses the question of whether complex lipids and polysaccharides are general metamorphic cues for cnidarian larvae.
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Affiliation(s)
- Huijuan Guo
- Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Jena, Germany
| | - Maja Rischer
- Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Jena, Germany
| | - Martin Westermann
- Electron Microscopy Centre, Friedrich Schiller University Jena, Jena, Germany
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Jena, Germany
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Parisi MG, Parrinello D, Stabili L, Cammarata M. Cnidarian Immunity and the Repertoire of Defense Mechanisms in Anthozoans. BIOLOGY 2020; 9:E283. [PMID: 32932829 PMCID: PMC7563517 DOI: 10.3390/biology9090283] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/04/2020] [Accepted: 09/04/2020] [Indexed: 02/07/2023]
Abstract
Anthozoa is the most specious class of the phylum Cnidaria that is phylogenetically basal within the Metazoa. It is an interesting group for studying the evolution of mutualisms and immunity, for despite their morphological simplicity, Anthozoans are unexpectedly immunologically complex, with large genomes and gene families similar to those of the Bilateria. Evidence indicates that the Anthozoan innate immune system is not only involved in the disruption of harmful microorganisms, but is also crucial in structuring tissue-associated microbial communities that are essential components of the cnidarian holobiont and useful to the animal's health for several functions including metabolism, immune defense, development, and behavior. Here, we report on the current state of the art of Anthozoan immunity. Like other invertebrates, Anthozoans possess immune mechanisms based on self/non-self-recognition. Although lacking adaptive immunity, they use a diverse repertoire of immune receptor signaling pathways (PRRs) to recognize a broad array of conserved microorganism-associated molecular patterns (MAMP). The intracellular signaling cascades lead to gene transcription up to endpoints of release of molecules that kill the pathogens, defend the self by maintaining homeostasis, and modulate the wound repair process. The cells play a fundamental role in immunity, as they display phagocytic activities and secrete mucus, which acts as a physicochemical barrier preventing or slowing down the proliferation of potential invaders. Finally, we describe the current state of knowledge of some immune effectors in Anthozoan species, including the potential role of toxins and the inflammatory response in the Mediterranean Anthozoan Anemonia viridis following injection of various foreign particles differing in type and dimensions, including pathogenetic bacteria.
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Affiliation(s)
- Maria Giovanna Parisi
- Department of Earth and Marine Sciences, University of Palermo, 90128 Palermo, Italy;
| | - Daniela Parrinello
- Department of Earth and Marine Sciences, University of Palermo, 90128 Palermo, Italy;
| | - Loredana Stabili
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy;
| | - Matteo Cammarata
- Department of Earth and Marine Sciences, University of Palermo, 90128 Palermo, Italy;
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Stabili L, Parisi MG, Parrinello D, Cammarata M. Cnidarian Interaction with Microbial Communities: From Aid to Animal's Health to Rejection Responses. Mar Drugs 2018; 16:E296. [PMID: 30142922 PMCID: PMC6164757 DOI: 10.3390/md16090296] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 08/11/2018] [Accepted: 08/16/2018] [Indexed: 02/07/2023] Open
Abstract
The phylum Cnidaria is an ancient branch in the tree of metazoans. Several species exert a remarkable longevity, suggesting the existence of a developed and consistent defense mechanism of the innate immunity capable to overcome the potential repeated exposure to microbial pathogenic agents. Increasing evidence indicates that the innate immune system in Cnidarians is not only involved in the disruption of harmful microorganisms, but also is crucial in structuring tissue-associated microbial communities that are essential components of the Cnidarian holobiont and useful to the animal's health for several functions, including metabolism, immune defense, development, and behavior. Sometimes, the shifts in the normal microbiota may be used as "early" bio-indicators of both environmental changes and/or animal disease. Here the Cnidarians relationships with microbial communities and the potential biotechnological applications are summarized and discussed.
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Affiliation(s)
- Loredana Stabili
- Istituto per l'Ambiente Marino Costiero, U.O.S. di Taranto, CNR, Via Roma 3, 74123 Taranto, Italy.
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, via Prov.le Lecce Monteroni, 73100 Lecce, Italy.
| | - Maria Giovanna Parisi
- Laboratory of Marine Immunobiology, Dipartimento delle Scienze della Terra e del Mare, Università di Palermo, Viale delle Scienze Ed. 16, 90128 Palermo, Italy.
| | - Daniela Parrinello
- Laboratory of Marine Immunobiology, Dipartimento delle Scienze della Terra e del Mare, Università di Palermo, Viale delle Scienze Ed. 16, 90128 Palermo, Italy.
| | - Matteo Cammarata
- Laboratory of Marine Immunobiology, Dipartimento delle Scienze della Terra e del Mare, Università di Palermo, Viale delle Scienze Ed. 16, 90128 Palermo, Italy.
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Rentzsch F, Layden M, Manuel M. The cellular and molecular basis of cnidarian neurogenesis. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2016; 6. [PMID: 27882698 PMCID: PMC6680159 DOI: 10.1002/wdev.257] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 08/30/2016] [Accepted: 09/21/2016] [Indexed: 12/22/2022]
Abstract
Neurogenesis initiates during early development and it continues through later developmental stages and in adult animals to enable expansion, remodeling, and homeostasis of the nervous system. The generation of nerve cells has been analyzed in detail in few bilaterian model organisms, leaving open many questions about the evolution of this process. As the sister group to bilaterians, cnidarians occupy an informative phylogenetic position to address the early evolution of cellular and molecular aspects of neurogenesis and to understand common principles of neural development. Here we review studies in several cnidarian model systems that have revealed significant similarities and interesting differences compared to neurogenesis in bilaterian species, and between different cnidarian taxa. Cnidarian neurogenesis is currently best understood in the sea anemone Nematostella vectensis, where it includes epithelial neural progenitor cells that express transcription factors of the soxB and atonal families. Notch signaling regulates the number of these neural progenitor cells, achaete‐scute and dmrt genes are required for their further development and Wnt and BMP signaling appear to be involved in the patterning of the nervous system. In contrast to many vertebrates and Drosophila, cnidarians have a high capacity to generate neurons throughout their lifetime and during regeneration. Utilizing this feature of cnidarian biology will likely allow gaining new insights into the similarities and differences of embryonic and regenerative neurogenesis. The use of different cnidarian model systems and their expanding experimental toolkits will thus continue to provide a better understanding of evolutionary and developmental aspects of nervous system formation. WIREs Dev Biol 2017, 6:e257. doi: 10.1002/wdev.257 This article is categorized under:
Gene Expression and Transcriptional Hierarchies > Cellular Differentiation Signaling Pathways > Cell Fate Signaling Comparative Development and Evolution > Organ System Comparisons Between Species
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Affiliation(s)
- Fabian Rentzsch
- Sars Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | | | - Michaël Manuel
- Sorbonne Universités, UMPC Univ Paris 06, CNRS, Evolution Paris-Seine, Institut de Biologie Paris-Seine (IBPS), Paris, France
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Leclère L, Copley RR, Momose T, Houliston E. Hydrozoan insights in animal development and evolution. Curr Opin Genet Dev 2016; 39:157-167. [DOI: 10.1016/j.gde.2016.07.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 06/02/2016] [Accepted: 07/07/2016] [Indexed: 12/21/2022]
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Anderson DA, Walz ME, Weil E, Tonellato P, Smith MC. RNA-Seq of the Caribbean reef-building coral Orbicella faveolata (Scleractinia-Merulinidae) under bleaching and disease stress expands models of coral innate immunity. PeerJ 2016; 4:e1616. [PMID: 26925311 PMCID: PMC4768675 DOI: 10.7717/peerj.1616] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 01/01/2016] [Indexed: 12/16/2022] Open
Abstract
Climate change-driven coral disease outbreaks have led to widespread declines in coral populations. Early work on coral genomics established that corals have a complex innate immune system, and whole-transcriptome gene expression studies have revealed mechanisms by which the coral immune system responds to stress and disease. The present investigation expands bioinformatic data available to study coral molecular physiology through the assembly and annotation of a reference transcriptome of the Caribbean reef-building coral, Orbicella faveolata. Samples were collected during a warm water thermal anomaly, coral bleaching event and Caribbean yellow band disease outbreak in 2010 in Puerto Rico. Multiplex sequencing of RNA on the Illumina GAIIx platform and de novo transcriptome assembly by Trinity produced 70,745,177 raw short-sequence reads and 32,463 O. faveolata transcripts, respectively. The reference transcriptome was annotated with gene ontologies, mapped to KEGG pathways, and a predicted proteome of 20,488 sequences was generated. Protein families and signaling pathways that are essential in the regulation of innate immunity across Phyla were investigated in-depth. Results were used to develop models of evolutionarily conserved Wnt, Notch, Rig-like receptor, Nod-like receptor, and Dicer signaling. O. faveolata is a coral species that has been studied widely under climate-driven stress and disease, and the present investigation provides new data on the genes that putatively regulate its immune system.
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Affiliation(s)
- David A Anderson
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Marine Sciences, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico, United States of America
| | - Marcus E Walz
- Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee , Milwaukee, Wisconsin , United States of America
| | - Ernesto Weil
- Department of Marine Sciences, University of Puerto Rico at Mayagüez , Mayagüez, Puerto Rico , United States of America
| | - Peter Tonellato
- Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America; Department of Biomedical Informatics, Harvard Medical School, Harvard University, Boston, Massachusetts, United States of America
| | - Matthew C Smith
- School of Freshwater Sciences, University of Wisconsin-Milwaukee , Milwaukee, Wisconsin , United States of America
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De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes. G3-GENES GENOMES GENETICS 2015; 5:2441-52. [PMID: 26384772 PMCID: PMC4632063 DOI: 10.1534/g3.115.020164] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Many nonmodel species exemplify important biological questions but lack the sequence resources required to study the genes and genomic regions underlying traits of interest. Reef-building corals are famously sensitive to rising seawater temperatures, motivating ongoing research into their stress responses and long-term prospects in a changing climate. A comprehensive understanding of these processes will require extending beyond the sequenced coral genome (Acropora digitifera) to encompass diverse coral species and related anthozoans. Toward that end, we have assembled and annotated reference transcriptomes to develop catalogs of gene sequences for three scleractinian corals (Fungia scutaria, Montastraea cavernosa, Seriatopora hystrix) and a temperate anemone (Anthopleura elegantissima). High-throughput sequencing of cDNA libraries produced ~20-30 million reads per sample, and de novo assembly of these reads produced ~75,000-110,000 transcripts from each sample with size distributions (mean ~1.4 kb, N50 ~2 kb), comparable to the distribution of gene models from the coral genome (mean ~1.7 kb, N50 ~2.2 kb). Each assembly includes matches for more than half the gene models from A. digitifera (54-67%) and many reasonably complete transcripts (~5300-6700) spanning nearly the entire gene (ortholog hit ratios ≥0.75). The catalogs of gene sequences developed in this study made it possible to identify hundreds to thousands of orthologs across diverse scleractinian species and related taxa. We used these sequences for phylogenetic inference, recovering known relationships and demonstrating superior performance over phylogenetic trees constructed using single mitochondrial loci. The resources developed in this study provide gene sequences and genetic markers for several anthozoan species. To enhance the utility of these resources for the research community, we developed searchable databases enabling researchers to rapidly recover sequences for genes of interest. Our analysis of de novo assembly quality highlights metrics that we expect will be useful for evaluating the relative quality of other de novo transcriptome assemblies. The identification of orthologous sequences and phylogenetic reconstruction demonstrates the feasibility of these methods for clarifying the substantial uncertainties in the existing scleractinian phylogeny.
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Ocampo ID, Cadavid Gutierrez LF. MECHANISMS OF IMMUNE RESPONSES IN CNIDARIANS. ACTA BIOLÓGICA COLOMBIANA 2014. [DOI: 10.15446/abc.v20n2.46728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Pante E, Abdelkrim J, Viricel A, Gey D, France SC, Boisselier MC, Samadi S. Use of RAD sequencing for delimiting species. Heredity (Edinb) 2014; 114:450-9. [PMID: 25407078 DOI: 10.1038/hdy.2014.105] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 09/12/2014] [Accepted: 09/16/2014] [Indexed: 11/10/2022] Open
Abstract
RAD-tag sequencing is a promising method for conducting genome-wide evolutionary studies. However, to date, only a handful of studies empirically tested its applicability above the species level. In this communication, we use RAD tags to contribute to the delimitation of species within a diverse genus of deep-sea octocorals, Chrysogorgia, for which few classical genetic markers have proved informative. Previous studies have hypothesized that single mitochondrial haplotypes can be used to delimit Chrysogorgia species. On the basis of two lanes of Illumina sequencing, we inferred phylogenetic relationships among 12 putative species that were delimited using mitochondrial data, comparing two RAD analysis pipelines (Stacks and PyRAD). The number of homologous RAD loci decreased dramatically with increasing divergence, as >70% of loci are lost when comparing specimens separated by two mutations on the 700-nt long mitochondrial phylogeny. Species delimitation hypotheses based on the mitochondrial mtMutS gene are largely supported, as six out of nine putative species represented by more than one colony were recovered as discrete, well-supported clades. Significant genetic structure (correlating with geography) was detected within one putative species, suggesting that individuals characterized by the same mtMutS haplotype may belong to distinct species. Conversely, three mtMutS haplotypes formed one well-supported clade within which no population structure was detected, also suggesting that intraspecific variation exists at mtMutS in Chrysogorgia. Despite an impressive decrease in the number of homologous loci across clades, RAD data helped us to fine-tune our interpretations of classical mitochondrial markers used in octocoral species delimitation, and discover previously undetected diversity.
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Affiliation(s)
- E Pante
- Laboratoire LIENSs, UMR 7266 CNRS-Université de La Rochelle, La Rochelle, France
| | - J Abdelkrim
- 1] Département Systématique et Evolution, UMS 2700 MNHN-CNRS, SSM, Muséum national d'Histoire naturelle, Paris, France [2] ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France
| | - A Viricel
- Laboratoire LIENSs, UMR 7266 CNRS-Université de La Rochelle, La Rochelle, France
| | - D Gey
- Département Systématique et Evolution, UMS 2700 MNHN-CNRS, SSM, Muséum national d'Histoire naturelle, Paris, France
| | - S C France
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - M C Boisselier
- 1] Département Systématique et Evolution, UMS 2700 MNHN-CNRS, SSM, Muséum national d'Histoire naturelle, Paris, France [2] ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France
| | - S Samadi
- ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France
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Hensel K, Lotan T, Sanders SM, Cartwright P, Frank U. Lineage-specific evolution of cnidarian Wnt ligands. Evol Dev 2014; 16:259-69. [PMID: 25123972 DOI: 10.1111/ede.12089] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We have studied the evolution of Wnt genes in cnidarians and the expression pattern of all Wnt ligands in the hydrozoan Hydractinia echinata. Current views favor a scenario in which 12 Wnt sub-families were jointly inherited by cnidarians and bilaterians from their last common ancestor. Our phylogenetic analyses clustered all medusozoan genes in distinct, well-supported clades, but many orthologous relationships between medusozoan Wnts and anthozoan and bilaterian Wnt genes were poorly supported. Only seven anthozoan genes, Wnt2, Wnt4, Wnt5, Wnt6, Wnt 10, Wnt11, and Wnt16 were recovered with strong support with bilaterian genes and of those, only the Wnt2, Wnt5, Wnt11, and Wnt16 clades also included medusozoan genes. Although medusozoan Wnt8 genes clustered with anthozoan and bilaterian genes, this was not well supported. In situ hybridization studies revealed poor conservation of expression patterns of putative Wnt orthologs within Cnidaria. In polyps, only Wnt1, Wnt3, and Wnt7 were expressed at the same position in the studied cnidarian models Hydra, Hydractinia, and Nematostella. Different expression patterns are consistent with divergent functions. Our data do not fully support previous assertions regarding Wnt gene homology, and suggest a more complex history of Wnt family genes than previously suggested. This includes high rates of sequence divergence and lineage-specific duplications of Wnt genes within medusozoans, followed by functional divergence over evolutionary time scales.
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Affiliation(s)
- Katrin Hensel
- School of Natural Sciences and Regenerative Medicine Institute, National University of Ireland, Galway, Ireland
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Plachetzki DC, Sabrina Pankey M, Johnson BR, Ronne EJ, Kopp A, Grosberg RK. Gene co-expression modules underlying polymorphic and monomorphic zooids in the colonial hydrozoan, Hydractinia symbiolongicarpus. Integr Comp Biol 2014; 54:276-83. [PMID: 24935986 DOI: 10.1093/icb/icu080] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Advances in sequencing technology have forced a quantitative revolution in Evolutionary Biology. One important feature of this renaissance is that comprehensive genomic resources can be obtained quickly for almost any taxon, thus speeding the development of new model organisms. Here, we analyze 20 RNA-seq libraries from morphologically, sexually, and genetically distinct polyp types from the gonochoristic colonial hydrozoan, Hydractinia symbiolongicarpus (Cnidaria). Analyses of these data using weighted gene co-expression networks highlight deeply conserved genetic elements of animal spermatogenesis and demonstrate the utility of these methods in identifying modules of genes that correlate with different zooid types across various statistical contrasts. RNA-seq data and analytical scripts described here are deposited in publicly available databases.
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Affiliation(s)
- David C Plachetzki
- *Department of Molecular, Cellular and Biomedical Sciences, The University of New Hampshire, Durham, NH 03801, USA; Department of Ecology Evolution and Marine Biology, The University of California at Santa Barbara, Santa Barbara, CA 93106, USA; Department of Entomology, The University of California at Davis, Davis, CA 95616, USA; Department of Evolution and Ecology, Center for Population Biology, The University of California at Davis, Davis, CA 95616, USA
| | - M Sabrina Pankey
- *Department of Molecular, Cellular and Biomedical Sciences, The University of New Hampshire, Durham, NH 03801, USA; Department of Ecology Evolution and Marine Biology, The University of California at Santa Barbara, Santa Barbara, CA 93106, USA; Department of Entomology, The University of California at Davis, Davis, CA 95616, USA; Department of Evolution and Ecology, Center for Population Biology, The University of California at Davis, Davis, CA 95616, USA
| | - Brian R Johnson
- *Department of Molecular, Cellular and Biomedical Sciences, The University of New Hampshire, Durham, NH 03801, USA; Department of Ecology Evolution and Marine Biology, The University of California at Santa Barbara, Santa Barbara, CA 93106, USA; Department of Entomology, The University of California at Davis, Davis, CA 95616, USA; Department of Evolution and Ecology, Center for Population Biology, The University of California at Davis, Davis, CA 95616, USA
| | - Eric J Ronne
- *Department of Molecular, Cellular and Biomedical Sciences, The University of New Hampshire, Durham, NH 03801, USA; Department of Ecology Evolution and Marine Biology, The University of California at Santa Barbara, Santa Barbara, CA 93106, USA; Department of Entomology, The University of California at Davis, Davis, CA 95616, USA; Department of Evolution and Ecology, Center for Population Biology, The University of California at Davis, Davis, CA 95616, USA
| | - Artyom Kopp
- *Department of Molecular, Cellular and Biomedical Sciences, The University of New Hampshire, Durham, NH 03801, USA; Department of Ecology Evolution and Marine Biology, The University of California at Santa Barbara, Santa Barbara, CA 93106, USA; Department of Entomology, The University of California at Davis, Davis, CA 95616, USA; Department of Evolution and Ecology, Center for Population Biology, The University of California at Davis, Davis, CA 95616, USA
| | - Richard K Grosberg
- *Department of Molecular, Cellular and Biomedical Sciences, The University of New Hampshire, Durham, NH 03801, USA; Department of Ecology Evolution and Marine Biology, The University of California at Santa Barbara, Santa Barbara, CA 93106, USA; Department of Entomology, The University of California at Davis, Davis, CA 95616, USA; Department of Evolution and Ecology, Center for Population Biology, The University of California at Davis, Davis, CA 95616, USA
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Stefanik DJ, Lubinski TJ, Granger BR, Byrd AL, Reitzel AM, DeFilippo L, Lorenc A, Finnerty JR. Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian. BMC Genomics 2014; 15:71. [PMID: 24467778 PMCID: PMC3909931 DOI: 10.1186/1471-2164-15-71] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 12/11/2013] [Indexed: 12/20/2022] Open
Abstract
Background The lined sea anemone Edwardsiella lineata is an informative model system for evolutionary-developmental studies of parasitism. In this species, it is possible to compare alternate developmental pathways leading from a larva to either a free-living polyp or a vermiform parasite that inhabits the mesoglea of a ctenophore host. Additionally, E. lineata is confamilial with the model cnidarian Nematostella vectensis, providing an opportunity for comparative genomic, molecular and organismal studies. Description We generated a reference transcriptome for E. lineata via high-throughput sequencing of RNA isolated from five developmental stages (parasite; parasite-to-larva transition; larva; larva-to-adult transition; adult). The transcriptome comprises 90,440 contigs assembled from >15 billion nucleotides of DNA sequence. Using a molecular clock approach, we estimated the divergence between E. lineata and N. vectensis at 215–364 million years ago. Based on gene ontology and metabolic pathway analyses and gene family surveys (bHLH-PAS, deiodinases, Fox genes, LIM homeodomains, minicollagens, nuclear receptors, Sox genes, and Wnts), the transcriptome of E. lineata is comparable in depth and completeness to N. vectensis. Analyses of protein motifs and revealed extensive conservation between the proteins of these two edwardsiid anemones, although we show the NF-κB protein of E. lineata reflects the ancestral structure, while the NF-κB protein of N. vectensis has undergone a split that separates the DNA-binding domain from the inhibitory domain. All contigs have been deposited in a public database (EdwardsiellaBase), where they may be searched according to contig ID, gene ontology, protein family motif (Pfam), enzyme commission number, and BLAST. The alignment of the raw reads to the contigs can also be visualized via JBrowse. Conclusions The transcriptomic data and database described here provide a platform for studying the evolutionary developmental genomics of a derived parasitic life cycle. In addition, these data from E. lineata will aid in the interpretation of evolutionary novelties in gene sequence or structure that have been reported for the model cnidarian N. vectensis (e.g., the split NF-κB locus). Finally, we include custom computational tools to facilitate the annotation of a transcriptome based on high-throughput sequencing data obtained from a “non-model system.”
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Affiliation(s)
| | | | | | | | | | | | | | - John R Finnerty
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA.
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Tucker RP, Adams JC. Adhesion networks of cnidarians: a postgenomic view. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 308:323-77. [PMID: 24411175 DOI: 10.1016/b978-0-12-800097-7.00008-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cell-extracellular matrix (ECM) and cell-cell adhesion systems are fundamental to the multicellularity of metazoans. Members of phylum Cnidaria were classified historically by their radial symmetry as an outgroup to bilaterian animals. Experimental study of Hydra and jellyfish has fascinated zoologists for many years. Laboratory studies, based on dissection, biochemical isolations, or perturbations of the living organism, have identified the ECM layer of cnidarians (mesoglea) and its components as important determinants of stem cell properties, cell migration and differentiation, tissue morphogenesis, repair, and regeneration. Studies of the ultrastructure and functions of intercellular gap and septate junctions identified parallel roles for these structures in intercellular communication and morphogenesis. More recently, the sequenced genomes of sea anemone Nematostella vectensis, Hydra magnipapillata, and coral Acropora digitifera have opened up a new frame of reference for analyzing the cell-ECM and cell-cell adhesion molecules of cnidarians and examining their conservation with bilaterians. This chapter integrates a review of literature on the structure and functions of cell-ECM and cell-cell adhesion systems in cnidarians with current analyses of genome-encoded repertoires of adhesion molecules. The postgenomic perspective provides a fresh view on fundamental similarities between cnidarian and bilaterian animals and is impelling wider adoption of species from phylum Cnidaria as model organisms.
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Affiliation(s)
- Richard P Tucker
- Department of Cell Biology and Human Anatomy, University of California, Davis, California, USA.
| | - Josephine C Adams
- School of Biochemistry, University of Bristol, Bristol, United Kingdom.
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Kanska J, Frank U. New roles for Nanos in neural cell fate determination revealed by studies in a cnidarian. J Cell Sci 2013; 126:3192-203. [PMID: 23659997 DOI: 10.1242/jcs.127233] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nanos is a pan-metazoan germline marker, important for germ cell development and maintenance. In flies, Nanos also acts in posterior and neural development, but these functions have not been demonstrated experimentally in other animals. Using the cnidarian Hydractinia we have uncovered novel roles for Nanos in neural cell fate determination. Ectopic expression of Nanos2 increased the numbers of embryonic stinging cell progenitors, but decreased the numbers of neurons. Downregulation of Nanos2 had the opposite effect. Furthermore, Nanos2 blocked maturation of committed, post-mitotic nematoblasts. Hence, Nanos2 acts as a switch between two differentiation pathways, increasing the numbers of nematoblasts at the expense of neuroblasts, but preventing nematocyte maturation. Nanos2 ectopic expression also caused patterning defects, but these were not associated with deregulation of Wnt signaling, showing that the basic anterior-posterior polarity remained intact, and suggesting that numerical imbalance between nematocytes and neurons might have caused these defects, affecting axial patterning only indirectly. We propose that the functions of Nanos in germ cells and in neural development are evolutionarily conserved, but its role in posterior patterning is an insect or arthropod innovation.
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Affiliation(s)
- Justyna Kanska
- School of Natural Sciences and Regenerative Medicine Institute (REMEDI), National University of Ireland, Galway, Ireland
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Wenger Y, Galliot B. RNAseq versus genome-predicted transcriptomes: a large population of novel transcripts identified in an Illumina-454 Hydra transcriptome. BMC Genomics 2013; 14:204. [PMID: 23530871 PMCID: PMC3764976 DOI: 10.1186/1471-2164-14-204] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 03/14/2013] [Indexed: 01/11/2023] Open
Abstract
Background Evolutionary studies benefit from deep sequencing technologies that generate
genomic and transcriptomic sequences from a variety of organisms. Genome
sequencing and RNAseq have complementary strengths. In this study, we
present the assembly of the most complete Hydra transcriptome to
date along with a comparative analysis of the specific features of RNAseq
and genome-predicted transcriptomes currently available in the freshwater
hydrozoan Hydra vulgaris. Results To produce an accurate and extensive Hydra transcriptome, we
combined Illumina and 454 Titanium reads, giving the primacy to Illumina
over 454 reads to correct homopolymer errors. This strategy yielded an
RNAseq transcriptome that contains 48’909 unique sequences including
splice variants, representing approximately 24’450 distinct genes.
Comparative analysis to the available genome-predicted transcriptomes
identified 10’597 novel Hydra transcripts that encode 529
evolutionarily-conserved proteins. The annotation of 170 human orthologs
points to critical functions in protein biosynthesis, FGF and TOR signaling,
vesicle transport, immunity, cell cycle regulation, cell death,
mitochondrial metabolism, transcription and chromatin regulation. However, a
majority of these novel transcripts encodes short ORFs, at least 767 of them
corresponding to pseudogenes. This RNAseq transcriptome also lacks
11’270 predicted transcripts that correspond either to silent genes or
to genes expressed below the detection level of this study. Conclusions We established a simple and powerful strategy to combine Illumina and 454
reads and we produced, with genome assistance, an extensive and accurate
Hydra transcriptome. The comparative analysis of the RNAseq
transcriptome with genome-predicted transcriptomes lead to the
identification of large populations of novel as well as missing transcripts
that might reflect Hydra-specific evolutionary events.
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Affiliation(s)
- Yvan Wenger
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
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Lin X, Zhang J, Li Y, Luo H, Wu Q, Sun C, Song J, Li X, Wei J, Lu A, Qian Z, Khan IA, Chen S. Functional genomics of a living fossil tree, Ginkgo, based on next-generation sequencing technology. PHYSIOLOGIA PLANTARUM 2011; 143:207-18. [PMID: 21834857 DOI: 10.1111/j.1399-3054.2011.01500.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Ginkgo biloba is monotypic species native to China and has old, dioecious, medicinally important characteristics. The functional genes related to these characteristics have not been effectively explored due to a limited number of expressed sequence tags (ESTs) from Ginkgo. To discover novel functional genes efficiently and to understand the development of a living fossil tree, Ginkgo, we used massive parallel pyrosequencing on the Roche 454 GS FLX Titanium platform to generate 64 057 ESTs. The ESTs combined with the 21 590 Ginkgo ESTs in genbank were assembled into 22 304 unique putative transcripts, in which 13 922 novel unique putative transcripts were identified by 454 sequencing. After being assigned to putative functions with Gene Ontology terms, a detailed view of the Ginkgo biological systems was displayed, including characterization of unique putative transcripts with homology to known key enzymes and transcription factors involved in ginkgolide/bilobalide and flavonoid biosynthetic pathways, as well as unique putative transcripts related to development, response to disease and defence. The fact that three full-length Ginkgo genes encoding key enzymes were found and cloned, suggests that high-throughput sequencing technology is superior to traditional gene-by-gene approach in discovery of genes. Additionally, a total of 204 simple sequence repeat motifs were detected. Our study not only lays the foundations for transcriptome-led studies in biosynthetic mechanisms, but also contributes significantly to the understanding of functional genomics and development in non-model plants.
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Affiliation(s)
- Xiaohan Lin
- The Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Houliston E, Momose T, Manuel M. Clytia hemisphaerica: a jellyfish cousin joins the laboratory. Trends Genet 2010; 26:159-67. [DOI: 10.1016/j.tig.2010.01.008] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2009] [Revised: 01/24/2010] [Accepted: 01/25/2010] [Indexed: 11/29/2022]
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