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Ettensohn CA, Guerrero-Santoro J, Khor JM. Lessons from a transcription factor: Alx1 provides insights into gene regulatory networks, cellular reprogramming, and cell type evolution. Curr Top Dev Biol 2022; 146:113-148. [PMID: 35152981 DOI: 10.1016/bs.ctdb.2021.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The skeleton-forming cells of sea urchins and other echinoderms have been studied by developmental biologists as models of cell specification and morphogenesis for many decades. The gene regulatory network (GRN) deployed in the embryonic skeletogenic cells of euechinoid sea urchins is one of the best understood in any developing animal. Recent comparative studies have leveraged the information contained in this GRN, bringing renewed attention to the diverse patterns of skeletogenesis within the phylum and the evolutionary basis for this diversity. The homeodomain-containing transcription factor, Alx1, was originally shown to be a core component of the skeletogenic GRN of the sea urchin embryo. Alx1 has since been found to be key regulator of skeletal cell identity throughout the phylum. As such, Alx1 is currently serving as a lens through which multiple developmental processes are being investigated. These include not only GRN organization and evolution, but also cell reprogramming, cell type evolution, and the gene regulatory control of morphogenesis. This review summarizes our current state of knowledge concerning Alx1 and highlights the insights it is yielding into these important developmental and evolutionary processes.
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Affiliation(s)
- Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States.
| | | | - Jian Ming Khor
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
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2
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Eckmair B, Jin C, Karlsson NG, Abed-Navandi D, Wilson IBH, Paschinger K. Glycosylation at an evolutionary nexus: the brittle star Ophiactis savignyi expresses both vertebrate and invertebrate N-glycomic features. J Biol Chem 2020; 295:3173-3188. [PMID: 32001617 DOI: 10.1074/jbc.ra119.011703] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/17/2020] [Indexed: 12/21/2022] Open
Abstract
Echinoderms are among the most primitive deuterostomes and have been used as model organisms to understand chordate biology because of their close evolutionary relationship to this phylogenetic group. However, there are almost no data available regarding the N-glycomic capacity of echinoderms, which are otherwise known to produce a diverse set of species-specific glycoconjugates, including ones heavily modified by fucose, sulfate, and sialic acid residues. To increase the knowledge of diversity of carbohydrate structures within this phylum, here we conducted an in-depth analysis of N-glycans from a brittle star (Ophiactis savignyi) as an example member of the class Ophiuroidea. To this end, we performed a multi-step N-glycan analysis by HPLC and various exoglyosidase and chemical treatments in combination with MALDI-TOF MS and MS/MS. Using this approach, we found a wealth of hybrid and complex oligosaccharide structures reminiscent of those in higher vertebrates as well as some classical invertebrate glycan structures. 70% of these N-glycans were anionic, carrying either sialic acid, sulfate, or phosphate residues. In terms of glycophylogeny, our data position the brittle star between invertebrates and vertebrates and confirm the high diversity of N-glycosylation in lower organisms.
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Affiliation(s)
- Barbara Eckmair
- Department für Chemie, Universität für Bodenkultur Wien, 1190 Wien, Austria
| | - Chunsheng Jin
- Institutionen för Biomedicin, Göteborgs Universitet, 405 30 Göteborg, Sweden
| | - Niclas G Karlsson
- Institutionen för Biomedicin, Göteborgs Universitet, 405 30 Göteborg, Sweden
| | | | - Iain B H Wilson
- Department für Chemie, Universität für Bodenkultur Wien, 1190 Wien, Austria
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3
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Vanbeselaere J, Jin C, Eckmair B, Wilson IBH, Paschinger K. Sulfated and sialylated N-glycans in the echinoderm Holothuria atra reflect its marine habitat and phylogeny. J Biol Chem 2020; 295:3159-3172. [PMID: 31969392 DOI: 10.1074/jbc.ra119.011701] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/17/2020] [Indexed: 01/14/2023] Open
Abstract
Among the earliest deuterostomes, the echinoderms are an evolutionary important group of ancient marine animals. Within this phylum, the holothuroids (sea cucumbers) are known to produce a wide range of glycoconjugate biopolymers with apparent benefits to health; therefore, they are of economic and culinary interest throughout the world. Other than their highly modified glycosaminoglycans (e.g. fucosylated chondroitin sulfate and fucoidan), nothing is known about their protein-linked glycosylation. Here we used multistep N-glycan fractionation to efficiently separate anionic and neutral N-glycans before analyzing the N-glycans of the black sea cucumber (Holothuria atra) by MS in combination with enzymatic and chemical treatments. These analyses showed the presence of various fucosylated, phosphorylated, sialylated, and multiply sulfated moieties as modifications of oligomannosidic, hybrid, and complex-type N-glycans. The high degree of sulfation and fucosylation parallels the modifications observed previously on holothuroid glycosaminoglycans. Compatible with its phylogenetic position, H. atra not only expresses vertebrate motifs such as sulfo- and sialyl-Lewis A epitopes but displays a high degree of anionic substitution of its glycans, as observed in other marine invertebrates. Thus, as for other echinoderms, the phylum- and order-specific aspects of this species' N-glycosylation reveal both invertebrate- and vertebrate-like features.
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Affiliation(s)
- Jorick Vanbeselaere
- Department of Chemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Chunsheng Jin
- Institute of Biomedicine, Sahlgrenska Academy, Göteborg University, 405 30 Göteborg, Sweden
| | - Barbara Eckmair
- Department of Chemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Iain B H Wilson
- Department of Chemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria.
| | - Katharina Paschinger
- Department of Chemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
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Erkenbrack EM, Thompson JR. Cell type phylogenetics informs the evolutionary origin of echinoderm larval skeletogenic cell identity. Commun Biol 2019; 2:160. [PMID: 31069269 PMCID: PMC6499829 DOI: 10.1038/s42003-019-0417-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/04/2019] [Indexed: 01/19/2023] Open
Abstract
The multiplicity of cell types comprising multicellular organisms begs the question as to how cell type identities evolve over time. Cell type phylogenetics informs this question by comparing gene expression of homologous cell types in distantly related taxa. We employ this approach to inform the identity of larval skeletogenic cells of echinoderms, a clade for which there are phylogenetically diverse datasets of spatial gene expression patterns. We determined ancestral spatial expression patterns of alx1, ets1, tbr, erg, and vegfr, key components of the skeletogenic gene regulatory network driving identity of the larval skeletogenic cell. Here we show ancestral state reconstructions of spatial gene expression of extant eleutherozoan echinoderms support homology and common ancestry of echinoderm larval skeletogenic cells. We propose larval skeletogenic cells arose in the stem lineage of eleutherozoans during a cell type duplication event that heterochronically activated adult skeletogenic cells in a topographically distinct tissue in early development.
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Affiliation(s)
- Eric M. Erkenbrack
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511 USA
- Yale Systems Biology Institute, Yale University, West Haven, CT 06516 USA
| | - Jeffrey R. Thompson
- Department of Geosciences, Baylor University, Waco, TX 76706 USA
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089-0740 USA
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Zandawala M, Moghul I, Yañez Guerra LA, Delroisse J, Abylkassimova N, Hugall AF, O'Hara TD, Elphick MR. Discovery of novel representatives of bilaterian neuropeptide families and reconstruction of neuropeptide precursor evolution in ophiuroid echinoderms. Open Biol 2018; 7:rsob.170129. [PMID: 28878039 PMCID: PMC5627052 DOI: 10.1098/rsob.170129] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/27/2017] [Indexed: 11/12/2022] Open
Abstract
Neuropeptides are a diverse class of intercellular signalling molecules that mediate neuronal regulation of many physiological and behavioural processes. Recent advances in genome/transcriptome sequencing are enabling identification of neuropeptide precursor proteins in species from a growing variety of animal taxa, providing new insights into the evolution of neuropeptide signalling. Here, detailed analysis of transcriptome sequence data from three brittle star species, Ophionotus victoriae, Amphiura filiformis and Ophiopsila aranea, has enabled the first comprehensive identification of neuropeptide precursors in the class Ophiuroidea of the phylum Echinodermata. Representatives of over 30 bilaterian neuropeptide precursor families were identified, some of which occur as paralogues. Furthermore, homologues of endothelin/CCHamide, eclosion hormone, neuropeptide-F/Y and nucleobinin/nesfatin were discovered here in a deuterostome/echinoderm for the first time. The majority of ophiuroid neuropeptide precursors contain a single copy of a neuropeptide, but several precursors comprise multiple copies of identical or non-identical, but structurally related, neuropeptides. Here, we performed an unprecedented investigation of the evolution of neuropeptide copy number over a period of approximately 270 Myr by analysing sequence data from over 50 ophiuroid species, with reference to a robust phylogeny. Our analysis indicates that the composition of neuropeptide ‘cocktails’ is functionally important, but with plasticity over long evolutionary time scales.
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Affiliation(s)
- Meet Zandawala
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Ismail Moghul
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Luis Alfonso Yañez Guerra
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Jérôme Delroisse
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Nikara Abylkassimova
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Andrew F Hugall
- Museums Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia
| | - Timothy D O'Hara
- Museums Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia
| | - Maurice R Elphick
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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6
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Dylus DV, Czarkwiani A, Blowes LM, Elphick MR, Oliveri P. Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution. Genome Biol 2018; 19:26. [PMID: 29490679 PMCID: PMC5831733 DOI: 10.1186/s13059-018-1402-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/01/2018] [Indexed: 12/13/2022] Open
Abstract
Background 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/. Results 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. Conclusions 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. Electronic supplementary material The online version of this article (10.1186/s13059-018-1402-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David V Dylus
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK.,CoMPLEX/SysBio, UCL, Gower Street, London, WC1E 6BT, UK.,Present address: Department of Computational Biology, UNIL, Genopode, 1005, Lausanne, Switzerland
| | - Anna Czarkwiani
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Liisa M Blowes
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.,Present address: Centre for Cell Biology & Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Maurice R Elphick
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Paola Oliveri
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK. .,Centre for Life's Origins and Evolution (CLOE), UCL, Gower Street, London, WC1E 6BT, UK.
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7
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Gaitán-Espitia JD, Hofmann GE. Gene expression profiling during the embryo-to-larva transition in the giant red sea urchin Mesocentrotus franciscanus. Ecol Evol 2017; 7:2798-2811. [PMID: 28428870 PMCID: PMC5395446 DOI: 10.1002/ece3.2850] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 01/20/2017] [Accepted: 02/01/2017] [Indexed: 01/24/2023] Open
Abstract
In echinoderms, major morphological transitions during early development are attributed to different genetic interactions and changes in global expression patterns that shape the regulatory program for the specification of embryonic territories. In order more thoroughly to understand these biological and molecular processes, we examined the transcriptome structure and expression profiles during the embryo‐to‐larva transition of a keystone species, the giant red sea urchin Mesocentrotus franciscanus. Using a de novo assembly approach, we obtained 176,885 transcripts from which 60,439 (34%) had significant alignments to known proteins. From these transcripts, ~80% were functionally annotated allowing the identification of ~2,600 functional, structural, and regulatory genes involved in developmental process. Analysis of expression profiles between gastrula and pluteus stages of M. franciscanus revealed 791 differentially expressed genes with 251 GO overrepresented terms. For gastrula, up‐regulated GO terms were mainly linked to cell differentiation and signal transduction involved in cell cycle checkpoints. In the pluteus stage, major GO terms were associated with phosphoprotein phosphatase activity, muscle contraction, and olfactory behavior, among others. Our evolutionary comparative analysis revealed that several of these genes and functional pathways are highly conserved among echinoids, holothuroids, and ophiuroids.
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Affiliation(s)
| | - Gretchen E Hofmann
- Department of Ecology, Evolution and Marine Biology University of California Santa Barbara CA USA
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8
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Delroisse J, Mallefet J, Flammang P. De Novo Adult Transcriptomes of Two European Brittle Stars: Spotlight on Opsin-Based Photoreception. PLoS One 2016; 11:e0152988. [PMID: 27119739 PMCID: PMC4847921 DOI: 10.1371/journal.pone.0152988] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 03/22/2016] [Indexed: 11/19/2022] Open
Abstract
Next generation sequencing (NGS) technology allows to obtain a deeper and more complete view of transcriptomes. For non-model or emerging model marine organisms, NGS technologies offer a great opportunity for rapid access to genetic information. In this study, paired-end Illumina HiSeqTM technology has been employed to analyse transcriptomes from the arm tissues of two European brittle star species, Amphiura filiformis and Ophiopsila aranea. About 48 million Illumina reads were generated and 136,387 total unigenes were predicted from A. filiformis arm tissues. For O. aranea arm tissues, about 47 million reads were generated and 123,324 total unigenes were obtained. Twenty-four percent of the total unigenes from A. filiformis show significant matches with sequences present in reference online databases, whereas, for O. aranea, this percentage amounts to 23%. In both species, around 50% of the predicted annotated unigenes were significantly similar to transcripts from the purple sea urchin, the closest species to date that has undergone complete genome sequencing and annotation. GO, COG and KEGG analyses were performed on predicted brittle star unigenes. We focused our analyses on the phototransduction actors involved in light perception. Firstly, two new echinoderm opsins were identified in O. aranea: one rhabdomeric opsin (homologous to vertebrate melanopsin) and one RGR opsin. The RGR-opsin is supposed to be involved in retinal regeneration while the r-opsin is suspected to play a role in visual-like behaviour. Secondly, potential phototransduction actors were identified in both transcriptomes using the fly (rhabdomeric) and mammal (ciliary) classical phototransduction pathways as references. Finally, the sensitivity of O.aranea to monochromatic light was investigated to complement data available for A. filiformis. The presence of microlens-like structures at the surface of dorsal arm plate of O. aranea could potentially explain phototactic behaviour differences between the two species. The results confirm (i) the ability of these brittle stars to perceive light using opsin-based photoreception, (ii) suggest the co-occurrence of both rhabdomeric and ciliary photoreceptors, and (iii) emphasise the complexity of light perception in this echinoderm class.
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Affiliation(s)
- Jérôme Delroisse
- School of Biological & Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Jérôme Mallefet
- Catholic University of Louvain-La-Neuve, Marine Biology Laboratory, Place croix du Sud, Louvain-La-Neuve–Belgium
| | - Patrick Flammang
- University of Mons—UMONS, Research Institute for Biosciences, Biology of Marine Organisms and Biomimetics, Mons, Belgium
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Dylus DV, Czarkwiani A, Stångberg J, Ortega-Martinez O, Dupont S, Oliveri P. Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks. EvoDevo 2016; 7:2. [PMID: 26759711 PMCID: PMC4709884 DOI: 10.1186/s13227-015-0039-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 12/21/2015] [Indexed: 11/20/2022] Open
Abstract
Background The evolutionary mechanisms involved in shaping complex gene regulatory networks (GRN) that encode for morphologically similar structures in distantly related animals remain elusive. In this context, echinoderm larval skeletons found in brittle stars and sea urchins provide an ideal system. Here, we characterize for the first time the development of the larval skeleton in the ophiuroid Amphiura filiformis and compare it systematically with its counterpart in sea urchin. Results We show that ophiuroids and euechinoids, that split at least 480 Million years ago (Mya), have remarkable similarities in tempo and mode of skeletal development. Despite morphological and ontological similarities, our high-resolution study of the dynamics of genetic regulatory states in A. filiformis highlights numerous differences in the architecture of their underlying GRNs. Importantly, the A.filiformispplx, the closest gene to the sea urchin double negative gate (DNG) repressor pmar1, fails to drive the skeletogenic program in sea urchin, showing important evolutionary differences in protein function. hesC, the second repressor of the DNG, is co-expressed with most of the genes that are repressed in sea urchin, indicating the absence of direct repression of tbr, ets1/2, and delta in A. filiformis. Furthermore, the absence of expression in later stages of brittle star skeleton development of key regulatory genes, such as foxb and dri, shows significantly different regulatory states. Conclusion Our data fill up an important gap in the picture of larval mesoderm in echinoderms and allows us to explore the evolutionary implications relative to the recently established phylogeny of echinoderm classes. In light of recent studies on other echinoderms, our data highlight a high evolutionary plasticity of the same nodes throughout evolution of echinoderm skeletogenesis. Finally, gene duplication, protein function diversification, and cis-regulatory element evolution all contributed to shape the regulatory program for larval skeletogenesis in different branches of echinoderms. Electronic supplementary material The online version of this article (doi:10.1186/s13227-015-0039-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David Viktor Dylus
- Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London, WC1E 6BT UK ; CoMPLEX/SysBio, UCL, Gower Street, London, WC1E 6BT UK ; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Anna Czarkwiani
- Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London, WC1E 6BT UK
| | - Josefine Stångberg
- Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London, WC1E 6BT UK ; Research Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Olga Ortega-Martinez
- Department of Biological and Environmental Sciences, Sven Lovén Centre for Marine Sciences, University of Gothenburg, Kristineberg 566, 451 78 Fiskebäckskil, Sweden
| | - Sam Dupont
- Department of Biological and Environmental Sciences, Sven Lovén Centre for Marine Sciences, University of Gothenburg, Kristineberg 566, 451 78 Fiskebäckskil, Sweden
| | - Paola Oliveri
- Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London, WC1E 6BT UK
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Cameron RA, Kudtarkar P, Gordon SM, Worley KC, Gibbs RA. Do echinoderm genomes measure up? Mar Genomics 2015; 22:1-9. [PMID: 25701080 PMCID: PMC4489978 DOI: 10.1016/j.margen.2015.02.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/05/2015] [Accepted: 02/06/2015] [Indexed: 11/19/2022]
Abstract
Echinoderm genome sequences are a corpus of useful information about a clade of animals that serve as research models in fields ranging from marine ecology to cell and developmental biology. Genomic information from echinoids has contributed to insights into the gene interactions that drive the developmental process at the molecular level. Such insights often rely heavily on genomic information and the kinds of questions that can be asked thus depend on the quality of the sequence information. Here we describe the history of echinoderm genomic sequence assembly and present details about the quality of the data obtained. All of the sequence information discussed here is posted on the echinoderm information web system, Echinobase.org.
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Affiliation(s)
- R Andrew Cameron
- Division of Biology 139-74, California Institute of Technology, Pasadena, CA, USA.
| | - Parul Kudtarkar
- Division of Biology 139-74, California Institute of Technology, Pasadena, CA, USA
| | - Susan M Gordon
- Division of Biology 139-74, California Institute of Technology, Pasadena, CA, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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11
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Reich A, Dunn C, Akasaka K, Wessel G. Phylogenomic analyses of Echinodermata support the sister groups of Asterozoa and Echinozoa. PLoS One 2015; 10:e0119627. [PMID: 25794146 PMCID: PMC4368666 DOI: 10.1371/journal.pone.0119627] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/12/2015] [Indexed: 12/01/2022] Open
Abstract
Echinoderms (sea urchins, sea stars, brittle stars, sea lilies and sea cucumbers) are a group of diverse organisms, second in number within deuterostome species to only the chordates. Echinoderms serve as excellent model systems for developmental biology due to their diverse developmental mechanisms, tractable laboratory use, and close phylogenetic distance to chordates. In addition, echinoderms are very well represented in the fossil record, including some larval features, making echinoderms a valuable system for studying evolutionary development. The internal relationships of Echinodermata have not been consistently supported across phylogenetic analyses, however, and this has hindered the study of other aspects of their biology. In order to test echinoderm phylogenetic relationships, we sequenced 23 de novo transcriptomes from all five clades of echinoderms. Using multiple phylogenetic methods at a variety of sampling depths we have constructed a well-supported phylogenetic tree of Echinodermata, including support for the sister groups of Asterozoa (sea stars and brittle stars) and Echinozoa (sea urchins and sea cucumbers). These results will help inform developmental and evolutionary studies specifically in echinoderms and deuterostomes in general.
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Affiliation(s)
- Adrian Reich
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Casey Dunn
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
| | - Koji Akasaka
- Misaki Marine Biological Station, University of Tokyo, Miura, Japan
| | - Gary Wessel
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
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12
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Examination of the skeletal proteome of the brittle star Ophiocoma wendtii reveals overall conservation of proteins but variation in spicule matrix proteins. Proteome Sci 2015; 13:7. [PMID: 25705131 PMCID: PMC4336488 DOI: 10.1186/s12953-015-0064-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 01/20/2015] [Indexed: 11/21/2022] Open
Abstract
Background While formation of mineralized tissue is characteristic of many animal taxa, the proteins that interact with mineral are diverse and appear in many cases to be of independent origin. Extracellular matrix proteins involved in mineralization do share some common features. They tend to be disordered, secreted proteins with repetitive, low complexity. The genes encoding these proteins are often duplicated and undergo concerted evolution, further diversifying the repetitive domains. This makes it difficult to identify mineralization genes and the proteins they encode using bioinformatics techniques. Here we describe the use of proteomics to identify mineralization genes in an ophiuroid echinoderm, Ophiocoma wendtii (O. wendtii). Results We have isolated the occluded proteins within the mineralized tissue of the brittle star Ophiocoma wendtii. The proteins were analyzed both unfractionated and separated on SDS-PAGE gels. Each slice was analyzed using mass spectroscopy and the amino acid sequence of the most prevalent peptides was obtained. This was compared to both an embryonic transcriptome from the gastrula stage when skeleton is being formed and a tube foot (an adult mineralized tissue) transcriptome. Thirty eight proteins were identified which matched known proteins or protein domains in the NCBI databases. These include C-type lectins, ECM proteins, Kazal-type protease inhibitors, matrix metalloproteases as well as more common cellular proteins. Many of these are similar to those found in the sea urchin Strongylocentrotus purpuratus (S. purpuratus) skeleton. We did not, however, identify clear homologs to the sea urchin spicule matrix proteins, and the number of C-type lectin containing genes was much reduced compared to sea urchins. Also notably absent was MSP-130. Conclusions Our results show an overall conservation of the types of proteins found in the mineralized tissues of two divergent groups of echinoderms, as well as in mineralized tissues in general. However, the extensive gene duplication and concerted evolution seen in the spicule matrix proteins found in the sea urchin skeleton was not observed in the brittle star. Electronic supplementary material The online version of this article (doi:10.1186/s12953-015-0064-7) contains supplementary material, which is available to authorized users.
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Telford MJ, Lowe CJ, Cameron CB, Ortega-Martinez O, Aronowicz J, Oliveri P, Copley RR. Phylogenomic analysis of echinoderm class relationships supports Asterozoa. Proc Biol Sci 2015; 281:rspb.2014.0479. [PMID: 24850925 DOI: 10.1098/rspb.2014.0479] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
While some aspects of the phylogeny of the five living echinoderm classes are clear, the position of the ophiuroids (brittlestars) relative to asteroids (starfish), echinoids (sea urchins) and holothurians (sea cucumbers) is controversial. Ophiuroids have a pluteus-type larva in common with echinoids giving some support to an ophiuroid/echinoid/holothurian clade named Cryptosyringida. Most molecular phylogenetic studies, however, support an ophiuroid/asteroid clade (Asterozoa) implying either convergent evolution of the pluteus or reversals to an auricularia-type larva in asteroids and holothurians. A recent study of 10 genes from four of the five echinoderm classes used 'phylogenetic signal dissection' to separate alignment positions into subsets of (i) suboptimal, heterogeneously evolving sites (invariant plus rapidly changing) and (ii) the remaining optimal, homogeneously evolving sites. Along with most previous molecular phylogenetic studies, their set of heterogeneous sites, expected to be more prone to systematic error, support Asterozoa. The homogeneous sites, in contrast, support an ophiuroid/echinoid grouping, consistent with the cryptosyringid clade, leading them to posit homology of the ophiopluteus and echinopluteus. Our new dataset comprises 219 genes from all echinoderm classes; analyses using probabilistic Bayesian phylogenetic methods strongly support Asterozoa. The most reliable, slowly evolving quartile of genes also gives highest support for Asterozoa; this support diminishes in second and third quartiles and the fastest changing quartile places the ophiuroids close to the root. Using phylogenetic signal dissection, we find heterogenous sites support an unlikely grouping of Ophiuroidea + Holothuria while homogeneous sites again strongly support Asterozoa. Our large and taxonomically complete dataset finds no support for the cryptosyringid hypothesis; in showing strong support for the Asterozoa, our preferred topology leaves the question of homology of pluteus larvae open.
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Affiliation(s)
- Maximilian J Telford
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Christopher J Lowe
- Hopkins Marine Station, Department of Biology, Stanford University, 120 Oceanview Boulevard, Pacific Grove, CA 93950, USA
| | - Christopher B Cameron
- Départment de Sciences Biologiques, Université de Montréal, Pavillion Marie-Victorin, C.P. 6128, Succ. Centre-ville, Montréal, Québec, Canada H3C 3J7
| | - Olga Ortega-Martinez
- Department of Biological and Environmental Sciences, Sven Lovén Centre for Marine Sciences, University of Gothenburg, Kristineberg 566, Fiskebäckskil 451 78, Sweden
| | - Jochanan Aronowicz
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60650, USA
| | - Paola Oliveri
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Richard R Copley
- CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Observatoire Océanographique, Villefranche-sur-mer 06230, France Sorbonne Universites, UPMC Univ Paris 06, Laboratoire de Biologie du Developpement de Villefranche-sur-mer, Observatoire Oceanographique, Villefranche-sur-mer 06230, France
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McIntyre DC, Lyons DC, Martik M, McClay DR. Branching out: origins of the sea urchin larval skeleton in development and evolution. Genesis 2014; 52:173-85. [PMID: 24549853 PMCID: PMC3990003 DOI: 10.1002/dvg.22756] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 02/14/2014] [Accepted: 02/14/2014] [Indexed: 11/08/2022]
Abstract
It is a challenge to understand how the information encoded in DNA is used to build a three-dimensional structure. To explore how this works the assembly of a relatively simple skeleton has been examined at multiple control levels. The skeleton of the sea urchin embryo consists of a number of calcite rods produced by 64 skeletogenic cells. The ectoderm supplies spatial cues for patterning, essentially telling the skeletogenic cells where to position themselves and providing the factors for skeletal growth. Here, we describe the information known about how this works. First the ectoderm must be patterned so that the signaling cues are released from precise positions. The skeletogenic cells respond by initiating skeletogenesis immediately beneath two regions (one on the right and the other on the left side). Growth of the skeletal rods requires additional signaling from defined ectodermal locations, and the skeletogenic cells respond to produce a membrane-bound template in which the calcite crystal grows. Important in this process are three signals, fibroblast growth factor, vascular endothelial growth factor, and Wnt5. Each is necessary for explicit tasks in skeleton production.
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Affiliation(s)
| | | | - Megan Martik
- Department of Biology, Duke University, Durham, NC
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