1
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Galià-Camps C, Carreras C, Pascual M, Greve C, Schell T, Turon X, Palacín C, Pérez-Portela R, Wangensteen OS, Pegueroles C. Chromosome-level genome assembly and annotation of the black sea urchin Arbacia lixula (Linnaeus, 1758). DNA Res 2024; 31:dsae020. [PMID: 38908014 PMCID: PMC11310861 DOI: 10.1093/dnares/dsae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/23/2024] [Accepted: 06/21/2024] [Indexed: 06/24/2024] Open
Abstract
The black sea urchin (Arbacia lixula) is a keystone species inhabiting the coastal shallow waters of the Mediterranean Sea, which is a key driver of littoral communities' structure. Here, we present the first genome assembly and annotation of this species, standing as the first Arbacioida genome, including both nuclear and mitochondrial genomes. To obtain a chromosome-level assembly, we used a combination of PacBio high fidelity (HiFi) reads and chromatin capture reads (Omni-C). In addition, we generated a high-quality nuclear annotation of both coding and non-coding genes, by using published RNA-Seq data from several individuals of A. lixula and gene models from closely related species. The nuclear genome assembly has a total span of 607.91 Mb, being consistent with its experimentally estimated genome size. The assembly contains 22 chromosome-scale scaffolds (96.52% of the total length), which coincides with its known karyotype. A total of 72,767 transcripts were predicted from the nuclear genome, 24,171 coding, and 48,596 non-coding that included lncRNA, snoRNA, and tRNAs. The circularized mitochondrial genome had 15,740 bp comprising 13 protein-coding genes, 2 rRNA, and 22 tRNA. This reference genome will enhance ongoing A. lixula studies and benefit the wider sea urchin scientific community.
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Affiliation(s)
- Carles Galià-Camps
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Carlos Carreras
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Marta Pascual
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Carola Greve
- Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Senckenberg Forschungsinstitut und Naturmuseum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Tilman Schell
- Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Senckenberg Forschungsinstitut und Naturmuseum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Xavier Turon
- Department of Marine Ecology, Centre for Advanced Studies of Blanes, Spanish National Research Council (CEAB, CSIC), Blanes, Spain
| | - Creu Palacín
- Institut de Recerca de la Biodiversitat (IRBio), Faculty of Biology, University of Barcelona, Barcelona, Spain
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Rocío Pérez-Portela
- Institut de Recerca de la Biodiversitat (IRBio), Faculty of Biology, University of Barcelona, Barcelona, Spain
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Owen S Wangensteen
- Institut de Recerca de la Biodiversitat (IRBio), Faculty of Biology, University of Barcelona, Barcelona, Spain
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Cinta Pegueroles
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Faculty of Biology, University of Barcelona, Barcelona, Spain
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2
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Parey E, Ortega-Martinez O, Delroisse J, Piovani L, Czarkwiani A, Dylus D, Arya S, Dupont S, Thorndyke M, Larsson T, Johannesson K, Buckley KM, Martinez P, Oliveri P, Marlétaz F. The brittle star genome illuminates the genetic basis of animal appendage regeneration. Nat Ecol Evol 2024; 8:1505-1521. [PMID: 39030276 PMCID: PMC11310086 DOI: 10.1038/s41559-024-02456-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/29/2024] [Indexed: 07/21/2024]
Abstract
Species within nearly all extant animal lineages are capable of regenerating body parts. However, it remains unclear whether the gene expression programme controlling regeneration is evolutionarily conserved. Brittle stars are a species-rich class of echinoderms with outstanding regenerative abilities, but investigations into the genetic bases of regeneration in this group have been hindered by the limited genomic resources. Here we report a chromosome-scale genome assembly for the brittle star Amphiura filiformis. We show that the brittle star genome is the most rearranged among echinoderms sequenced so far, featuring a reorganized Hox cluster reminiscent of the rearrangements observed in sea urchins. In addition, we performed an extensive profiling of gene expression during brittle star adult arm regeneration and identified sequential waves of gene expression governing wound healing, proliferation and differentiation. We conducted comparative transcriptomic analyses with other invertebrate and vertebrate models for appendage regeneration and uncovered hundreds of genes with conserved expression dynamics, particularly during the proliferative phase of regeneration. Our findings emphasize the crucial importance of echinoderms to detect long-range expression conservation between vertebrates and classical invertebrate regeneration model systems.
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Affiliation(s)
- Elise Parey
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - Olga Ortega-Martinez
- Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Jérôme Delroisse
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Laura Piovani
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Anna Czarkwiani
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Technische Universität Dresden, Center for Regenerative Therapies Dresden (CRTD), Dresden, Germany
| | - David Dylus
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Roche Pharmaceutical Research and Early Development (pRED), Cardiovascular and Metabolism, Immunology, Infectious Disease, and Ophthalmology (CMI2O), F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Srishti Arya
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- MRC Laboratory of Medical Sciences, Imperial College London, London, UK
| | - Samuel Dupont
- Department of Biology and Environmental Science, University of Gothenburg, Kristineberg Marine Research Station, Fiskebäckskil, Sweden
- IAEA Marine Environment Laboratories, Radioecology Laboratory, Quai Antoine 1er, Monaco
| | - Michael Thorndyke
- Department of Biology and Environmental Science, University of Gothenburg, Kristineberg Marine Research Station, Fiskebäckskil, Sweden
| | - Tomas Larsson
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kerstin Johannesson
- Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | | | - Pedro Martinez
- Departament de Genètica, Microbiologia, i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Paola Oliveri
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - Ferdinand Marlétaz
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
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3
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Loubet-Senear K, Srivastava M. Brittle star genome provides information on the evolution of regeneration. Nat Ecol Evol 2024; 8:1385-1386. [PMID: 39030275 DOI: 10.1038/s41559-024-02459-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2024]
Affiliation(s)
- Kaitlyn Loubet-Senear
- Department of Molecular and Cell Biology, Harvard University, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA.
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4
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Lin CY, Marlétaz F, Pérez-Posada A, Martínez-García PM, Schloissnig S, Peluso P, Conception GT, Bump P, Chen YC, Chou C, Lin CY, Fan TP, Tsai CT, Gómez Skarmeta JL, Tena JJ, Lowe CJ, Rank DR, Rokhsar DS, Yu JK, Su YH. Chromosome-level genome assemblies of 2 hemichordates provide new insights into deuterostome origin and chromosome evolution. PLoS Biol 2024; 22:e3002661. [PMID: 38829909 PMCID: PMC11175523 DOI: 10.1371/journal.pbio.3002661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/13/2024] [Accepted: 05/03/2024] [Indexed: 06/05/2024] Open
Abstract
Deuterostomes are a monophyletic group of animals that includes Hemichordata, Echinodermata (together called Ambulacraria), and Chordata. The diversity of deuterostome body plans has made it challenging to reconstruct their ancestral condition and to decipher the genetic changes that drove the diversification of deuterostome lineages. Here, we generate chromosome-level genome assemblies of 2 hemichordate species, Ptychodera flava and Schizocardium californicum, and use comparative genomic approaches to infer the chromosomal architecture of the deuterostome common ancestor and delineate lineage-specific chromosomal modifications. We show that hemichordate chromosomes (1N = 23) exhibit remarkable chromosome-scale macrosynteny when compared to other deuterostomes and can be derived from 24 deuterostome ancestral linkage groups (ALGs). These deuterostome ALGs in turn match previously inferred bilaterian ALGs, consistent with a relatively short transition from the last common bilaterian ancestor to the origin of deuterostomes. Based on this deuterostome ALG complement, we deduced chromosomal rearrangement events that occurred in different lineages. For example, a fusion-with-mixing event produced an Ambulacraria-specific ALG that subsequently split into 2 chromosomes in extant hemichordates, while this homologous ALG further fused with another chromosome in sea urchins. Orthologous genes distributed in these rearranged chromosomes are enriched for functions in various developmental processes. We found that the deeply conserved Hox clusters are located in highly rearranged chromosomes and that maintenance of the clusters are likely due to lower densities of transposable elements within the clusters. We also provide evidence that the deuterostome-specific pharyngeal gene cluster was established via the combination of 3 pre-assembled microsyntenic blocks. We suggest that since chromosomal rearrangement events and formation of new gene clusters may change the regulatory controls of developmental genes, these events may have contributed to the evolution of diverse body plans among deuterostomes.
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Affiliation(s)
- Che-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Ferdinand Marlétaz
- Center for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Alberto Pérez-Posada
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Pedro Manuel Martínez-García
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | | | - Paul Peluso
- Pacific Biosciences, Menlo Park, California, United States of America
| | | | - Paul Bump
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, California, United States of America
| | - Yi-Chih Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Cindy Chou
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Ching-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Tzu-Pei Fan
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Chang-Tai Tsai
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - José Luis Gómez Skarmeta
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Juan J. Tena
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Christopher J. Lowe
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, California, United States of America
- Chan-Zuckerberg Biohub, San Francisco, California, United States of America
| | - David R. Rank
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Daniel S. Rokhsar
- Chan-Zuckerberg Biohub, San Francisco, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
- Molecular Genetics Unit, Okinawa Institute for Science and Technology, Onna, Japan
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
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5
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Komoto T, Ikeo K, Yaguchi S, Yamamoto T, Sakamoto N, Awazu A. Assembly of continuous high-resolution draft genome sequence of Hemicentrotus pulcherrimus using long-read sequencing. Dev Growth Differ 2024; 66:297-304. [PMID: 38634255 DOI: 10.1111/dgd.12924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/13/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024]
Abstract
The update of the draft genome assembly of sea urchin, Hemicentrotus pulcherrimus, which is widely studied in East Asia as a model organism of early development, was performed using Oxford nanopore long-read sequencing. The updated assembly provided ~600-Mb genome sequences divided into 2,163 contigs with N50 = 516 kb. BUSCO completeness score and transcriptome model mapping ratio (TMMR) of the present assembly were obtained as 96.5% and 77.8%, respectively. These results were more continuous with higher resolution than those by the previous version of H. pulcherrimus draft genome, HpulGenome_v1, where the number of scaffolds = 16,251 with a total of ~100 Mb, N50 = 143 kb, BUSCO completeness score = 86.1%, and TMMR = 55.4%. The obtained genome contained 36,055 gene models that were consistent with those in other echinoderms. Additionally, two tandem repeat sequences of early histone gene locus containing 47 copies and 34 copies of all histone genes, and 185 of the homologous sequences of the interspecifically conserved region of the Ars insulator, ArsInsC, were obtained. These results provide further advance for genome-wide research of development, gene regulation, and intranuclear structural dynamics of multicellular organisms using H. pulcherrimus.
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Affiliation(s)
- Tetsushi Komoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Kazuho Ikeo
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Shizuoka, Japan
| | - Shunsuke Yaguchi
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Japan
| | - Takashi Yamamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Higashi-Hiroshima, Japan
| | - Naoaki Sakamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Higashi-Hiroshima, Japan
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Higashi-Hiroshima, Japan
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6
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Massri AJ, Berrio A, Afanassiev A, Greenstreet L, Pipho K, Byrne M, Schiebinger G, McClay DR, Wray GA. Single-cell transcriptomics reveals evolutionary reconfiguration of embryonic cell fate specification in the sea urchin Heliocidaris erythrogramma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591752. [PMID: 38746376 PMCID: PMC11092583 DOI: 10.1101/2024.04.30.591752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Altered regulatory interactions during development likely underlie a large fraction of phenotypic diversity within and between species, yet identifying specific evolutionary changes remains challenging. Analysis of single-cell developmental transcriptomes from multiple species provides a powerful framework for unbiased identification of evolutionary changes in developmental mechanisms. Here, we leverage a "natural experiment" in developmental evolution in sea urchins, where a major life history switch recently evolved in the lineage leading to Heliocidaris erythrogramma, precipitating extensive changes in early development. Comparative analyses of scRNA-seq developmental time courses from H. erythrogramma and Lytechinus variegatus (representing the derived and ancestral states respectively) reveals numerous evolutionary changes in embryonic patterning. The earliest cell fate specification events, and the primary signaling center are co-localized in the ancestral dGRN but remarkably, in H. erythrogramma they are spatially and temporally separate. Fate specification and differentiation are delayed in most embryonic cell lineages, although in some cases, these processes are conserved or even accelerated. Comparative analysis of regulator-target gene co-expression is consistent with many specific interactions being preserved but delayed in H. erythrogramma, while some otherwise widely conserved interactions have likely been lost. Finally, specific patterning events are directly correlated with evolutionary changes in larval morphology, suggesting that they are directly tied to the life history shift. Together, these findings demonstrate that comparative scRNA-seq developmental time courses can reveal a diverse set of evolutionary changes in embryonic patterning and provide an efficient way to identify likely candidate regulatory interactions for subsequent experimental validation.
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Affiliation(s)
- Abdull J Massri
- Department of Biology, Duke University, Durham, NC 27701 USA
| | | | - Anton Afanassiev
- Department of Mathematics, University of British Colombia, Vancouver, BC V6T 1Z4 Canada
| | - Laura Greenstreet
- Department of Mathematics, University of British Colombia, Vancouver, BC V6T 1Z4 Canada
| | - Krista Pipho
- Department of Biology, Duke University, Durham, NC 27701 USA
| | - Maria Byrne
- School of Life and Environmental Sciences, Sydney University, Sydney, NSW Australia
| | - Geoffrey Schiebinger
- Department of Mathematics, University of British Colombia, Vancouver, BC V6T 1Z4 Canada
| | - David R McClay
- Department of Biology, Duke University, Durham, NC 27701 USA
| | - Gregory A Wray
- Department of Biology, Duke University, Durham, NC 27701 USA
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7
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Chromosomal-level genome assembly of the long-spined sea urchin Diadema setosum (Leske, 1778). GIGABYTE 2024; 2024:gigabyte121. [PMID: 38707632 PMCID: PMC11066563 DOI: 10.46471/gigabyte.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/14/2024] [Indexed: 05/07/2024] Open
Abstract
The long-spined sea urchin Diadema setosum is an algal and coral feeder widely distributed in the Indo-Pacific that can cause severe bioerosion on the reef community. However, the lack of genomic information has hindered the study of its ecology and evolution. Here, we report the chromosomal-level genome (885.8 Mb) of the long-spined sea urchin D. setosum using a combination of PacBio long-read sequencing and Omni-C scaffolding technology. The assembled genome contains a scaffold N50 length of 38.3 Mb, 98.1% of complete BUSCO (Geno, metazoa_odb10) genes (the single copy score is 97.8% and the duplication score is 0.3%), and 98.6% of the sequences are anchored to 22 pseudo-molecules/chromosomes. A total of 27,478 gene models have were annotated, reaching a total of 28,414 transcripts, including 5,384 tRNA and 23,030 protein-coding genes. The high-quality genome of D. setosum presented here is a valuable resource for the ecological and evolutionary studies of this coral reef-associated sea urchin.
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8
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Hijaze E, Gildor T, Seidel R, Layous M, Winter M, Bertinetti L, Politi Y, Ben-Tabou de-Leon S. ROCK and the actomyosin network control biomineral growth and morphology during sea urchin skeletogenesis. eLife 2024; 12:RP89080. [PMID: 38573316 PMCID: PMC10994658 DOI: 10.7554/elife.89080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
Biomineralization had apparently evolved independently in different phyla, using distinct minerals, organic scaffolds, and gene regulatory networks (GRNs). However, diverse eukaryotes from unicellular organisms, through echinoderms to vertebrates, use the actomyosin network during biomineralization. Specifically, the actomyosin remodeling protein, Rho-associated coiled-coil kinase (ROCK) regulates cell differentiation and gene expression in vertebrates' biomineralizing cells, yet, little is known on ROCK's role in invertebrates' biomineralization. Here, we reveal that ROCK controls the formation, growth, and morphology of the calcite spicules in the sea urchin larva. ROCK expression is elevated in the sea urchin skeletogenic cells downstream of the Vascular Endothelial Growth Factor (VEGF) signaling. ROCK inhibition leads to skeletal loss and disrupts skeletogenic gene expression. ROCK inhibition after spicule formation reduces the spicule elongation rate and induces ectopic spicule branching. Similar skeletogenic phenotypes are observed when ROCK is inhibited in a skeletogenic cell culture, indicating that these phenotypes are due to ROCK activity specifically in the skeletogenic cells. Reduced skeletal growth and enhanced branching are also observed under direct perturbations of the actomyosin network. We propose that ROCK and the actomyosin machinery were employed independently, downstream of distinct GRNs, to regulate biomineral growth and morphology in Eukaryotes.
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Affiliation(s)
- Eman Hijaze
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of HaifaHaifaIsrael
| | - Tsvia Gildor
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of HaifaHaifaIsrael
| | - Ronald Seidel
- B CUBE Center for Molecular Bioengineering, Technische Universität DresdenDresdenGermany
| | - Majed Layous
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of HaifaHaifaIsrael
| | - Mark Winter
- Department of Electrical Engineering, Computer Science and Mathematics, Technische Universiteit DelftDelftNetherlands
| | - Luca Bertinetti
- B CUBE Center for Molecular Bioengineering, Technische Universität DresdenDresdenGermany
| | - Yael Politi
- B CUBE Center for Molecular Bioengineering, Technische Universität DresdenDresdenGermany
| | - Smadar Ben-Tabou de-Leon
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of HaifaHaifaIsrael
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9
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Sakamoto N, Watanabe K, Awazu A, Yamamoto T. CRISPR-Cas9-Mediated Gene Knockout in a Non-Model Sea Urchin, Heliocidaris crassispina. Zoolog Sci 2024; 41:159-166. [PMID: 38587910 DOI: 10.2108/zs230052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/25/2023] [Indexed: 04/10/2024]
Abstract
Sea urchins have been used as model organisms in developmental biology research and the genomes of several sea urchin species have been sequenced. Recently, genome editing technologies have become available for sea urchins, and methods for gene knockout using the CRISPRCas9 system have been established. Heliocidaris crassispina is an important marine fishery resource with edible gonads. Although H. crassispina has been used as a biological research material, its genome has not yet been published, and it is a non-model sea urchin for molecular biology research. However, as recent advances in genome editing technology have facilitated genome modification in non-model organisms, we applied genome editing using the CRISPR-Cas9 system to H. crassispina. In this study, we targeted genes encoding ETS transcription factor (HcEts) and pigmentation-related polyketide synthase (HcPks1). Gene fragments were isolated using primers designed by inter-specific sequence comparisons within Echinoidea. When Ets gene was targeted using two sgRNAs, one successfully introduced mutations and impaired skeletogenesis. In the Pks1 gene knockout, when two sgRNAs targeting the close vicinity of the site corresponding to the target site that showed 100% mutagenesis efficiency of the Pks1 gene in Hemicentrotus pulcherrimus, mutagenesis was not observed. However, two other sgRNAs targeting distant sites efficiently introduced mutations. In addition, Pks1 knockout H. crassispina exhibited an albino phenotype in the pluteus larvae and adult sea urchins after metamorphosis. This indicates that the CRISPRCas9 system can be used to modify the genome of the non-model sea urchin H. crassispina.
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Affiliation(s)
- Naoaki Sakamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan,
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Kaichi Watanabe
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Akinori Awazu
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
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10
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Fernández-Boo S, Machado A, Castro LFC, Azeredo R, Costas B. Unravelling the main immune repertoire of Paracentrotus lividus following Vibrio anguillarum bath challenge. FISH & SHELLFISH IMMUNOLOGY 2024; 147:109431. [PMID: 38346567 DOI: 10.1016/j.fsi.2024.109431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/23/2024]
Abstract
Paracentrotus lividus is the most abundant echinoid species in the North East Atlantic Ocean and Mediterranean Sea. Although there is abundant genomic information of the species, there is no deep characterisation of the genes involved in the immune response. Here, a reference transcriptome of male and female coelomocytes was produced. The generated P. lividus transcriptome assembly has 203,511 transcripts, N50 transcript length of 1079 bp, and more than 90% estimated gene completeness in Eukaryota and Metazoa BUSCO databases, respectively. Differential gene expression analyses showed 54 and 55 up-regulated genes in P. lividus female and male coelomocyte tissues, respectively. These results suggest a similar immune gene repertoire between sexes. To examine the immune response, P. lividus was challenged with Vibrio anguillarum, one of the candidate pathogens for bald disease. Immune parameters were evaluated at cell and humoral levels, as well as the expression analysis of immune related genes at an early response stage. No differences were found at cellular and humoral levels with the exception of the increase of nitric oxide in perivisceral fluid of challenged animals. At the gene expression level, a total of 2721 genes were upregulated in challenged animals, 13.6 times higher expression than control group. Our analysis revealed that four major KEGG pathways were enriched in challenged animals: Autophagy (KEGG:04140), Endocytosis (KEGG:04144), Phagosome (KEGG:04145) and Protein processing in endoplasmic reticulum (KEGG:04141). Several toll-like receptors (TLR), scavenger receptors cysteine-rich (SRCR) or nucleotide-binding oligomerisation domain like receptors (NLR) were identified as major family genes for pathogen recognition and immune defence. This study provides a valuable transcriptomic resource and unfolds the molecular basis of immune response to V. anguillarum exposure. Overall, our findings contribute to the conservation effort of the P. lividus populations, as well as its sustainable exploitation in an aquaculture context.
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Affiliation(s)
- Sergio Fernández-Boo
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR). Terminal de Cruzeiros Do Porto de Leixões, Av. General Norton de Matos S/n, 4450-208, Matosinhos, Portugal.
| | - André Machado
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR). Terminal de Cruzeiros Do Porto de Leixões, Av. General Norton de Matos S/n, 4450-208, Matosinhos, Portugal
| | - L Filipe C Castro
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR). Terminal de Cruzeiros Do Porto de Leixões, Av. General Norton de Matos S/n, 4450-208, Matosinhos, Portugal; Departamento de Biologia, Universidade Do Porto, Rua Do Campo Alegre, S/n, Edifício FC4, 4169-007, Porto, Portugal
| | - Rita Azeredo
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR). Terminal de Cruzeiros Do Porto de Leixões, Av. General Norton de Matos S/n, 4450-208, Matosinhos, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS-UP), Universidade Do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Benjamin Costas
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR). Terminal de Cruzeiros Do Porto de Leixões, Av. General Norton de Matos S/n, 4450-208, Matosinhos, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS-UP), Universidade Do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
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11
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Perillo M, Sepe RM, Paganos P, Toscano A, Annunziata R. Sea cucumbers: an emerging system in evo-devo. EvoDevo 2024; 15:3. [PMID: 38368336 PMCID: PMC10874539 DOI: 10.1186/s13227-023-00220-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/24/2023] [Indexed: 02/19/2024] Open
Abstract
A challenge for evolutionary developmental (evo-devo) biology is to expand the breadth of research organisms used to investigate how animal diversity has evolved through changes in embryonic development. New experimental systems should couple a relevant phylogenetic position with available molecular tools and genomic resources. As a phylum of the sister group to chordates, echinoderms extensively contributed to our knowledge of embryonic patterning, organ development and cell-type evolution. Echinoderms display a variety of larval forms with diverse shapes, making them a suitable group to compare the evolution of embryonic developmental strategies. However, because of the laboratory accessibility and the already available techniques, most studies focus on sea urchins and sea stars mainly. As a comparative approach, the field would benefit from including information on other members of this group, like the sea cucumbers (holothuroids), for which little is known on the molecular basis of their development. Here, we review the spawning and culture methods, the available morphological and molecular information, and the current state of genomic and transcriptomic resources on sea cucumbers. With the goal of making this system accessible to the broader community, we discuss how sea cucumber embryos and larvae can be a powerful system to address the open questions in evo-devo, including understanding the origins of bilaterian structures.
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Affiliation(s)
- Margherita Perillo
- Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, 7 MBL St., Woods Hole, MA, 02543, USA.
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| | - Rosa Maria Sepe
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Periklis Paganos
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Alfonso Toscano
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
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12
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Costantini M, Esposito R, Ruocco N, Caramiello D, Cordella A, Ventola GM, Zupo V. De Novo Assembly of the Genome of the Sea Urchin Paracentrotus lividus (Lamarck 1816). Int J Mol Sci 2024; 25:1685. [PMID: 38338963 PMCID: PMC10855541 DOI: 10.3390/ijms25031685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
The Mediterranean purple sea urchin Paracentrotus lividus (Lamarck 1816) is a remarkable model system for molecular, evolutionary and cell biology studies, particularly in the field of developmental biology. We sequenced the genome, performed a de novo assembly, and analysed the assembly content. The genome of P. lividus was sequenced using Illumina NextSeq 500 System (Illumina) in a 2 × 150 paired-end format. More than 30,000 open reading frames (ORFs), (more than 8000 are unique), were identified and analysed to provide molecular tools accessible for the scientific community. In particular, several genes involved in complex innate immune responses, oxidative metabolism, signal transduction, and kinome, as well as genes regulating the membrane receptors, were identified in the P. lividus genome. In this way, the employment of the Mediterranean sea urchin for investigations and comparative analyses was empowered, leading to the explanation of cis-regulatory networks and their evolution in a key developmental model occupying an important evolutionary position with respect to vertebrates and humans.
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Affiliation(s)
- Maria Costantini
- Stazione Zoologica Anton Dohrn, Department of Ecosustainable Marine Biotechnology, Via Ammiraglio Ferdinando Acton n. 55, 80133 Napoli, Italy;
| | - Roberta Esposito
- Stazione Zoologica Anton Dohrn, Department of Ecosustainable Marine Biotechnology, Via Ammiraglio Ferdinando Acton n. 55, 80133 Napoli, Italy;
| | - Nadia Ruocco
- Stazione Zoologica Anton Dohrn, Department of Ecosustainable Marine Biotechnology, Calabria Marine Centre, C.da Torre Spaccata, 87071 Amendolara, Italy;
| | - Davide Caramiello
- Stazione Zoologica Anton Dohrn, Department of Marine Animal Conservation and Public Engagement, Villa Comunale, 1, 80121 Naples, Italy;
| | - Angela Cordella
- Genomix4Life S.r.l., Baronissi, 84081 Salerno, Italy; (A.C.); (G.M.V.)
- Genome Research Center for Health-CRGS, Baronissi, 84081 Salerno, Italy
| | | | - Valerio Zupo
- Stazione Zoologica Anton Dohrn, Department of Ecosustainable Marine Biotechnology, Ischia Marine Centre, 80121 Naples, Italy
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Drozdov A, Lebedev E, Adonin L. Comparative Analysis of Bivalve and Sea Urchin Genetics and Development: Investigating the Dichotomy in Bilateria. Int J Mol Sci 2023; 24:17163. [PMID: 38138992 PMCID: PMC10742642 DOI: 10.3390/ijms242417163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/19/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
This comprehensive review presents a comparative analysis of early embryogenesis in Protostomia and Deuterostomia, the first of which exhibit a mosaic pattern of development, where cells are fated deterministically, while Deuterostomia display a regulatory pattern of development, where the fate of cells is indeterminate. Despite these fundamental differences, there are common transcriptional mechanisms that underline their evolutionary linkages, particularly in the field of functional genomics. By elucidating both conserved and unique regulatory strategies, this review provides essential insights into the comparative embryology and developmental dynamics of these groups. The objective of this review is to clarify the shared and distinctive characteristics of transcriptional regulatory mechanisms. This will contribute to the extensive areas of functional genomics, evolutionary biology and developmental biology, and possibly lay the foundation for future research and discussion on this seminal topic.
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Affiliation(s)
- Anatoliy Drozdov
- Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Egor Lebedev
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia;
| | - Leonid Adonin
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia;
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
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Bronchain O, Ducos B, Putzer H, Delagrange M, Laalami S, Philippe-Caraty L, Saroul K, Ciapa B. Natural antisense transcription of presenilin in sea urchin reveals a possible role for natural antisense transcription in the general control of gene expression during development. J Cell Sci 2023; 136:jcs261284. [PMID: 37345489 DOI: 10.1242/jcs.261284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023] Open
Abstract
One presenilin gene (PSEN) is expressed in the sea urchin embryo, in the vegetal pole of the gastrula and then mainly in cilia cells located around the digestive system of the pluteus, as we recently have reported. PSEN expression must be accurately regulated for correct execution of these two steps of development. While investigating PSEN expression changes in embryos after expansion of endoderm with LiCl or of ectoderm with Zn2+ by whole-mount in situ hybridization (WISH) and quantitative PCR (qPCR), we detected natural antisense transcription of PSEN. We then found that Endo16 and Wnt5, markers of endo-mesoderm, and of Hnf6 and Gsc, markers of ectoderm, are also sense and antisense transcribed. We discuss that general gene expression could depend on both sense and antisense transcription. This mechanism, together with the PSEN gene, should be included in gene regulatory networks (GRNs) that theorize diverse processes in this species. We suggest that it would also be relevant to investigate natural antisense transcription of PSEN in the field of Alzheimer's disease (AD) where the role of human PSEN1 and PSEN2 is well known.
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Affiliation(s)
- Odile Bronchain
- Paris-Saclay Institute of Neuroscience, CNRS, UMR CNRS 9197, Université Paris-Saclay, 75005 Paris, France
| | - Bertrand Ducos
- High Throughput qPCR Core Facility of the ENS, Université PSL, IBENS, Laboratoire de Physique de l'Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France
| | - Harald Putzer
- CNRS, Université Paris Cité, Expression Génétique Microbienne, IBPC, 75005 Paris, France
| | - Marine Delagrange
- High Throughput qPCR Core Facility of the ENS, Université PSL, IBENS, Laboratoire de Physique de l'Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France
| | - Soumaya Laalami
- CNRS, Université Paris Cité, Expression Génétique Microbienne, IBPC, 75005 Paris, France
| | - Laetitia Philippe-Caraty
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Krystel Saroul
- Institut CURIE, Université Paris-Saclay, INSERM U932, Immunité et Cancer, 91400 Orsay, France
| | - Brigitte Ciapa
- Paris-Saclay Institute of Neuroscience, CNRS, UMR CNRS 9197, Université Paris-Saclay, 75005 Paris, France
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