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Shook EN, Barlow GT, Garcia-Rosales D, Gibbons CJ, Montague TG. Dynamic skin behaviors in cephalopods. Curr Opin Neurobiol 2024; 86:102876. [PMID: 38652980 DOI: 10.1016/j.conb.2024.102876] [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: 11/01/2023] [Revised: 03/11/2024] [Accepted: 03/23/2024] [Indexed: 04/25/2024]
Abstract
The coleoid cephalopods (cuttlefish, octopus, and squid) are a group of soft-bodied mollusks that exhibit a wealth of complex behaviors, including dynamic camouflage, object mimicry, skin-based visual communication, and dynamic body patterns during sleep. Many of these behaviors are visually driven and engage the animals' color changing skin, a pixelated display that is directly controlled by neurons projecting from the brain. Thus, cephalopod skin provides a direct readout of neural activity in the brain. During camouflage, cephalopods recreate on their skin an approximation of what they see, providing a window into perceptual processes in the brain. Additionally, cephalopods communicate their internal state during social encounters using innate skin patterns, and create waves of pigmentation on their skin during periods of arousal. Thus, by leveraging the visual displays of cephalopods, we can gain insight into how the external world is represented in the brain and how this representation is transformed into a recapitulation of the world on the skin. Here, we describe the rich skin behaviors of the coleoid cephalopods, what is known about cephalopod neuroanatomy, and how advancements in gene editing, machine learning, optical imaging, and electrophysiological tools may provide an opportunity to explore the neural bases of these fascinating behaviors.
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Affiliation(s)
- Erica N Shook
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - George Thomas Barlow
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Daniella Garcia-Rosales
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Connor J Gibbons
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Tessa G Montague
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA.
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2
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Hegarty BE, Gruenhagen GW, Johnson ZV, Baker CM, Streelman JT. Spatially resolved cell atlas of the teleost telencephalon and deep homology of the vertebrate forebrain. Commun Biol 2024; 7:612. [PMID: 38773256 PMCID: PMC11109250 DOI: 10.1038/s42003-024-06315-1] [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: 09/21/2023] [Accepted: 05/10/2024] [Indexed: 05/23/2024] Open
Abstract
The telencephalon has undergone remarkable diversification and expansion throughout vertebrate evolution, exhibiting striking variations in structural and functional complexity. Nevertheless, fundamental features are shared across vertebrate taxa, such as the presence of distinct regions including the pallium, subpallium, and olfactory structures. Teleost fishes have a uniquely "everted" telencephalon, which has confounded comparisons of their brain regions to other vertebrates. Here we combine spatial transcriptomics and single nucleus RNA-sequencing to generate a spatially-resolved transcriptional atlas of the Mchenga conophorus cichlid fish telencephalon. We then compare cell-types and anatomical regions in the cichlid telencephalon with those in amphibians, reptiles, birds, and mammals. We uncover striking transcriptional similarities between cell-types in the fish telencephalon and subpallial, hippocampal, and cortical cell-types in tetrapods, and find support for partial eversion of the teleost telencephalon. Ultimately, our work lends new insights into the organization and evolution of conserved cell-types and regions in the vertebrate forebrain.
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Affiliation(s)
- Brianna E Hegarty
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - George W Gruenhagen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| | - Zachary V Johnson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, 30329, USA
| | - Cristina M Baker
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jeffrey T Streelman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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3
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Goodheart JA, Rio RA, Taraporevala NF, Fiorenza RA, Barnes SR, Morrill K, Jacob MAC, Whitesel C, Masterson P, Batzel GO, Johnston HT, Ramirez MD, Katz PS, Lyons DC. A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes. BMC Biol 2024; 22:9. [PMID: 38233809 PMCID: PMC10795318 DOI: 10.1186/s12915-024-01814-3] [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: 08/07/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum have long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. RESULTS The final assembled and filtered Berghia genome is comparable to other high-quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes) and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. CONCLUSIONS Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.
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Affiliation(s)
- Jessica A Goodheart
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
| | - Robin A Rio
- Bioengineering Department, Stanford University, Stanford, CA, USA
| | - Neville F Taraporevala
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | - Rose A Fiorenza
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Seth R Barnes
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kevin Morrill
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mark Allan C Jacob
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Carl Whitesel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Park Masterson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Grant O Batzel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hereroa T Johnston
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - M Desmond Ramirez
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Paul S Katz
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Deirdre C Lyons
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
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4
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Rogers TF, Yalçın G, Briseno J, Vijayan N, Nyholm SV, Simakov O. Gene modelling and annotation for the Hawaiian bobtail squid, Euprymna scolopes. Sci Data 2024; 11:40. [PMID: 38184621 PMCID: PMC10771462 DOI: 10.1038/s41597-023-02903-8] [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: 08/15/2023] [Accepted: 12/28/2023] [Indexed: 01/08/2024] Open
Abstract
Coleoid cephalopods possess numerous complex, species-specific morphological and behavioural adaptations, e.g., a uniquely structured nervous system that is the largest among the invertebrates. The Hawaiian bobtail squid (Euprymna scolopes) is one of the most established cephalopod species. With its recent publication of the chromosomal-scale genome assembly and regulatory genomic data, it also emerges as a key model for cephalopod gene regulation and evolution. However, the latest genome assembly has been lacking a native gene model set. Our manuscript describes the generation of new long-read transcriptomic data and, made using this combined with a plethora of publicly available transcriptomic and protein sequence data, a new reference annotation for E. scolopes.
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Affiliation(s)
- Thea F Rogers
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria.
| | - Gözde Yalçın
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - John Briseno
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Nidhi Vijayan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Spencer V Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria
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5
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Baden T, Briseño J, Coffing G, Cohen-Bodénès S, Courtney A, Dickerson D, Dölen G, Fiorito G, Gestal C, Gustafson T, Heath-Heckman E, Hua Q, Imperadore P, Kimbara R, Król M, Lajbner Z, Lichilín N, Macchi F, McCoy MJ, Nishiguchi MK, Nyholm SV, Otjacques E, Pérez-Ferrer PA, Ponte G, Pungor JR, Rogers TF, Rosenthal JJC, Rouressol L, Rubas N, Sanchez G, Santos CP, Schultz DT, Seuntjens E, Songco-Casey JO, Stewart IE, Styfhals R, Tuanapaya S, Vijayan N, Weissenbacher A, Zifcakova L, Schulz G, Weertman W, Simakov O, Albertin CB. Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology. Integr Comp Biol 2023; 63:1226-1239. [PMID: 37370232 PMCID: PMC10755191 DOI: 10.1093/icb/icad087] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Few animal groups can claim the level of wonder that cephalopods instill in the minds of researchers and the general public. Much of cephalopod biology, however, remains unexplored: the largest invertebrate brain, difficult husbandry conditions, and complex (meta-)genomes, among many other things, have hindered progress in addressing key questions. However, recent technological advancements in sequencing, imaging, and genetic manipulation have opened new avenues for exploring the biology of these extraordinary animals. The cephalopod molecular biology community is thus experiencing a large influx of researchers, emerging from different fields, accelerating the pace of research in this clade. In the first post-pandemic event at the Cephalopod International Advisory Council (CIAC) conference in April 2022, over 40 participants from all over the world met and discussed key challenges and perspectives for current cephalopod molecular biology and evolution. Our particular focus was on the fields of comparative and regulatory genomics, gene manipulation, single-cell transcriptomics, metagenomics, and microbial interactions. This article is a result of this joint effort, summarizing the latest insights from these emerging fields, their bottlenecks, and potential solutions. The article highlights the interdisciplinary nature of the cephalopod-omics community and provides an emphasis on continuous consolidation of efforts and collaboration in this rapidly evolving field.
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Affiliation(s)
- Tom Baden
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - John Briseño
- Molecular and Cell Biology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Gabrielle Coffing
- Biology Department: Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| | - Sophie Cohen-Bodénès
- Laboratoire des Systèmes Perceptifs, Département d'Etudes Cognitives, Ecole Normale Supérieure, PSL University, CNRS, 75005 Paris, France
| | - Amy Courtney
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Dominick Dickerson
- Friday Harbor Laboratory, University of Washington, Seattle, WA 98250, USA
| | - Gül Dölen
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
| | - Camino Gestal
- Laboratory of Marine Molecular Pathobiology, Institute of Marine Research (IIM), Spanish National Research Council (CSIC), Vigo 36208, Spain
| | | | - Elizabeth Heath-Heckman
- Departments of Integrative Biology and Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Qiaz Hua
- Department of Ecology and Evolution, University of Adelaide, Adelaide, South Australia 5000, Australia
| | - Pamela Imperadore
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
| | - Ryosuke Kimbara
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Miura, Kanagawa 238-0225, Japan
| | - Mirela Król
- Adam Mickiewicz University in Poznań, Poznań 61-712, Poland
| | - Zdeněk Lajbner
- Physics and Biology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami District, Okinawa 904-0495, Japan
| | - Nicolás Lichilín
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Filippo Macchi
- Program in Biology, New York University Abu Dhabi, P.O. Box 129188 Abu Dhabi, United Arab Emirates
| | - Matthew J McCoy
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Michele K Nishiguchi
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, 5200 N. Lake Blvd., Merced, CA 95343, USA
| | - Spencer V Nyholm
- Molecular and Cell Biology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Eve Otjacques
- MARE—Marine and Environmental Sciences Centre & ARNET—Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Av. Nossa Senhora do Cabo, 939, 2750-374 Cascais, Portugal
- Division of Biosphere Sciences and Engineering, Carnegie Institution for Science, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Pedro Antonio Pérez-Ferrer
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, 5200 N. Lake Blvd., Merced, CA 95343, USA
| | - Giovanna Ponte
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
| | - Judit R Pungor
- Biology Department: Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| | - Thea F Rogers
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Joshua J C Rosenthal
- Marine Biological Laboratory, The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, MA 02543-1015, USA
| | - Lisa Rouressol
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Noelle Rubas
- Department of Molecular Biosciences and Bioengineering, University of Hawaii Manoa, Honolulu, HI 96822, USA
| | - Gustavo Sanchez
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Catarina Pereira Santos
- MARE—Marine and Environmental Sciences Centre & ARNET—Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Av. Nossa Senhora do Cabo, 939, 2750-374 Cascais, Portugal
| | - Darrin T Schultz
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Jeremea O Songco-Casey
- Biology Department: Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| | - Ian Erik Stewart
- Neural Circuits and Behaviour Lab, Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin 13125, Germany
| | - Ruth Styfhals
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Surangkana Tuanapaya
- Laboratory of genetics and applied breeding of molluscs, Fisheries College, Ocean University of China, Qingdao 266100, China
| | - Nidhi Vijayan
- Molecular and Cell Biology Department, University of Connecticut, Storrs, CT 06269, USA
| | | | - Lucia Zifcakova
- Physics and Biology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami District, Okinawa 904-0495, Japan
| | | | - Willem Weertman
- Friday Harbor Laboratory, University of Washington, Seattle, WA 98250, USA
| | - Oleg Simakov
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Caroline B Albertin
- Marine Biological Laboratory, The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, MA 02543-1015, USA
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6
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Bump P, Lubeck L. Marine Invertebrates One Cell at A Time: Insights from Single-Cell Analysis. Integr Comp Biol 2023; 63:999-1009. [PMID: 37188638 PMCID: PMC10714908 DOI: 10.1093/icb/icad034] [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: 02/27/2023] [Revised: 04/25/2023] [Accepted: 05/05/2023] [Indexed: 05/17/2023] Open
Abstract
Over the past decade, single-cell RNA-sequencing (scRNA-seq) has made it possible to study the cellular diversity of a broad range of organisms. Technological advances in single-cell isolation and sequencing have expanded rapidly, allowing the transcriptomic profile of individual cells to be captured. As a result, there has been an explosion of cell type atlases created for many different marine invertebrate species from across the tree of life. Our focus in this review is to synthesize current literature on marine invertebrate scRNA-seq. Specifically, we provide perspectives on key insights from scRNA-seq studies, including descriptive studies of cell type composition, how cells respond in dynamic processes such as development and regeneration, and the evolution of new cell types. Despite these tremendous advances, there also lie several challenges ahead. We discuss the important considerations that are essential when making comparisons between experiments, or between datasets from different species. Finally, we address the future of single-cell analyses in marine invertebrates, including combining scRNA-seq data with other 'omics methods to get a fuller understanding of cellular complexities. The full diversity of cell types across marine invertebrates remains unknown and understanding this diversity and evolution will provide rich areas for future study.
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Affiliation(s)
- Paul Bump
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Lauren Lubeck
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
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7
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Destanović D, Schultz DT, Styfhals R, Cruz F, Gómez-Garrido J, Gut M, Gut I, Fiorito G, Simakov O, Alioto TS, Ponte G, Seuntjens E. A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797). G3 (BETHESDA, MD.) 2023; 13:jkad220. [PMID: 37850903 PMCID: PMC10700109 DOI: 10.1093/g3journal/jkad220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/18/2023] [Indexed: 10/19/2023]
Abstract
Cephalopods are emerging animal models and include iconic species for studying the link between genomic innovations and physiological and behavioral complexities. Coleoid cephalopods possess the largest nervous system among invertebrates, both for cell counts and brain-to-body ratio. Octopus vulgaris has been at the center of a long-standing tradition of research into diverse aspects of cephalopod biology, including behavioral and neural plasticity, learning and memory recall, regeneration, and sophisticated cognition. However, no chromosome-scale genome assembly was available for O. vulgaris to aid in functional studies. To fill this gap, we sequenced and assembled a chromosome-scale genome of the common octopus, O. vulgaris. The final assembly spans 2.8 billion basepairs, 99.34% of which are in 30 chromosome-scale scaffolds. Hi-C heatmaps support a karyotype of 1n = 30 chromosomes. Comparisons with other octopus species' genomes show a conserved octopus karyotype and a pattern of local genome rearrangements between species. This new chromosome-scale genome of O. vulgaris will further facilitate research in all aspects of cephalopod biology, including various forms of plasticity and the neural machinery underlying sophisticated cognition, as well as an understanding of cephalopod evolution.
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Affiliation(s)
- Dalila Destanović
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1030, Austria
| | - Darrin T Schultz
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1030, Austria
| | - Ruth Styfhals
- Department of Biology, Lab of Developmental Neurobiology, Animal Physiology and Neurobiology Division, KU Leuven, Leuven 3000, Belgium
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples 80121, Italy
| | - Fernando Cruz
- Centro Nacional de Análisis Genómico (CNAG), Barcelona 08028, Spain
| | | | - Marta Gut
- Centro Nacional de Análisis Genómico (CNAG), Barcelona 08028, Spain
| | - Ivo Gut
- Centro Nacional de Análisis Genómico (CNAG), Barcelona 08028, Spain
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples 80121, Italy
| | - Oleg Simakov
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1030, Austria
| | - Tyler S Alioto
- Centro Nacional de Análisis Genómico (CNAG), Barcelona 08028, Spain
| | - Giovanna Ponte
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples 80121, Italy
| | - Eve Seuntjens
- Department of Biology, Lab of Developmental Neurobiology, Animal Physiology and Neurobiology Division, KU Leuven, Leuven 3000, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven 3000, Belgium
- Leuven Brain Institute, KU Leuven, Leuven 3000, Belgium
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8
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Valamparamban GF, Spéder P. Homemade: building the structure of the neurogenic niche. Front Cell Dev Biol 2023; 11:1275963. [PMID: 38107074 PMCID: PMC10722289 DOI: 10.3389/fcell.2023.1275963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023] Open
Abstract
Neural stem/progenitor cells live in an intricate cellular environment, the neurogenic niche, which supports their function and enables neurogenesis. The niche is made of a diversity of cell types, including neurons, glia and the vasculature, which are able to signal to and are structurally organised around neural stem/progenitor cells. While the focus has been on how individual cell types signal to and influence the behaviour of neural stem/progenitor cells, very little is actually known on how the niche is assembled during development from multiple cellular origins, and on the role of the resulting topology on these cells. This review proposes to draw a state-of-the art picture of this emerging field of research, with the aim to expose our knowledge on niche architecture and formation from different animal models (mouse, zebrafish and fruit fly). We will span its multiple aspects, from the existence and importance of local, adhesive interactions to the potential emergence of larger-scale topological properties through the careful assembly of diverse cellular and acellular components.
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Affiliation(s)
| | - Pauline Spéder
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Structure and Signals in the Neurogenic Niche, Paris, France
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9
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Liao IJY, Lu TM, Chen ME, Luo YJ. Spiralian genomics and the evolution of animal genome architecture. Brief Funct Genomics 2023; 22:498-508. [PMID: 37507111 DOI: 10.1093/bfgp/elad029] [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: 05/05/2023] [Revised: 06/27/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Recent developments in sequencing technologies have greatly improved our knowledge of phylogenetic relationships and genomic architectures throughout the tree of life. Spiralia, a diverse clade within Protostomia, is essential for understanding the evolutionary history of parasitism, gene conversion, nervous systems and animal body plans. In this review, we focus on the current hypotheses of spiralian phylogeny and investigate the impact of long-read sequencing on the quality of genome assemblies. We examine chromosome-level assemblies to highlight key genomic features that have driven spiralian evolution, including karyotype, synteny and the Hox gene organization. In addition, we show how chromosome rearrangement has influenced spiralian genomic structures. Although spiralian genomes have undergone substantial changes, they exhibit both conserved and lineage-specific features. We recommend increasing sequencing efforts and expanding functional genomics research to deepen insights into spiralian biology.
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10
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Piovani L, Marlétaz F. Single-cell transcriptomics refuels the exploration of spiralian biology. Brief Funct Genomics 2023; 22:517-524. [PMID: 37609674 PMCID: PMC10658179 DOI: 10.1093/bfgp/elad038] [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: 06/05/2023] [Revised: 07/31/2023] [Accepted: 08/08/2023] [Indexed: 08/24/2023] Open
Abstract
Spiralians represent the least studied superclade of bilaterian animals, despite exhibiting the widest diversity of organisms. Although spiralians include iconic organisms, such as octopus, earthworms and clams, a lot remains to be discovered regarding their phylogeny and biology. Here, we review recent attempts to apply single-cell transcriptomics, a new pioneering technology enabling the classification of cell types and the characterisation of their gene expression profiles, to several spiralian taxa. We discuss the methodological challenges and requirements for applying this approach to marine organisms and explore the insights that can be brought by such studies, both from a biomedical and evolutionary perspective. For instance, we show that single-cell sequencing might help solve the riddle of the homology of larval forms across spiralians, but also to better characterise and compare the processes of regeneration across taxa. We highlight the capacity of single-cell to investigate the origin of evolutionary novelties, as the mollusc shell or the cephalopod visual system, but also to interrogate the conservation of the molecular fingerprint of cell types at long evolutionary distances. We hope that single-cell sequencing will open a new window in understanding the biology of spiralians, and help renew the interest for these overlooked but captivating organisms.
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Affiliation(s)
- Laura Piovani
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution & Environment, University College London, Gower Street, London, UK
| | - Ferdinand Marlétaz
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution & Environment, University College London, Gower Street, London, UK
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11
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Voss G, Rosenthal JJC. High-level RNA editing diversifies the coleoid cephalopod brain proteome. Brief Funct Genomics 2023; 22:525-532. [PMID: 37981860 DOI: 10.1093/bfgp/elad034] [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: 06/11/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 11/21/2023] Open
Abstract
Coleoid cephalopods (octopus, squid and cuttlefish) have unusually complex nervous systems. The coleoid nervous system is also the only one currently known to recode the majority of expressed proteins through A-to-I RNA editing. The deamination of adenosine by adenosine deaminase acting on RNA (ADAR) enzymes produces inosine, which is interpreted as guanosine during translation. If this occurs in an open reading frame, which is the case for tens of thousands of editing sites in coleoids, it can recode the encoded protein. Here, we describe recent findings aimed at deciphering the mechanisms underlying high-level recoding and its adaptive potential. We describe the complement of ADAR enzymes in cephalopods, including a recently discovered novel domain in sqADAR1. We further summarize current evidence supporting an adaptive role of high-level RNA recoding in coleoids, and review recent studies showing that a large proportion of recoding sites is temperature-sensitive. Despite these new findings, the mechanisms governing the high level of RNA recoding in coleoid cephalopods remain poorly understood. Recent advances using genome editing in squid may provide useful tools to further study A-to-I RNA editing in these animals.
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Affiliation(s)
- Gjendine Voss
- The Eugene Bell Center, The Marine Biological Laboratory, 7 MBL Street, Woods Hole MA 02543, United States
| | - Joshua J C Rosenthal
- The Eugene Bell Center, The Marine Biological Laboratory, 7 MBL Street, Woods Hole MA 02543, United States
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12
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Goodheart JA, Rio RA, Taraporevala NF, Fiorenza RA, Barnes SR, Morrill K, Jacob MAC, Whitesel C, Masterson P, Batzel GO, Johnston HT, Ramirez MD, Katz PS, Lyons DC. A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552006. [PMID: 38014205 PMCID: PMC10680569 DOI: 10.1101/2023.08.04.552006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum has long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. The final assembled and filtered Berghia genome is comparable to other high quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes), and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.
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Affiliation(s)
- Jessica A. Goodheart
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Robin A. Rio
- Bioengineering Department, Stanford University, Stanford, CA, USA
| | - Neville F. Taraporevala
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | - Rose A. Fiorenza
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Seth R. Barnes
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kevin Morrill
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mark Allan C. Jacob
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Carl Whitesel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Park Masterson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Grant O. Batzel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hereroa T. Johnston
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - M. Desmond Ramirez
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Paul S. Katz
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Deirdre C. Lyons
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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13
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Pungor JR, Niell CM. The neural basis of visual processing and behavior in cephalopods. Curr Biol 2023; 33:R1106-R1118. [PMID: 37875093 PMCID: PMC10664291 DOI: 10.1016/j.cub.2023.08.093] [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] [Indexed: 10/26/2023]
Abstract
Coleoid cephalopods (octopuses, squids and cuttlefishes) are the only branch of the animal kingdom outside of vertebrates to have evolved both a large brain and camera-type eyes. They are highly dependent on vision, with the majority of their brain devoted to visual processing. Their excellent vision supports a range of advanced visually guided behaviors, from navigation and prey capture, to the ability to camouflage based on their surroundings. However, their brain organization is radically different from that of vertebrates, as well as other invertebrates, providing a unique opportunity to explore how a novel neural architecture for vision is organized and functions. Relatively few studies have examined the cephalopod visual system using current neuroscience approaches, to the extent that there has not even been a measurement of single-cell receptive fields in their central visual system. Therefore, there remains a tremendous amount that is unknown about the neural basis of vision in these extraordinary animals. Here, we review the existing knowledge of the organization and function of the cephalopod visual system to provide a framework for examining the neural circuits and computational mechanisms mediating their remarkable visual capabilities.
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Affiliation(s)
- Judit R Pungor
- Department of Biology and Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Cristopher M Niell
- Department of Biology and Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
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14
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Barrera Grijalba CC, Rodríguez Monje SV, Gestal C, Wollesen T. Octopod Hox genes and cephalopod plesiomorphies. Sci Rep 2023; 13:15492. [PMID: 37726311 PMCID: PMC10509229 DOI: 10.1038/s41598-023-42435-0] [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: 06/30/2023] [Accepted: 09/10/2023] [Indexed: 09/21/2023] Open
Abstract
Few other invertebrates captivate our attention as cephalopods do. Octopods, cuttlefish, and squids amaze with their behavior and sophisticated body plans that belong to the most intriguing among mollusks. Little is, however, known about their body plan formation and the role of Hox genes. The latter homeobox genes pattern the anterior-posterior body axis and have only been studied in a single decapod species so far. Here, we study developmental Hox and ParaHox gene expression in Octopus vulgaris. Hox genes are expressed in a near-to-staggered fashion, among others in homologous organs of cephalopods such as the stellate ganglia, the arms, or funnel. As in other mollusks Hox1 is expressed in the nascent octopod shell rudiment. While ParaHox genes are expressed in an evolutionarily conserved fashion, Hox genes are also expressed in some body regions that are considered homologous among mollusks such as the cephalopod arms and funnel with the molluscan foot. We argue that cephalopod Hox genes are recruited to a lesser extent into the formation of non-related organ systems than previously thought and emphasize that despite all morphological innovations molecular data still reveal the ancestral molluscan heritage of cephalopods.
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Affiliation(s)
| | - Sonia Victoria Rodríguez Monje
- Department of Evolutionary Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Camino Gestal
- Institute of Marine Research (IIM-CSIC), Eduardo Cabello 6, 36208, Vigo, Spain
| | - Tim Wollesen
- Department of Evolutionary Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
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15
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Rauniyar K, Bokharaie H, Jeltsch M. Expansion and collapse of VEGF diversity in major clades of the animal kingdom. Angiogenesis 2023; 26:437-461. [PMID: 37017884 PMCID: PMC10328876 DOI: 10.1007/s10456-023-09874-9] [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: 01/20/2023] [Accepted: 03/17/2023] [Indexed: 04/06/2023]
Abstract
Together with the platelet-derived growth factors (PDGFs), the vascular endothelial growth factors (VEGFs) form the PDGF/VEGF subgroup among cystine knot growth factors. The evolutionary relationships within this subgroup have not been examined thoroughly to date. Here, we comprehensively analyze the PDGF/VEGF growth factors throughout all animal phyla and propose a phylogenetic tree. Vertebrate whole-genome duplications play a role in expanding PDGF/VEGF diversity, but several limited duplications are necessary to account for the temporal pattern of emergence. The phylogenetically oldest PDGF/VEGF-like growth factor likely featured a C-terminus with a BR3P signature, a hallmark of the modern-day lymphangiogenic growth factors VEGF-C and VEGF-D. Some younger VEGF genes, such as VEGFB and PGF, appeared completely absent in important vertebrate clades such as birds and amphibia, respectively. In contrast, individual PDGF/VEGF gene duplications frequently occurred in fish on top of the known fish-specific whole-genome duplications. The lack of precise counterparts for human genes poses limitations but also offers opportunities for research using organisms that diverge considerably from humans. Sources for the graphical abstract: 326 MYA and older [1]; 72-240 MYA [2]; 235-65 MYA [3].
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Affiliation(s)
- Khushbu Rauniyar
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Biocenter 2, (Viikinkaari 5E), P.O. Box. 56, 00790, Helsinki, Finland
| | - Honey Bokharaie
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Biocenter 2, (Viikinkaari 5E), P.O. Box. 56, 00790, Helsinki, Finland
| | - Michael Jeltsch
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Biocenter 2, (Viikinkaari 5E), P.O. Box. 56, 00790, Helsinki, Finland.
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Wihuri Research Institute, Helsinki, Finland.
- Helsinki One Health, University of Helsinki, Helsinki, Finland.
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16
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Hegarty BE, Gruenhagen GW, Johnson ZV, Baker CM, Streelman JT. Spatially resolved cell atlas of the teleost telencephalon and deep homology of the vertebrate forebrain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.20.549873. [PMID: 37503039 PMCID: PMC10370212 DOI: 10.1101/2023.07.20.549873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The telencephalon has undergone remarkable diversification and expansion throughout vertebrate evolution, exhibiting striking differences in structural and functional complexity. Nevertheless, fundamental features are shared across vertebrate taxa, such as the presence of distinct regions including the pallium, subpallium, and olfactory structures. Teleost fishes have a uniquely 'everted' telencephalon, which has made it challenging to compare brain regions in fish to those in other vertebrates. Here we combine spatial transcriptomics and single-nucleus RNA-sequencing to generate a spatially-resolved transcriptional atlas of the cichlid fish telencephalon. We then compare cell-types and anatomical regions in the cichlid telencephalon with those in amphibians, reptiles, birds, and mammals. We uncover striking transcriptional similarities between cell populations in the fish telencephalon and subpallial, hippocampal, and cortical cell populations in tetrapods. Ultimately, our work lends new insights into the organization and evolution of conserved cell-types and regions in the vertebrate forebrain.
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Affiliation(s)
- Brianna E Hegarty
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332
| | - George W Gruenhagen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332
| | - Zachary V Johnson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329
- Department of Psychiatry & Behavioral Sciences, Emory University, Atlanta, GA 30329
| | - Cristina M Baker
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jeffrey T Streelman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332
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17
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Pungor JR, Allen VA, Songco-Casey JO, Niell CM. Functional organization of visual responses in the octopus optic lobe. Curr Biol 2023; 33:2784-2793.e3. [PMID: 37343556 PMCID: PMC11056276 DOI: 10.1016/j.cub.2023.05.069] [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: 02/23/2023] [Revised: 04/24/2023] [Accepted: 05/30/2023] [Indexed: 06/23/2023]
Abstract
Cephalopods are highly visual animals with camera-type eyes, large brains, and a rich repertoire of visually guided behaviors. However, the cephalopod brain evolved independently from those of other highly visual species, such as vertebrates; therefore, the neural circuits that process sensory information are profoundly different. It is largely unknown how their powerful but unique visual system functions, as there have been no direct neural measurements of visual responses in the cephalopod brain. In this study, we used two-photon calcium imaging to record visually evoked responses in the primary visual processing center of the octopus central brain, the optic lobe, to determine how basic features of the visual scene are represented and organized. We found spatially localized receptive fields for light (ON) and dark (OFF) stimuli, which were retinotopically organized across the optic lobe, demonstrating a hallmark of visual system organization shared across many species. An examination of these responses revealed transformations of the visual representation across the layers of the optic lobe, including the emergence of the OFF pathway and increased size selectivity. We also identified asymmetries in the spatial processing of ON and OFF stimuli, which suggest unique circuit mechanisms for form processing that may have evolved to suit the specific demands of processing an underwater visual scene. This study provides insight into the neural processing and functional organization of the octopus visual system, highlighting both shared and unique aspects, and lays a foundation for future studies of the neural circuits that mediate visual processing and behavior in cephalopods.
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Affiliation(s)
- Judit R Pungor
- Department of Biology and Institute of Neuroscience, University of Oregon, Eugene, OR 97405, USA.
| | - V Angelique Allen
- Department of Biology and Institute of Neuroscience, University of Oregon, Eugene, OR 97405, USA
| | - Jeremea O Songco-Casey
- Department of Biology and Institute of Neuroscience, University of Oregon, Eugene, OR 97405, USA
| | - Cristopher M Niell
- Department of Biology and Institute of Neuroscience, University of Oregon, Eugene, OR 97405, USA.
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18
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Montague TG, Rieth IJ, Gjerswold-Selleck S, Garcia-Rosales D, Aneja S, Elkis D, Zhu N, Kentis S, Rubino FA, Nemes A, Wang K, Hammond LA, Emiliano R, Ober RA, Guo J, Axel R. A brain atlas for the camouflaging dwarf cuttlefish, Sepia bandensis. Curr Biol 2023:S0960-9822(23)00757-1. [PMID: 37343557 DOI: 10.1016/j.cub.2023.06.007] [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: 04/11/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/23/2023]
Abstract
The coleoid cephalopods (cuttlefish, octopus, and squid) are a group of soft-bodied marine mollusks that exhibit an array of interesting biological phenomena, including dynamic camouflage, complex social behaviors, prehensile regenerating arms, and large brains capable of learning, memory, and problem-solving.1,2,3,4,5,6,7,8,9,10 The dwarf cuttlefish, Sepia bandensis, is a promising model cephalopod species due to its small size, substantial egg production, short generation time, and dynamic social and camouflage behaviors.11 Cuttlefish dynamically camouflage to their surroundings by changing the color, pattern, and texture of their skin. Camouflage is optically driven and is achieved by expanding and contracting hundreds of thousands of pigment-filled saccules (chromatophores) in the skin, which are controlled by motor neurons emanating from the brain. We generated a dwarf cuttlefish brain atlas using magnetic resonance imaging (MRI), deep learning, and histology, and we built an interactive web tool (https://www.cuttlebase.org/) to host the data. Guided by observations in other cephalopods,12,13,14,15,16,17,18,19,20 we identified 32 brain lobes, including two large optic lobes (75% the total volume of the brain), chromatophore lobes whose motor neurons directly innervate the chromatophores of the color-changing skin, and a vertical lobe that has been implicated in learning and memory. The brain largely conforms to the anatomy observed in other Sepia species and provides a valuable tool for exploring the neural basis of behavior in the experimentally facile dwarf cuttlefish.
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Affiliation(s)
- Tessa G Montague
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA.
| | - Isabelle J Rieth
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Sabrina Gjerswold-Selleck
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Daniella Garcia-Rosales
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Sukanya Aneja
- Interactive Telecommunications Program, New York University, New York, NY 10003, USA
| | - Dana Elkis
- Interactive Telecommunications Program, New York University, New York, NY 10003, USA
| | - Nanyan Zhu
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Sabrina Kentis
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Frederick A Rubino
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Adriana Nemes
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Katherine Wang
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Luke A Hammond
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Roselis Emiliano
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Rebecca A Ober
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Jia Guo
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Richard Axel
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA.
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19
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Ahuja N, Hwaun E, Pungor JR, Rafiq R, Nemes S, Sakmar T, Vogt MA, Grasse B, Diaz Quiroz J, Montague TG, Null RW, Dallis DN, Gavriouchkina D, Marletaz F, Abbo L, Rokhsar DS, Niell CM, Soltesz I, Albertin CB, Rosenthal JJC. Creation of an albino squid line by CRISPR-Cas9 and its application for in vivo functional imaging of neural activity. Curr Biol 2023:S0960-9822(23)00739-X. [PMID: 37343558 DOI: 10.1016/j.cub.2023.05.066] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/17/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023]
Abstract
Cephalopods are remarkable among invertebrates for their cognitive abilities, adaptive camouflage, novel structures, and propensity for recoding proteins through RNA editing. Due to the lack of genetically tractable cephalopod models, however, the mechanisms underlying these innovations are poorly understood. Genome editing tools such as CRISPR-Cas9 allow targeted mutations in diverse species to better link genes and function. One emerging cephalopod model, Euprymna berryi, produces large numbers of embryos that can be easily cultured throughout their life cycle and has a sequenced genome. As proof of principle, we used CRISPR-Cas9 in E. berryi to target the gene for tryptophan 2,3 dioxygenase (TDO), an enzyme required for the formation of ommochromes, the pigments present in the eyes and chromatophores of cephalopods. CRISPR-Cas9 ribonucleoproteins targeting tdo were injected into early embryos and then cultured to adulthood. Unexpectedly, the injected specimens were pigmented, despite verification of indels at the targeted sites by sequencing in injected animals (G0s). A homozygote knockout line for TDO, bred through multiple generations, was also pigmented. Surprisingly, a gene encoding indoleamine 2,3, dioxygenase (IDO), an enzyme that catalyzes the same reaction as TDO in vertebrates, was also present in E. berryi. Double knockouts of both tdo and ido with CRISPR-Cas9 produced an albino phenotype. We demonstrate the utility of these albinos for in vivo imaging of Ca2+ signaling in the brain using two-photon microscopy. These data show the feasibility of making gene knockout cephalopod lines that can be used for live imaging of neural activity in these behaviorally sophisticated organisms.
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Affiliation(s)
- Namrata Ahuja
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Ernie Hwaun
- Department of Neurosurgery and Stanford Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Judit R Pungor
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Ruhina Rafiq
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Sal Nemes
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Taylor Sakmar
- Marine Resources Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Miranda A Vogt
- Marine Resources Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Bret Grasse
- Marine Resources Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Juan Diaz Quiroz
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Tessa G Montague
- Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Ryan W Null
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Danielle N Dallis
- Marine Resources Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Daria Gavriouchkina
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0412, Japan
| | - Ferdinand Marletaz
- Centre for Life's Origin & Evolution, Department of Ecology, Evolution & Environment, University College London, WC1E 6BT London, UK
| | - Lisa Abbo
- Marine Resources Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Daniel S Rokhsar
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0412, Japan; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Ivan Soltesz
- Department of Neurosurgery and Stanford Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Caroline B Albertin
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
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20
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Imperadore P, Cagnin S, Allegretti V, Millino C, Raffini F, Fiorito G, Ponte G. Transcriptome-wide selection and validation of a solid set of reference genes for gene expression studies in the cephalopod mollusk Octopus vulgaris. Front Mol Neurosci 2023; 16:1091305. [PMID: 37266373 PMCID: PMC10230085 DOI: 10.3389/fnmol.2023.1091305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 02/20/2023] [Indexed: 06/03/2023] Open
Abstract
Octopus vulgaris is a cephalopod mollusk and an active marine predator that has been at the center of a number of studies focused on the understanding of neural and biological plasticity. Studies on the machinery involved in e.g., learning and memory, regeneration, and neuromodulation are required to shed light on the conserved and/or unique mechanisms that these animals have evolved. Analysis of gene expression is one of the most essential means to expand our understanding of biological machinery, and the selection of an appropriate set of reference genes is the prerequisite for the quantitative real-time polymerase chain reaction (qRT-PCR). Here we selected 77 candidate reference genes (RGs) from a pool of stable and relatively high-expressed transcripts identified from the full-length transcriptome of O. vulgaris, and we evaluated their expression stabilities in different tissues through geNorm, NormFinder, Bestkeeper, Delta-CT method, and RefFinder. Although various algorithms provided different assemblages of the most stable reference genes for the different kinds of tissues tested here, a comprehensive ranking revealed RGs specific to the nervous system (Ov-RNF7 and Ov-RIOK2) and Ov-EIF2A and Ov-CUL1 across all considered tissues. Furthermore, we validated RGs by assessing the expression profiles of nine target genes (Ov-Naa15, Ov-Ltv1, Ov-CG9286, Ov-EIF3M, Ov-NOB1, Ov-CSDE1, Ov-Abi2, Ov-Homer2, and Ov-Snx20) in different areas of the octopus nervous system (gastric ganglion, as control). Our study allowed us to identify the most extensive set of stable reference genes currently available for the nervous system and appendages of adult O. vulgaris.
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Affiliation(s)
- Pamela Imperadore
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, Padova, Italy
- CIR-Myo Myology Center, University of Padova, Padova, Italy
| | - Vittoria Allegretti
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | | | - Francesca Raffini
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Giovanna Ponte
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
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21
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Como CN, Kim S, Siegenthaler J. Stuck on you: Meninges cellular crosstalk in development. Curr Opin Neurobiol 2023; 79:102676. [PMID: 36773497 PMCID: PMC10023464 DOI: 10.1016/j.conb.2023.102676] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 02/11/2023]
Abstract
The spatial and temporal development of the brain, overlying meninges (fibroblasts, vasculature and immune cells) and calvarium are highly coordinated. In particular, the timing of meningeal fibroblasts into molecularly distinct pia, arachnoid and dura subtypes coincides with key developmental events in the brain and calvarium. Further, the meninges are positioned to influence development of adjacent structures and do so via depositing basement membrane and producing molecular cues to regulate brain and calvarial development. Here, we review the current knowledge of how meninges development aligns with events in the brain and calvarium and meningeal fibroblast "crosstalk" with these structures. We summarize outstanding questions and how the use of non-mammalian models to study the meninges will substantially advance the field of meninges biology.
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Affiliation(s)
- Christina N Como
- Department of Pediatrics Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Neuroscience Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. https://twitter.com/ChristinaComo
| | - Sol Kim
- Department of Pediatrics Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Cell Biology, Stem Cells, and Development Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Julie Siegenthaler
- Department of Pediatrics Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Cell Biology, Stem Cells, and Development Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Neuroscience Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; University of Colorado, School of Medicine Department of Pediatrics 12800 East 19th Ave MS-8313 Aurora, CO 80045, USA.
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22
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Pungor JR, Allen VA, Songco-Casey JO, Niell CM. Functional organization of visual responses in the octopus optic lobe. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528734. [PMID: 36824726 PMCID: PMC9949128 DOI: 10.1101/2023.02.16.528734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Cephalopods are highly visual animals with camera-type eyes, large brains, and a rich repertoire of visually guided behaviors. However, the cephalopod brain evolved independently from that of other highly visual species, such as vertebrates, and therefore the neural circuits that process sensory information are profoundly different. It is largely unknown how their powerful but unique visual system functions, since there have been no direct neural measurements of visual responses in the cephalopod brain. In this study, we used two-photon calcium imaging to record visually evoked responses in the primary visual processing center of the octopus central brain, the optic lobe, to determine how basic features of the visual scene are represented and organized. We found spatially localized receptive fields for light (ON) and dark (OFF) stimuli, which were retinotopically organized across the optic lobe, demonstrating a hallmark of visual system organization shared across many species. Examination of these responses revealed transformations of the visual representation across the layers of the optic lobe, including the emergence of the OFF pathway and increased size selectivity. We also identified asymmetries in the spatial processing of ON and OFF stimuli, which suggest unique circuit mechanisms for form processing that may have evolved to suit the specific demands of processing an underwater visual scene. This study provides insight into the neural processing and functional organization of the octopus visual system, highlighting both shared and unique aspects, and lays a foundation for future studies of the neural circuits that mediate visual processing and behavior in cephalopods. Highlights The functional organization and visual response properties of the cephalopod visual system are largely unknownUsing calcium imaging, we performed mapping of visual responses in the octopus optic lobeVisual responses demonstrate localized ON and OFF receptive fields with retinotopic organizationON/OFF pathways and size selectivity emerge across layers of the optic lobe and have distinct properties relative to other species.
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Affiliation(s)
- Judit R Pungor
- Department of Biology and Institute of Neuroscience, University of Oregon, Eugene OR 97405
| | - V Angelique Allen
- Department of Biology and Institute of Neuroscience, University of Oregon, Eugene OR 97405
| | - Jeremea O Songco-Casey
- Department of Biology and Institute of Neuroscience, University of Oregon, Eugene OR 97405
| | - Cristopher M Niell
- Department of Biology and Institute of Neuroscience, University of Oregon, Eugene OR 97405
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23
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De Sio F, Imperadore P. Deciphering regeneration through non-model animals: A century of experiments on cephalopod mollusks and an outlook at the future. Front Cell Dev Biol 2023; 10:1072382. [PMID: 36699008 PMCID: PMC9868252 DOI: 10.3389/fcell.2022.1072382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
The advent of marine stations in the last quarter of the 19th Century has given biologists the possibility of observing and experimenting upon myriad marine organisms. Among them, cephalopod mollusks have attracted great attention from the onset, thanks to their remarkable adaptability to captivity and a great number of biologically unique features including a sophisticate behavioral repertoire, remarkable body patterning capacities under direct neural control and the complexity of nervous system rivalling vertebrates. Surprisingly, the capacity to regenerate tissues and complex structures, such as appendages, albeit been known for centuries, has been understudied over the decades. Here, we will first review the limited in number, but fundamental studies on the subject published between 1920 and 1970 and discuss what they added to our knowledge of regeneration as a biological phenomenon. We will also speculate on how these relate to their epistemic and disciplinary context, setting the base for the study of regeneration in the taxon. We will then frame the peripherality of cephalopods in regeneration studies in relation with their experimental accessibility, and in comparison, with established models, either simpler (such as planarians), or more promising in terms of translation (urodeles). Last, we will explore the potential and growing relevance of cephalopods as prospective models of regeneration today, in the light of the novel opportunities provided by technological and methodological advances, to reconsider old problems and explore new ones. The recent development of cutting-edge technologies made available for cephalopods, like genome editing, is allowing for a number of important findings and opening the way toward new promising avenues. The contribution offered by cephalopods will increase our knowledge on regenerative mechanisms through cross-species comparison and will lead to a better understanding of the complex cellular and molecular machinery involved, shedding a light on the common pathways but also on the novel strategies different taxa evolved to promote regeneration of tissues and organs. Through the dialogue between biological/experimental and historical/contextual perspectives, this article will stimulate a discussion around the changing relations between availability of animal models and their specificity, technical and methodological developments and scientific trends in contemporary biology and medicine.
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Affiliation(s)
- Fabio De Sio
- Heinrich Heine Universität, Institut für Geschichte, Theorie und Ethik der Medizin, Centre for Health and Society, Medizinische Fakultät, Düsseldorf, Germany,*Correspondence: Fabio De Sio, ; Pamela Imperadore, ,
| | - Pamela Imperadore
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy,Association for Cephalopod Research—CephRes, Napoli, Italy,*Correspondence: Fabio De Sio, ; Pamela Imperadore, ,
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24
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Duruz J, Sprecher M, Kaldun JC, Al-Soudy AS, Lischer HEL, van Geest G, Nicholson P, Bruggmann R, Sprecher SG. Molecular characterization of cell types in the squid Loligo vulgaris. eLife 2023; 12:80670. [PMID: 36594460 PMCID: PMC9839350 DOI: 10.7554/elife.80670] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023] Open
Abstract
Cephalopods are set apart from other mollusks by their advanced behavioral abilities and the complexity of their nervous systems. Because of the great evolutionary distance that separates vertebrates from cephalopods, it is evident that higher cognitive features have evolved separately in these clades despite the similarities that they share. Alongside their complex behavioral abilities, cephalopods have evolved specialized cells and tissues, such as the chromatophores for camouflage or suckers to grasp prey. Despite significant progress in genome and transcriptome sequencing, the molecular identities of cell types in cephalopods remain largely unknown. We here combine single-cell transcriptomics with in situ gene expression analysis to uncover cell type diversity in the European squid Loligo vulgaris. We describe cell types that are conserved with other phyla such as neurons, muscles, or connective tissues but also cephalopod-specific cells, such as chromatophores or sucker cells. Moreover, we investigate major components of the squid nervous system including progenitor and developing cells, differentiated cells of the brain and optic lobes, as well as sensory systems of the head. Our study provides a molecular assessment for conserved and novel cell types in cephalopods and a framework for mapping the nervous system of L. vulgaris.
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Affiliation(s)
- Jules Duruz
- Department of Biology, Institute of Zoology, University of FribourgFribourgSwitzerland
| | - Marta Sprecher
- Department of Biology, Institute of Zoology, University of FribourgFribourgSwitzerland
| | - Jenifer C Kaldun
- Department of Biology, Institute of Zoology, University of FribourgFribourgSwitzerland
| | - Al-Sayed Al-Soudy
- Department of Biology, Institute of Zoology, University of FribourgFribourgSwitzerland
| | - Heidi EL Lischer
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of BernBernSwitzerland
| | - Geert van Geest
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of BernBernSwitzerland
| | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of BernBernSwitzerland
| | - Simon G Sprecher
- Department of Biology, Institute of Zoology, University of FribourgFribourgSwitzerland
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25
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Jiang D, Liu Q, Sun J, Liu S, Fan G, Wang L, Zhang Y, Seim I, An S, Liu X, Li Q, Zheng X. The gold-ringed octopus (Amphioctopus fangsiao) genome and cerebral single-nucleus transcriptomes provide insights into the evolution of karyotype and neural novelties. BMC Biol 2022; 20:289. [PMID: 36575497 PMCID: PMC9795677 DOI: 10.1186/s12915-022-01500-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 12/08/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Coleoid cephalopods have distinctive neural and morphological characteristics compared to other invertebrates. Early studies reported massive genomic rearrangements occurred before the split of octopus and squid lineages (Proc Natl Acad Sci U S A 116:3030-5, 2019), which might be related to the neural innovations of their brain, yet the details remain elusive. Here we combine genomic and single-nucleus transcriptome analyses to investigate the octopod chromosome evolution and cerebral characteristics. RESULTS We present a chromosome-level genome assembly of a gold-ringed octopus, Amphioctopus fangsiao, and a single-nucleus transcriptome of its supra-esophageal brain. Chromosome-level synteny analyses estimate that the chromosomes of the ancestral octopods experienced multiple chromosome fission/fusion and loss/gain events by comparing with the nautilus genome as outgroup, and that a conserved genome organization was detected during the evolutionary process from the last common octopod ancestor to their descendants. Besides, protocadherin, GPCR, and C2H2 ZNF genes are thought to be highly related to the neural innovations in cephalopods (Nature 524:220-4, 2015), and the chromosome analyses pinpointed several collinear modes of these genes on the octopod chromosomes, such as the collinearity between PCDH and C2H2 ZNF, as well as between GPCR and C2H2 ZNF. Phylogenetic analyses show that the expansion of the octopod protocadherin genes is driven by a tandem-duplication mechanism on one single chromosome, including two separate expansions at 65 million years ago (Ma) and 8-14 Ma, respectively. Furthermore, we identify eight cell types (i.e., cholinergic and glutamatergic neurons) in the supra-esophageal brain of A. fangsiao, and the single-cell expression analyses reveal the co-expression of protocadherin and GPCR in specific neural cells, which may contribute to the neural development and signal transductions in the octopod brain. CONCLUSIONS The octopod genome analyses reveal the dynamic evolutionary history of octopod chromosomes and neural-related gene families. The single-nucleus transcriptomes of the supra-esophageal brain indicate their cellular heterogeneities and functional interactions with other tissues (i.e., gill), which provides a foundation for further octopod cerebral studies.
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Affiliation(s)
- Dianhang Jiang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Ocean University of China, Qingdao, 266003, China
- Institute of Evolution & Marine Biodiversity (IEMB), Qingdao, 266003, China
| | - Qun Liu
- BGI-QingDao, BGI-Shenzhen, Qingdao, 266555, China
| | - Jin Sun
- Institute of Evolution & Marine Biodiversity (IEMB), Qingdao, 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Ocean University of China, Qingdao, 266003, China
| | - Guangyi Fan
- BGI-QingDao, BGI-Shenzhen, Qingdao, 266555, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Lihua Wang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Ocean University of China, Qingdao, 266003, China
- Institute of Evolution & Marine Biodiversity (IEMB), Qingdao, 266003, China
| | - Yaolei Zhang
- BGI-QingDao, BGI-Shenzhen, Qingdao, 266555, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, 4000, Australia
| | - Shucai An
- The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xin Liu
- BGI-QingDao, BGI-Shenzhen, Qingdao, 266555, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Ocean University of China, Qingdao, 266003, China
| | - Xiaodong Zheng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution & Marine Biodiversity (IEMB), Qingdao, 266003, China.
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