Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology

Tom Baden¹, John Briseño², Gabrielle Coffing³, Sophie Cohen-Bodénès⁴, Amy Courtney⁵, Dominick Dickerson⁶, Gül Dölen⁷, Graziano Fiorito⁸, Camino Gestal⁹, Taryn Gustafson¹⁰, Elizabeth Heath-Heckman¹¹, Qiaz Hua¹², Pamela Imperadore⁸, Ryosuke Kimbara¹³, Mirela Król¹⁴, Zdeněk Lajbner¹⁵, Nicolás Lichilín¹⁶, Filippo Macchi¹⁷, Matthew J McCoy¹⁸, Michele K Nishiguchi¹⁹, Spencer V Nyholm², Eve Otjacques^{20

21}, Pedro Antonio Pérez-Ferrer¹⁹, Giovanna Ponte⁸, Judit R Pungor³, Thea F Rogers¹⁶, Joshua J C Rosenthal²², Lisa Rouressol¹⁶, Noelle Rubas²³, Gustavo Sanchez²⁴, Catarina Pereira Santos²⁰, Darrin T Schultz¹⁶, Eve Seuntjens²⁵, Jeremea O Songco-Casey³, Ian Erik Stewart²⁶, Ruth Styfhals²⁵, Surangkana Tuanapaya²⁷, Nidhi Vijayan², Anton Weissenbacher²⁸, Lucia Zifcakova¹⁵, Grace Schulz²⁹, Willem Weertman⁶, Oleg Simakov¹⁶, Caroline B Albertin²²

Affiliations

¹ School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK.
² Molecular and Cell Biology Department, University of Connecticut, Storrs, CT 06269, USA.
³ Biology Department: Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA.
⁴ Laboratoire des Systèmes Perceptifs, Département d'Etudes Cognitives, Ecole Normale Supérieure, PSL University, CNRS, 75005 Paris, France.
⁵ MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
⁶ Friday Harbor Laboratory, University of Washington, Seattle, WA 98250, USA.
⁷ Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21218, USA.
⁸ Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy.
⁹ Laboratory of Marine Molecular Pathobiology, Institute of Marine Research (IIM), Spanish National Research Council (CSIC), Vigo 36208, Spain.
¹⁰ University of Central Florida, Orlando, FL 32826, USA.
¹¹ Departments of Integrative Biology and Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
¹² Department of Ecology and Evolution, University of Adelaide, Adelaide, South Australia 5000, Australia.
¹³ Misaki Marine Biological Station, School of Science, The University of Tokyo, Miura, Kanagawa 238-0225, Japan.
¹⁴ Adam Mickiewicz University in Poznań, Poznań 61-712, Poland.
¹⁵ Physics and Biology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami District, Okinawa 904-0495, Japan.
¹⁶ Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria.
¹⁷ Program in Biology, New York University Abu Dhabi, P.O. Box 129188 Abu Dhabi, United Arab Emirates.
¹⁸ Department of Pathology, Stanford University, Stanford, CA 94305, USA.
¹⁹ Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, 5200 N. Lake Blvd., Merced, CA 95343, USA.
²⁰ 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.
²¹ Division of Biosphere Sciences and Engineering, Carnegie Institution for Science, 1200 E. California Blvd, Pasadena, CA 91125, USA.
²² Marine Biological Laboratory, The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, MA 02543-1015, USA.
²³ Department of Molecular Biosciences and Bioengineering, University of Hawaii Manoa, Honolulu, HI 96822, USA.
²⁴ Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
²⁵ Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven 3000, Belgium.
²⁶ Neural Circuits and Behaviour Lab, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin 13125, Germany.
²⁷ Laboratory of genetics and applied breeding of molluscs, Fisheries College, Ocean University of China, Qingdao 266100, China.
²⁸ Vienna Zoo, Maxingstraße 13b, 1130 Vienna, Austria.
²⁹ University of Chicago, Chicago, IL 60637, USA.

PMID: 37370232
PMCID: PMC10755191
DOI: 10.1093/icb/icad087

Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology

Tom Baden et al. Integr Comp Biol. 2023.

. 2023 Dec 29;63(6):1226-1239.

doi: 10.1093/icb/icad087.

Authors

Affiliations

¹ School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK.
² Molecular and Cell Biology Department, University of Connecticut, Storrs, CT 06269, USA.
³ Biology Department: Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA.
⁴ Laboratoire des Systèmes Perceptifs, Département d'Etudes Cognitives, Ecole Normale Supérieure, PSL University, CNRS, 75005 Paris, France.
⁵ MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
⁶ Friday Harbor Laboratory, University of Washington, Seattle, WA 98250, USA.
⁷ Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21218, USA.
⁸ Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy.
⁹ Laboratory of Marine Molecular Pathobiology, Institute of Marine Research (IIM), Spanish National Research Council (CSIC), Vigo 36208, Spain.
¹⁰ University of Central Florida, Orlando, FL 32826, USA.
¹¹ Departments of Integrative Biology and Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
¹² Department of Ecology and Evolution, University of Adelaide, Adelaide, South Australia 5000, Australia.
¹³ Misaki Marine Biological Station, School of Science, The University of Tokyo, Miura, Kanagawa 238-0225, Japan.
¹⁴ Adam Mickiewicz University in Poznań, Poznań 61-712, Poland.
¹⁵ Physics and Biology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami District, Okinawa 904-0495, Japan.
¹⁶ Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria.
¹⁷ Program in Biology, New York University Abu Dhabi, P.O. Box 129188 Abu Dhabi, United Arab Emirates.
¹⁸ Department of Pathology, Stanford University, Stanford, CA 94305, USA.
¹⁹ Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, 5200 N. Lake Blvd., Merced, CA 95343, USA.
²⁰ 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.
²¹ Division of Biosphere Sciences and Engineering, Carnegie Institution for Science, 1200 E. California Blvd, Pasadena, CA 91125, USA.
²² Marine Biological Laboratory, The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, MA 02543-1015, USA.
²³ Department of Molecular Biosciences and Bioengineering, University of Hawaii Manoa, Honolulu, HI 96822, USA.
²⁴ Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
²⁵ Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven 3000, Belgium.
²⁶ Neural Circuits and Behaviour Lab, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin 13125, Germany.
²⁷ Laboratory of genetics and applied breeding of molluscs, Fisheries College, Ocean University of China, Qingdao 266100, China.
²⁸ Vienna Zoo, Maxingstraße 13b, 1130 Vienna, Austria.
²⁹ University of Chicago, Chicago, IL 60637, USA.

PMID: 37370232
PMCID: PMC10755191
DOI: 10.1093/icb/icad087

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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Conflict of interest statement

The authors declare that there is no conflict of interest.

Figures

**Fig. 1**
Research questions addressable with emerging technologies for cephalopods. Numbers in brackets refer to the numbers assigned to the different types of cephalopods. (1) Bobtail squid, (2) Loliginid squid, (3) Cuttlefish, and (4) Octopus (Created with BioRender.com).

See this image and copyright information in PMC

References

1. Ahuja N, Hwaun E, Pungor JRet al. . 2023. Creation of an albino squid line by CRISPR-Cas9 and its application for in vivo functional imaging of neural activity. Curr Biol. S0960–9822: 00739–X..10.1016 - PubMed
1. Albertin CB, Bonnaud L, Brown CTet al. . 2012. Cephalopod genomics: a plan of strategies and organization. Stand Genom Sci. 7: 175–88. - PMC - PubMed
1. Albertin CB, Medina-Ruiz S, Mitros Tet al. . 2022. Genome and transcriptome mechanisms driving cephalopod evolution. Nat Commun. 13: 2427. - PMC - PubMed
1. Albertin CB, Simakov O, Mitros Tet al. . 2015. The octopus genome and the evolution of cephalopod neural and morphological novelties. Nature. 524: 220–4. - PMC - PubMed
1. Albertin CB, Simakov O. 2020. Cephalopod biology: at the intersection between genomic and organismal novelties. Annu Rev Anim Biosci. 8: 71–90. - PubMed

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Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology

Affiliations

Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Grants and funding

LinkOut - more resources

Full Text Sources

Miscellaneous