1
|
Olson CS, Schulz NG, Ragsdale CW. Neuronal segmentation in cephalopod arms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596333. [PMID: 38853825 PMCID: PMC11160704 DOI: 10.1101/2024.05.29.596333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The prehensile arms of the cephalopod are among these animals most remarkable features, but the neural circuitry governing arm and sucker movements remains largely unknown. We studied the neuronal organization of the adult axial nerve cord (ANC) of Octopus bimaculoides with molecular and cellular methods. The ANCs, which lie in the center of every arm, are the largest neuronal structures in the octopus, containing four times as many neurons as found in the central brain. In transverse cross section, the cell body layer (CBL) of the ANC wraps around its neuropil (NP) with little apparent segregation of sensory and motor neurons or nerve exits. Strikingly, when studied in longitudinal sections, the ANC is segmented. ANC neuronal cell bodies form columns separated by septa, with 15 segments overlying each pair of suckers. The segments underlie a modular organization to the ANC neuropil: neuronal cell bodies within each segment send the bulk of their processes directly into the adjoining neuropil, with some reaching the contralateral side. In addition, some nerve processes branch upon entering the NP, forming short-range projections to neighboring segments and mid-range projections to the ANC segments of adjoining suckers. The septa between the segments are employed as ANC nerve exits and as channels for ANC vasculature. Cellular analysis establishes that adjoining septa issue nerves with distinct fiber trajectories, which across two segments (or three septa) fully innervate the arm musculature. Sucker nerves also use the septa, setting up a nerve fiber "suckerotopy" in the sucker-side of the ANC. Comparative anatomy suggests a strong link between segmentation and flexible sucker-laden arms. In the squid Doryteuthis pealeii, the arms and the sucker-rich club of the tentacles have segments, but the sucker-poor stalk of the tentacles does not. The neural modules described here provide a new template for understanding the motor control of octopus soft tissues. In addition, this finding represents the first demonstration of nervous system segmentation in a mollusc.
Collapse
Affiliation(s)
- Cassady S. Olson
- Committee on Computational Neuroscience, The University of Chicago, Chicago, IL 60637
| | - Natalie Grace Schulz
- Committee on Development, Regeneration and Stem Cell Biology, The University of Chicago, Chicago, IL 60637
| | - Clifton W. Ragsdale
- Committee on Development, Regeneration and Stem Cell Biology, The University of Chicago, Chicago, IL 60637
- Department of Neurobiology, The University of Chicago, Chicago, IL 60637
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Yu H, Li Y, Han W, Bao L, Liu F, Ma Y, Pu Z, Zeng Q, Zhang L, Bao Z, Wang S. Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach. Nat Protoc 2024; 19:1623-1678. [PMID: 38514839 DOI: 10.1038/s41596-024-00966-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 12/20/2023] [Indexed: 03/23/2024]
Abstract
The forthcoming massive genome data generated by the Earth BioGenome Project will open up a new era of comparative genomics, for which genome synteny analysis provides an important framework. Profiling genome synteny represents an essential step in elucidating genome architecture, regulatory blocks/elements and their evolutionary history. Here we describe PanSyn, ( https://github.com/yhw320/PanSyn ), the most comprehensive and up-to-date genome synteny pipeline, providing step-by-step instructions and application examples to demonstrate its usage. PanSyn inherits both basic and advanced functions from existing popular tools, offering a user-friendly, highly customized approach for genome macrosynteny analysis and integrated pan-evolutionary and regulatory analysis of genome architecture, which are not yet available in public synteny software or tools. The advantages of PanSyn include: (i) advanced microsynteny analysis by functional profiling of microsynteny genes and associated regulatory elements; (ii) comprehensive macrosynteny analysis, including the inference of karyotype evolution from ancestors to extant species; and (iii) functional integration of microsynteny and macrosynteny for pan-evolutionary profiling of genome architecture and regulatory blocks, as well as integration with external functional genomics datasets from three- or four-dimensional genome and ENCODE projects. PanSyn requires basic knowledge of the Linux environment and Perl programming language and the ability to access a computer cluster, especially for large-scale genomic comparisons. Our protocol can be easily implemented by a competent graduate student or postdoc and takes several days to weeks to execute for dozens to hundreds of genomes. PanSyn provides yet the most comprehensive and powerful tool for integrated evolutionary and functional genomics.
Collapse
Affiliation(s)
- Hongwei Yu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuli Li
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
| | - Wentao Han
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lisui Bao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Fuyun Liu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuanting Ma
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhongqi Pu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lingling Zhang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
| | - Zhenmin Bao
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
- Laboratory for Marine Fisheries and Aquaculture, Laoshan Laboratory, Qingdao, China
| | - Shi Wang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
| |
Collapse
|
4
|
Schultz DT, Heath-Heckman EA, Winchell CJ, Kuo DH, Yu YS, Oberauer F, Kocot KM, Cho SJ, Simakov O, Weisblat DA. Acceleration of genome rearrangement in clitellate annelids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.12.593736. [PMID: 38798472 PMCID: PMC11118384 DOI: 10.1101/2024.05.12.593736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Comparisons of multiple metazoan genomes have revealed the existence of ancestral linkage groups (ALGs), genomic scaffolds sharing sets of orthologous genes that have been inherited from ancestral animals for hundreds of millions of years (Simakov et al. 2022; Schultz et al. 2023) These ALGs have persisted across major animal taxa including Cnidaria, Deuterostomia, Ecdysozoa and Spiralia. Notwithstanding this general trend of chromosome-scale conservation, ALGs have been obliterated by extensive genome rearrangements in certain groups, most notably including Clitellata (oligochaetes and leeches), a group of easily overlooked invertebrates that is of tremendous ecological, agricultural and economic importance (Charles 2019; Barrett 2016). To further investigate these rearrangements, we have undertaken a comparison of 12 clitellate genomes (including four newly sequenced species) and 11 outgroup representatives. We show that these rearrangements began at the base of the Clitellata (rather than progressing gradually throughout polychaete annelids), that the inter-chromosomal rearrangements continue in several clitellate lineages and that these events have substantially shaped the evolution of the otherwise highly conserved Hox cluster.
Collapse
Affiliation(s)
- Darrin T. Schultz
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Elizabeth A.C. Heath-Heckman
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Christopher J. Winchell
- Department of Molecular and Cell Biology, University of California, 385 Weill Hall, Berkeley, CA 94720-3200, USA
| | - Dian-Han Kuo
- Department of Life Science & Museum of Zoology, National Taiwan University, No. 1 Section 4 Roosevelt Rd., Taipei 10617, Taiwan
| | - Yun-sang Yu
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Fabian Oberauer
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Kevin M. Kocot
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
- Alabama Museum of Natural History, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Sung-Jin Cho
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - David A. Weisblat
- Department of Molecular and Cell Biology, University of California, 385 Weill Hall, Berkeley, CA 94720-3200, USA
| |
Collapse
|
5
|
Rangwala SH, Rudnev DV, Ananiev VV, Oh DH, Asztalos A, Benica B, Borodin EA, Bouk N, Evgeniev VI, Kodali VK, Lotov V, Mozes E, Omelchenko MV, Savkina S, Sukharnikov E, Virothaisakun J, Murphy TD, Pruitt KD, Schneider VA. The NCBI Comparative Genome Viewer (CGV) is an interactive visualization tool for the analysis of whole-genome eukaryotic alignments. PLoS Biol 2024; 22:e3002405. [PMID: 38713717 PMCID: PMC11101090 DOI: 10.1371/journal.pbio.3002405] [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: 10/12/2023] [Revised: 05/17/2024] [Accepted: 04/08/2024] [Indexed: 05/09/2024] Open
Abstract
We report a new visualization tool for analysis of whole-genome assembly-assembly alignments, the Comparative Genome Viewer (CGV) (https://ncbi.nlm.nih.gov/genome/cgv/). CGV visualizes pairwise same-species and cross-species alignments provided by National Center for Biotechnology Information (NCBI) using assembly alignment algorithms developed by us and others. Researchers can examine large structural differences spanning chromosomes, such as inversions or translocations. Users can also navigate to regions of interest, where they can detect and analyze smaller-scale deletions and rearrangements within specific chromosome or gene regions. RefSeq or user-provided gene annotation is displayed where available. CGV currently provides approximately 800 alignments from over 350 animal, plant, and fungal species. CGV and related NCBI viewers are undergoing active development to further meet needs of the research community in comparative genome visualization.
Collapse
Affiliation(s)
- Sanjida H. Rangwala
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Dmitry V. Rudnev
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Victor V. Ananiev
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Dong-Ha Oh
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Andrea Asztalos
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Barrett Benica
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Evgeny A. Borodin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Nathan Bouk
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Vladislav I. Evgeniev
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Vamsi K. Kodali
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Vadim Lotov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Eyal Mozes
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Marina V. Omelchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Sofya Savkina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Ekaterina Sukharnikov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Joël Virothaisakun
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Terence D. Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Kim D. Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Valerie A. Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| |
Collapse
|
6
|
Baverstock K. Responses to commentaries on "The gene: An appraisal". PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 188:31-42. [PMID: 38360273 DOI: 10.1016/j.pbiomolbio.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 02/02/2024] [Indexed: 02/17/2024]
Abstract
The central conclusions of "The Gene: An Appraisal" are that genetic variance does not underpin biological evolution, and, therefore, that genes are not Mendel's units of inheritance. In this response, I will address the criticisms I have received via commentaries on that paper by defending the following statements: 1. Epistasis does not explain the power-law fitness profile of the Long-Term Evolution Experiment (LTEE). The data from the evolution of natural systems displays the power-law form ubiquitously. Epistasis plays no role in evolution. 2. The common characteristics of living things (natural systems) are described by the principle of least action in de Maupertuis's original form, which is synonymous with the 2nd law of thermodynamics and Newton's 2nd law of motion in its complete form, i.e., F = dp/dt. Organisms strive to achieve free energy balance with their environments. 3. Based on an appraisal of the scientific environment between 1880 and 1911, I conclude that Johannsen's genotype conception was perhaps, the only option available to him. 4. The power-law fitness profile of the LTEE falsifies Fisher's Genetical Theory of Natural Selection, Johannsen's genotype conception, and the idea that 'Darwinian evolution' is an exception to the generic thermodynamic process of evolution in natural systems. 5. The use of the technique of genome-wide association to identify the causes and the likelihoods of inherited common diseases and behavioural traits is a 'wild goose chase' because genes are not the units of inheritance.
Collapse
Affiliation(s)
- Keith Baverstock
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio Campus, Kuopio, Finland.
| |
Collapse
|
7
|
Plessy C, Mansfield MJ, Bliznina A, Masunaga A, West C, Tan Y, Liu AW, Grašič J, Del Río Pisula MS, Sánchez-Serna G, Fabrega-Torrus M, Ferrández-Roldán A, Roncalli V, Navratilova P, Thompson EM, Onuma T, Nishida H, Cañestro C, Luscombe NM. Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species. Genome Res 2024; 34:426-440. [PMID: 38621828 PMCID: PMC11067885 DOI: 10.1101/gr.278295.123] [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: 07/19/2023] [Accepted: 02/28/2024] [Indexed: 04/17/2024]
Abstract
Genome structural variations within species are rare. How selective constraints preserve gene order and chromosome structure is a central question in evolutionary biology that remains unsolved. Our sequencing of several genomes of the appendicularian tunicate Oikopleura dioica around the globe reveals extreme genome scrambling caused by thousands of chromosomal rearrangements, although showing no obvious morphological differences between these animals. The breakpoint accumulation rate is an order of magnitude higher than in ascidian tunicates, nematodes, Drosophila, or mammals. Chromosome arms and sex-specific regions appear to be the primary unit of macrosynteny conservation. At the microsyntenic level, scrambling did not preserve operon structures, suggesting an absence of selective pressure to maintain them. The uncoupling of the genome scrambling with morphological conservation in O. dioica suggests the presence of previously unnoticed cryptic species and provides a new biological system that challenges our previous vision of speciation in which similar animals always share similar genome structures.
Collapse
Affiliation(s)
- Charles Plessy
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan;
| | - Michael J Mansfield
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Aleksandra Bliznina
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Aki Masunaga
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Charlotte West
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Yongkai Tan
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Andrew W Liu
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Jan Grašič
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - María Sara Del Río Pisula
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Gaspar Sánchez-Serna
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona 08028, Spain
| | - Marc Fabrega-Torrus
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona 08028, Spain
| | - Alfonso Ferrández-Roldán
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona 08028, Spain
| | - Vittoria Roncalli
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona 08028, Spain
| | - Pavla Navratilova
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, 779 00 Olomouc, Czech Republic
- Sars International Centre, University of Bergen, Bergen N-5008, Norway
| | - Eric M Thompson
- Sars International Centre, University of Bergen, Bergen N-5008, Norway
- Department of Biological Sciences, University of Bergen, Bergen N-5020, Norway
| | - Takeshi Onuma
- Faculty of Science, Kagoshima University, Kagoshima 890-0065, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Cristian Cañestro
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona 08028, Spain
| | - Nicholas M Luscombe
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| |
Collapse
|
8
|
McCoy MJ, Fire AZ. Parallel gene size and isoform expansion of ancient neuronal genes. Curr Biol 2024; 34:1635-1645.e3. [PMID: 38460513 PMCID: PMC11043017 DOI: 10.1016/j.cub.2024.02.021] [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: 08/22/2023] [Revised: 12/16/2023] [Accepted: 02/11/2024] [Indexed: 03/11/2024]
Abstract
How nervous systems evolved is a central question in biology. A diversity of synaptic proteins is thought to play a central role in the formation of specific synapses leading to nervous system complexity. The largest animal genes, often spanning hundreds of thousands of base pairs, are known to be enriched for expression in neurons at synapses and are frequently mutated or misregulated in neurological disorders and diseases. Although many of these genes have been studied independently in the context of nervous system evolution and disease, general principles underlying their parallel evolution remain unknown. To investigate this, we directly compared orthologous gene sizes across eukaryotes. By comparing relative gene sizes within organisms, we identified a distinct class of large genes with origins predating the diversification of animals and, in many cases, the emergence of neurons as dedicated cell types. We traced this class of ancient large genes through evolution and found orthologs of the large synaptic genes potentially driving the immense complexity of metazoan nervous systems, including in humans and cephalopods. Moreover, we found that while these genes are evolving under strong purifying selection, as demonstrated by low dN/dS ratios, they have simultaneously grown larger and gained the most isoforms in animals. This work provides a new lens through which to view this distinctive class of large and multi-isoform genes and demonstrates how intrinsic genomic properties, such as gene length, can provide flexibility in molecular evolution and allow groups of genes and their host organisms to evolve toward complexity.
Collapse
Affiliation(s)
- Matthew J McCoy
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA.
| | - Andrew Z Fire
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA.
| |
Collapse
|
9
|
Vijayan N, McAnulty SJ, Sanchez G, Jolly J, Ikeda Y, Nishiguchi MK, Réveillac E, Gestal C, Spady BL, Li DH, Burford BP, Kerwin AH, Nyholm SV. Evolutionary history influences the microbiomes of a female symbiotic reproductive organ in cephalopods. Appl Environ Microbiol 2024; 90:e0099023. [PMID: 38315021 PMCID: PMC10952459 DOI: 10.1128/aem.00990-23] [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: 06/14/2023] [Accepted: 12/09/2023] [Indexed: 02/07/2024] Open
Abstract
Many female squids and cuttlefishes have a symbiotic reproductive organ called the accessory nidamental gland (ANG) that hosts a bacterial consortium involved with egg defense against pathogens and fouling organisms. While the ANG is found in multiple cephalopod families, little is known about the global microbial diversity of these ANG bacterial symbionts. We used 16S rRNA gene community analysis to characterize the ANG microbiome from different cephalopod species and assess the relationship between host and symbiont phylogenies. The ANG microbiome of 11 species of cephalopods from four families (superorder: Decapodiformes) that span seven geographic locations was characterized. Bacteria of class Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia were found in all species, yet analysis of amplicon sequence variants by multiple distance metrics revealed a significant difference between ANG microbiomes of cephalopod families (weighted/unweighted UniFrac, Bray-Curtis, P = 0.001). Despite being collected from widely disparate geographic locations, members of the family Sepiolidae (bobtail squid) shared many bacterial taxa including (~50%) Opitutae (Verrucomicrobia) and Ruegeria (Alphaproteobacteria) species. Furthermore, we tested for phylosymbiosis and found a positive correlation between host phylogenetic distance and bacterial community dissimilarity (Mantel test r = 0.7). These data suggest that closely related sepiolids select for distinct symbionts from similar bacterial taxa. Overall, the ANGs of different cephalopod species harbor distinct microbiomes and thus offer a diverse symbiont community to explore antimicrobial activity and other functional roles in host fitness.IMPORTANCEMany aquatic organisms recruit microbial symbionts from the environment that provide a variety of functions, including defense from pathogens. Some female cephalopods (squids, bobtail squids, and cuttlefish) have a reproductive organ called the accessory nidamental gland (ANG) that contains a bacterial consortium that protects eggs from pathogens. Despite the wide distribution of these cephalopods, whether they share similar microbiomes is unknown. Here, we studied the microbial diversity of the ANG in 11 species of cephalopods distributed over a broad geographic range and representing 15-120 million years of host divergence. The ANG microbiomes shared some bacterial taxa, but each cephalopod species had unique symbiotic members. Additionally, analysis of host-symbiont phylogenies suggests that the evolutionary histories of the partners have been important in shaping the ANG microbiome. This study advances our knowledge of cephalopod-bacteria relationships and provides a foundation to explore defensive symbionts in other systems.
Collapse
Affiliation(s)
- Nidhi Vijayan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Sarah J. McAnulty
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Gustavo Sanchez
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
- Graduate School of Integrated Science for Life, Hiroshima University, Hiroshima, Japan
| | - Jeffrey Jolly
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
- Marine Climate Change Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Yuzuru Ikeda
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of Ryukyus, Ryukyus, Japan
| | - Michele K. Nishiguchi
- Department of Molecular and Cell Biology, University of California, Merced, California, USA
| | - Elodie Réveillac
- Littoral, Environnement et Sociétés (LIENSs), UMR 7266 CNRS–La Rochelle Université, La Rochelle, France
| | - Camino Gestal
- Institute of Marine Research (IIM), CSIC, Vigo, Spain
| | - Blake L. Spady
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- U.S. National Oceanic and Atmospheric Administration, National Environmental Satellite Data and Information Service, Center for Satellite Applications and Research, Coral Reef Watch, College Park, Maryland, USA
| | - Diana H. Li
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, New York, USA
| | - Benjamin P. Burford
- Institute of Marine Sciences, University of California, affiliated with the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Southwest Fisheries Science Center, Santa Cruz, California, USA
| | - Allison H. Kerwin
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Department of Biology, McDaniel College, Westminster, Maryland, USA
| | - Spencer V. Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| |
Collapse
|
10
|
Coffing GC, Tittes S, Small ST, Songco-Casey JO, Piscopo DM, Pungor JR, Miller AC, Niell CM, Kern AD. Cephalopod Sex Determination and its Ancient Evolutionary Origin Revealed by Chromosome-level Assembly of the California Two-Spot Octopus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.21.581452. [PMID: 38463997 PMCID: PMC10925132 DOI: 10.1101/2024.02.21.581452] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Sex chromosomes are critical elements of sexual reproduction in many animal and plant taxa, however they show incredible diversity and rapid turnover even within clades. Here, using a chromosome-level assembly generated with long read sequencing, we report the first evidence for genetic sex determination in cephalopods. We have uncovered a sex chromosome in California two-spot octopus (Octopus bimaculoides) in which males/females show ZZ/ZO karyotypes respectively. We show that the octopus Z chromosome is an evolutionary outlier with respect to divergence and repetitive element content as compared to other chromosomes and that it is present in all coleoid cephalopods that we have examined. Our results suggest that the cephalopod Z chromosome originated between 455 and 248 million years ago and has been conserved to the present, making it the among the oldest conserved animal sex chromosomes known.
Collapse
Affiliation(s)
- Gabrielle C. Coffing
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Silas Tittes
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Scott T. Small
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Jeremea O. Songco-Casey
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Denise M. Piscopo
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Judit R. Pungor
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Adam C. Miller
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Cristopher M. Niell
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Andrew D. Kern
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| |
Collapse
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Dissegna A, Borrelli L, Ponte G, Chiandetti C, Fiorito G. Octopus vulgaris Exhibits Interindividual Differences in Behavioural and Problem-Solving Performance. BIOLOGY 2023; 12:1487. [PMID: 38132313 PMCID: PMC10740590 DOI: 10.3390/biology12121487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 11/26/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
By presenting individual Octopus vulgaris with an extractive foraging problem with a puzzle box, we examined the possible correlation between behavioural performances (e.g., ease of adaptation to captive conditions, prevalence of neophobic and neophilic behaviours, and propensity to learn individually or by observing conspecifics), biotic (body and brain size, age, sex) and abiotic (seasonality and place of origin) factors. We found more neophilic animals showing shorter latencies to approach the puzzle box and higher probability of solving the task; also, shorter times to solve the task were correlated with better performance on the individual learning task. However, the most neophilic octopuses that approached the puzzle box more quickly did not reach the solution earlier than other individuals, suggesting that strong neophilic tendency may lead to suboptimal performance at some stages of the problem-solving process. In addition, seasonal and environmental characteristics of location of origin appear to influence the rate of expression of individual traits central to problem solving. Overall, our analysis provides new insights into the traits associated with problem solving in invertebrates and highlights the presence of adaptive mechanisms that promote population-level changes in octopuses' behavioural traits.
Collapse
Affiliation(s)
- Andrea Dissegna
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (A.D.); (C.C.)
| | - Luciana Borrelli
- Animal Physiology and Evolution Lab, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy;
| | - Giovanna Ponte
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy;
| | - Cinzia Chiandetti
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (A.D.); (C.C.)
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy;
| |
Collapse
|
16
|
Johansen M, Saenko S, Schilthuizen M, Blaxter M, Davison A. Fine mapping of the Cepaea nemoralis shell colour and mid-banded loci using a high-density linkage map. Heredity (Edinb) 2023; 131:327-337. [PMID: 37758900 PMCID: PMC10673960 DOI: 10.1038/s41437-023-00648-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
Molluscs are a highly speciose phylum that exhibits an astonishing array of colours and patterns, yet relatively little progress has been made in identifying the underlying genes that determine phenotypic variation. One prominent example is the land snail Cepaea nemoralis for which classical genetic studies have shown that around nine loci, several physically linked and inherited together as a 'supergene', control the shell colour and banding polymorphism. As a first step towards identifying the genes involved, we used whole-genome resequencing of individuals from a laboratory cross to construct a high-density linkage map, and then trait mapping to identify 95% confidence intervals for the chromosomal region that contains the supergene, specifically the colour locus (C), and the unlinked mid-banded locus (U). The linkage map is made up of 215,593 markers, ordered into 22 linkage groups, with one large group making up ~27% of the genome. The C locus was mapped to a ~1.3 cM region on linkage group 11, and the U locus was mapped to a ~0.7 cM region on linkage group 15. The linkage map will serve as an important resource for further evolutionary and population genomic studies of C. nemoralis and related species, as well as the identification of candidate genes within the supergene and for the mid-banding phenotype.
Collapse
Affiliation(s)
- Margrethe Johansen
- School of Life Sciences, University Park, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Suzanne Saenko
- Evolutionary Ecology, Naturalis Biodiversity Center, Leiden, 2333CR, The Netherlands
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden, 2333BE, The Netherlands
| | - Menno Schilthuizen
- Evolutionary Ecology, Naturalis Biodiversity Center, Leiden, 2333CR, The Netherlands
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden, 2333BE, The Netherlands
| | - Mark Blaxter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Angus Davison
- School of Life Sciences, University Park, University of Nottingham, Nottingham, NG7 2RD, UK
| |
Collapse
|
17
|
Yuasa HJ. Unusual Evolution of Cephalopod Tryptophan Indole-Lyases. J Mol Evol 2023; 91:912-921. [PMID: 38007709 DOI: 10.1007/s00239-023-10144-x] [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: 07/17/2023] [Accepted: 11/07/2023] [Indexed: 11/28/2023]
Abstract
Tryptophan indole-lyase (TIL), a pyridoxal-5-phosphate-dependent enzyme, catalyzes the hydrolysis of L-tryptophan (L-Trp) to indole and ammonium pyruvate. TIL is widely distributed among bacteria and bacterial TILs consist of a D2-symmetric homotetramer. On the other hand, TIL genes are also present in several metazoans. Cephalopods have two TILs, TILα and TILβ, which are believed to be derived from a gene duplication that occurred before octopus and squid diverged. However, both TILα and TILβ individually contain disruptive amino acid substitutions for TIL activity, and neither was active when expressed alone. When TILα and TILβ were coexpressed, however, they formed a heterotetramer that exhibited low TIL activity. The loss of TIL activity of the heterotetramer following site-directed mutagenesis strongly suggests that the active heterotetramer contains the TILα/TILβ heterodimer. Metazoan TILs generally have lower kcat values for L-Trp than those of bacterial TILs, but such low TIL activity may be rather suitable for metazoan physiology, where L-Trp is in high demand. Therefore, reduced activity may have been a less likely target for purifying selection in the evolution of cephalopod TILs. Meanwhile, the unusual evolution of cephalopod TILs may indicate the difficulty of post-gene duplication evolution of enzymes with catalytic sites contributed by multiple subunits, such as TIL.
Collapse
Affiliation(s)
- Hajime Julie Yuasa
- Laboratory of Biochemistry, Department of Chemistry and Biotechnology, Faculty of Science and Technology, National University Corporation Kochi University, Kochi, 780-8520, Japan.
| |
Collapse
|
18
|
Rangwala SH, Rudnev DV, Ananiev VV, Asztalos A, Benica B, Borodin EA, Bouk N, Evgeniev VI, Kodali VK, Lotov V, Mozes E, Oh DH, Omelchenko MV, Savkina S, Sukharnikov E, Virothaisakun J, Murphy TD, Pruitt KD, Schneider VA. Interactive visualization of whole eukaryote genome alignments using NCBI's Comparative Genome Viewer (CGV). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564672. [PMID: 38077029 PMCID: PMC10705539 DOI: 10.1101/2023.10.30.564672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
We report a new visualization tool for analysis of whole genome assembly-assembly alignments, the Comparative Genome Viewer (CGV) (https://ncbi.nlm.nih.gov/genome/cgv/). CGV visualizes pairwise same-species and cross-species alignments provided by NCBI using assembly alignment algorithms developed by us and others. Researchers can examine the alignments between the two assemblies using two alternate views: a chromosome ideogram-based view or a 2D genome dotplot. Whole genome alignment views expose large structural differences spanning chromosomes, such as inversions or translocations. Users can also navigate to regions of interest, where they can detect and analyze smaller-scale deletions and rearrangements within specific chromosome or gene regions. RefSeq or user-provided gene annotation is displayed in the ideogram view where available. CGV currently provides approximately 700 alignments from over 300 animal, plant, and fungal species. CGV and related NCBI viewers are undergoing active development to further meet needs of the research community in comparative genome visualization.
Collapse
Affiliation(s)
- Sanjida H Rangwala
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Dmitry V Rudnev
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Victor V Ananiev
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Andrea Asztalos
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Barrett Benica
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Evgeny A Borodin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Nathan Bouk
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Vladislav I Evgeniev
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Vamsi K Kodali
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Vadim Lotov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Eyal Mozes
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Dong-Ha Oh
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Marina V Omelchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Sofya Savkina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Ekaterina Sukharnikov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Joël Virothaisakun
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Terence D. Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Valerie A. Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA
| |
Collapse
|
19
|
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.
Collapse
|
20
|
Rogers TF, Simakov O. Emerging questions on the mechanisms and dynamics of 3D genome evolution in spiralians. Brief Funct Genomics 2023; 22:533-542. [PMID: 37815133 PMCID: PMC10658181 DOI: 10.1093/bfgp/elad043] [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: 04/29/2023] [Revised: 08/17/2023] [Accepted: 09/12/2023] [Indexed: 10/11/2023] Open
Abstract
Information on how 3D genome topology emerged in animal evolution, how stable it is during development, its role in the evolution of phenotypic novelties and how exactly it affects gene expression is highly debated. So far, data to address these questions are lacking with the exception of a few key model species. Several gene regulatory mechanisms have been proposed, including scenarios where genome topology has little to no impact on gene expression, and vice versa. The ancient and diverse clade of spiralians may provide a crucial testing ground for such mechanisms. Sprialians have followed distinct evolutionary trajectories, with some clades experiencing genome expansions and/or large-scale genome rearrangements, and others undergoing genome contraction, substantially impacting their size and organisation. These changes have been associated with many phenotypic innovations in this clade. In this review, we describe how emerging genome topology data, along with functional tools, allow for testing these scenarios and discuss their predicted outcomes.
Collapse
Affiliation(s)
- Thea F Rogers
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Montague TG. Neural control of cephalopod camouflage. Curr Biol 2023; 33:R1095-R1100. [PMID: 37875091 DOI: 10.1016/j.cub.2023.08.095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
In Die Another Day, James Bond receives an Aston Martin that can render itself invisible by dynamically reproducing the surroundings on the car's "polymer skin". In what is widely regarded as the worst Bond movie ever, the invisible car scene is cited as the moment the plot plunges into the truly absurd. But what if nature had actually invented such a technology, and did so hundreds of millions of years ago? The coleoid cephalopods - octopus, cuttlefish and squid - are living examples of dynamic camouflage. Their skin is covered with a high-resolution array of 'cellular pixels' (chromatophores) that are controlled by the brain. To disappear into their surroundings, cephalopods recreate an approximation of their environment on their skin by activating different combinations of colored chromatophores. However, unlike the fictional Bond car, whose surface is coated in tiny cameras to detect the environment, cephalopods don't see the world with their skin. Instead, the visual world is detected by the eyes, processed in the brain, and then used to activate motor commands that direct the skin's camouflage pattern. Thus, cephalopod skin patterns are an external manifestation of their internal perception of the world. How do cephalopods approximate the world with their skin? What can this teach us about how brains work? And which neurobiological tools will be needed to uncover the neural basis of camouflage?
Collapse
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.
| |
Collapse
|
23
|
Albertin CB, Katz PS. Evolution of cephalopod nervous systems. Curr Biol 2023; 33:R1087-R1091. [PMID: 37875089 PMCID: PMC10792511 DOI: 10.1016/j.cub.2023.08.092] [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
Giant brains have independently evolved twice on this planet, in vertebrates and in cephalopods (Figure 1A). Thus, the brains and nervous systems of cephalopods provide an important counterpoint to vertebrates in the search for generalities of brain organization and function. Their mere existence disproves various hypotheses proposed to explain the evolution of the mind and the human brain, such as cognition and large brains evolved only in long-lived animals with complex social systems and parental care, none of which is true of cephalopods. Therefore, it is worthwhile to review what is known about the evolution of cephalopod nervous systems to consider how it informs our understanding of general principles of brain evolution.
Collapse
Affiliation(s)
- Caroline B Albertin
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
| | - Paul S Katz
- Department of Biology, Neuroscience and Behavior Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA.
| |
Collapse
|
24
|
Song H, Wang Y, Shao H, Li Z, Hu P, Yap-Chiongco MK, Shi P, Zhang T, Li C, Wang Y, Ma P, Vinther J, Wang H, Kocot KM. Scaphopoda is the sister taxon to Bivalvia: Evidence of ancient incomplete lineage sorting. Proc Natl Acad Sci U S A 2023; 120:e2302361120. [PMID: 37738291 PMCID: PMC10556646 DOI: 10.1073/pnas.2302361120] [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: 02/13/2023] [Accepted: 08/18/2023] [Indexed: 09/24/2023] Open
Abstract
The almost simultaneous emergence of major animal phyla during the early Cambrian shaped modern animal biodiversity. Reconstructing evolutionary relationships among such closely spaced branches in the animal tree of life has proven to be a major challenge, hindering understanding of early animal evolution and the fossil record. This is particularly true in the species-rich and highly varied Mollusca where dramatic inconsistency among paleontological, morphological, and molecular evidence has led to a long-standing debate about the group's phylogeny and the nature of dozens of enigmatic fossil taxa. A critical step needed to overcome this issue is to supplement available genomic data, which is plentiful for well-studied lineages, with genomes from rare but key lineages, such as Scaphopoda. Here, by presenting chromosome-level genomes from both extant scaphopod orders and leveraging complete genomes spanning Mollusca, we provide strong support for Scaphopoda as the sister taxon of Bivalvia, revitalizing the morphology-based Diasoma hypothesis originally proposed 50 years ago. Our molecular clock analysis confidently dates the split between Bivalvia and Scaphopoda at ~520 Ma, prompting a reinterpretation of controversial laterally compressed Early Cambrian fossils, including Anabarella, Watsonella, and Mellopegma, as stem diasomes. Moreover, we show that incongruence in the phylogenetic placement of Scaphopoda in previous phylogenomic studies was due to ancient incomplete lineage sorting (ILS) that occurred during the rapid radiation of Conchifera. Our findings highlight the need to consider ILS as a potential source of error in deep phylogeny reconstruction, especially in the context of the unique nature of the Cambrian Explosion.
Collapse
Affiliation(s)
- Hao Song
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao266237, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Yunan Wang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Haojing Shao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Zhuoqing Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Pinli Hu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | | | - Pu Shi
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Tao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao266237, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Cui Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Yiguan Wang
- Institute of Ecology and Evolution, University of Edinburgh, EdinburghEH9 3FL, United Kingdom
| | - Peizhen Ma
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Jakob Vinther
- School of Biological Sciences, University of Bristol, BristolBS8 1TQ, United Kingdom
- School of Earth Sciences, University of Bristol, BristolBS8 1TQ, United Kingdom
| | - Haiyan Wang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao266237, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Kevin M. Kocot
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL35487
- Alabama Museum of Natural History, University of Alabama, Tuscaloosa, AL35487
| |
Collapse
|
25
|
Chavez Ramirez C, Khoo M, Lopez G M, Ferguson S, Walker S, Echeverri K. Comparison of Blastema Formation after Injury in Two Cephalopod Species. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000946. [PMID: 37799205 PMCID: PMC10550383 DOI: 10.17912/micropub.biology.000946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/04/2023] [Accepted: 09/19/2023] [Indexed: 10/07/2023]
Abstract
Regeneration is the ability to functionally replace significant amounts of lost tissue or whole appendages like arms, limbs or tentacles. The amount of tissue that can be regenerated varies among species, but regeneration is found in both invertebrate and vertebrate animals. Cephalopods have been broadly reported in the literature to regenerate their arms. There are over 800 species of Cephalopod; however, regeneration has only been documented in the literature in a few species (1). Here we compare arm regeneration in two species of cephalopod, the Octopus bimaculoides and the hummingbird bobtail squid Euprymna berryi.
Collapse
Affiliation(s)
| | - Miya Khoo
- University of Chicago, Chicago, Illinois, United States
| | - Marco Lopez G
- University of Chicago, Chicago, Illinois, United States
| | - Sophie Ferguson
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, Massachusetts, United States
| | - Sarah Walker
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, Massachusetts, United States
| | - Karen Echeverri
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, Massachusetts, United States
| |
Collapse
|
26
|
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.
Collapse
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.
| |
Collapse
|
27
|
McCoy MJ, Fire AZ. Ancient origins of complex neuronal genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534655. [PMID: 37034725 PMCID: PMC10081198 DOI: 10.1101/2023.03.28.534655] [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: 06/19/2023]
Abstract
How nervous systems evolved is a central question in biology. An increasing diversity of synaptic proteins is thought to play a central role in the formation of specific synapses leading to nervous system complexity. The largest animal genes, often spanning millions of base pairs, are known to be enriched for expression in neurons at synapses and are frequently mutated or misregulated in neurological disorders and diseases. While many of these genes have been studied independently in the context of nervous system evolution and disease, general principles underlying their parallel evolution remain unknown. To investigate this, we directly compared orthologous gene sizes across eukaryotes. By comparing relative gene sizes within organisms, we identified a distinct class of large genes with origins predating the diversification of animals and in many cases the emergence of dedicated neuronal cell types. We traced this class of ancient large genes through evolution and found orthologs of the large synaptic genes driving the immense complexity of metazoan nervous systems, including in humans and cephalopods. Moreover, we found that while these genes are evolving under strong purifying selection as demonstrated by low dN/dS scores, they have simultaneously grown larger and gained the most isoforms in animals. This work provides a new lens through which to view this distinctive class of large and multi-isoform genes and demonstrates how intrinsic genomic properties, such as gene length, can provide flexibility in molecular evolution and allow groups of genes and their host organisms to evolve toward complexity.
Collapse
Affiliation(s)
- Matthew J. McCoy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Andrew Z. Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
28
|
Song H, Li Z, Yang M, Shi P, Yu Z, Hu Z, Zhou C, Hu P, Zhang T. Chromosome-level genome assembly of the caenogastropod snail Rapana venosa. Sci Data 2023; 10:539. [PMID: 37587134 PMCID: PMC10432487 DOI: 10.1038/s41597-023-02459-7] [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: 03/31/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023] Open
Abstract
The carnivorous gastropod Rapana venosa (Valenciennes, 1846) is one of the most notorious ecological invaders worldwide. Here, we present the first high-quality chromosome-scale reference R. venosa genome obtained via PacBio sequencing, Illumina paired-end sequencing, and high-throughput chromosome conformation capture scaffolding. The assembled genome has a size of 2.30 Gb, with a scaffold N50 length of 64.63 Mb, and is anchored to 35 chromosomes. It contains 29,649 protein-coding genes, 77.22% of which were functionally annotated. Given its high heterozygosity (1.41%) and large proportion of repeat sequences (57.72%), it is one of the most complex genome assemblies. This chromosome-level genome assembly of R. venosa is an important resource for understanding molluscan evolutionary adaption and provides a genetic basis for its biological invasion control.
Collapse
Grants
- This research was supported by the National Natural Science Foundation of China (Grant No. 32002409, 42206086, 31972814, and 32002374), the China Postdoctoral Science Foundation (Grant No. 2021M703248), the China Agriculture Research System of MOF and MARA, and the Creative Team Project of the Laboratory for Marine Ecology and Environmental Science, Qingdao National for Marine Science and Technology (no. LMEESCTSP-2018). Hao Song was supported by the Young Elite Scientists Sponsorship Program by cst(Grant No. 2021QNRC001), and Youth Innovation Promotion Association by CAS. The funders had no role in the study design, data collection and analysis, decision to publish or preparation of the manuscript.
Collapse
Affiliation(s)
- Hao Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhuoqing Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meijie Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pu Shi
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenglin Yu
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Zhi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cong Zhou
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pengpeng Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
29
|
Rouressol L, Briseno J, Vijayan N, Chen GY, Ritschard EA, Sanchez G, Nyholm SV, McFall-Ngai MJ, Simakov O. Emergence of novel genomic regulatory regions associated with light-organ development in the bobtail squid. iScience 2023; 26:107091. [PMID: 37426346 PMCID: PMC10329180 DOI: 10.1016/j.isci.2023.107091] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/25/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023] Open
Abstract
Light organs (LO) with symbiotic bioluminescent bacteria are hallmarks of many bobtail squid species. These organs possess structural and functional features to modulate light, analogous to those found in coleoid eyes. Previous studies identified four transcription factors and modulators (SIX, EYA, PAX6, DAC) associated with both eyes and light organ development, suggesting co-option of a highly conserved gene regulatory network. Using available topological, open chromatin, and transcriptomic data, we explore the regulatory landscape around the four transcription factors as well as genes associated with LO and shared LO/eye expression. This analysis revealed several closely associated and putatively co-regulated genes. Comparative genomic analyses identified distinct evolutionary origins of these putative regulatory associations, with the DAC locus showing a unique topological and evolutionarily recent organization. We discuss different scenarios of modifications to genome topology and how these changes may have contributed to the evolutionary emergence of the light organ.
Collapse
Affiliation(s)
- Lisa Rouressol
- Department for Neurosciences and Developmental Biology, University of Vienna, Vienna 1030, Austria
- Department of Biosphere Sciences and Engineering, Carnegie Institution for Science, Pasadena, CA 91125, USA
| | - John Briseno
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Nidhi Vijayan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Grischa Y. Chen
- Department of Biosphere Sciences and Engineering, Carnegie Institution for Science, Pasadena, CA 91125, USA
| | - Elena A. Ritschard
- Department for Neurosciences and Developmental Biology, University of Vienna, Vienna 1030, Austria
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, NA, Italy
| | - Gustavo Sanchez
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan
| | - Spencer V. Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Margaret J. McFall-Ngai
- Department of Biosphere Sciences and Engineering, Carnegie Institution for Science, Pasadena, CA 91125, USA
| | - Oleg Simakov
- Department for Neurosciences and Developmental Biology, University of Vienna, Vienna 1030, Austria
| |
Collapse
|
30
|
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.
Collapse
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.
| | | |
Collapse
|
31
|
Rangan KJ, Reck-Peterson SL. RNA recoding in cephalopods tailors microtubule motor protein function. Cell 2023; 186:2531-2543.e11. [PMID: 37295401 PMCID: PMC10467349 DOI: 10.1016/j.cell.2023.04.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/05/2023] [Accepted: 04/24/2023] [Indexed: 06/12/2023]
Abstract
RNA editing is a widespread epigenetic process that can alter the amino acid sequence of proteins, termed "recoding." In cephalopods, most transcripts are recoded, and recoding is hypothesized to be an adaptive strategy to generate phenotypic plasticity. However, how animals use RNA recoding dynamically is largely unexplored. We investigated the function of cephalopod RNA recoding in the microtubule motor proteins kinesin and dynein. We found that squid rapidly employ RNA recoding in response to changes in ocean temperature, and kinesin variants generated in cold seawater displayed enhanced motile properties in single-molecule experiments conducted in the cold. We also identified tissue-specific recoded squid kinesin variants that displayed distinct motile properties. Finally, we showed that cephalopod recoding sites can guide the discovery of functional substitutions in non-cephalopod kinesin and dynein. Thus, RNA recoding is a dynamic mechanism that generates phenotypic plasticity in cephalopods and can inform the characterization of conserved non-cephalopod proteins.
Collapse
Affiliation(s)
- Kavita J Rangan
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA.
| | - Samara L Reck-Peterson
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
32
|
Birk MA, Liscovitch-Brauer N, Dominguez MJ, McNeme S, Yue Y, Hoff JD, Twersky I, Verhey KJ, Sutton RB, Eisenberg E, Rosenthal JJC. Temperature-dependent RNA editing in octopus extensively recodes the neural proteome. Cell 2023; 186:2544-2555.e13. [PMID: 37295402 PMCID: PMC10445230 DOI: 10.1016/j.cell.2023.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/24/2023] [Accepted: 05/04/2023] [Indexed: 06/12/2023]
Abstract
In poikilotherms, temperature changes challenge the integration of physiological function. Within the complex nervous systems of the behaviorally sophisticated coleoid cephalopods, these problems are substantial. RNA editing by adenosine deamination is a well-positioned mechanism for environmental acclimation. We report that the neural proteome of Octopus bimaculoides undergoes massive reconfigurations via RNA editing following a temperature challenge. Over 13,000 codons are affected, and many alter proteins that are vital for neural processes. For two highly temperature-sensitive examples, recoding tunes protein function. For synaptotagmin, a key component of Ca2+-dependent neurotransmitter release, crystal structures and supporting experiments show that editing alters Ca2+ binding. For kinesin-1, a motor protein driving axonal transport, editing regulates transport velocity down microtubules. Seasonal sampling of wild-caught specimens indicates that temperature-dependent editing occurs in the field as well. These data show that A-to-I editing tunes neurophysiological function in response to temperature in octopus and most likely other coleoids.
Collapse
Affiliation(s)
- Matthew A Birk
- Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Biology, Saint Francis University, Loretto, PA 15940, USA
| | | | - Matthew J Dominguez
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79410, USA
| | - Sean McNeme
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Yang Yue
- Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - J Damon Hoff
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Itamar Twersky
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Kristen J Verhey
- Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - R Bryan Sutton
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79410, USA
| | - Eli Eisenberg
- School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel.
| | | |
Collapse
|
33
|
Vallecillo-Viejo IC, Voss G, Albertin CB, Liscovitch-Brauer N, Eisenberg E, Rosenthal JJC. Squid express conserved ADAR orthologs that possess novel features. Front Genome Ed 2023; 5:1181713. [PMID: 37342458 PMCID: PMC10278661 DOI: 10.3389/fgeed.2023.1181713] [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: 03/07/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023] Open
Abstract
The coleoid cephalopods display unusually extensive mRNA recoding by adenosine deamination, yet the underlying mechanisms are not well understood. Because the adenosine deaminases that act on RNA (ADAR) enzymes catalyze this form of RNA editing, the structure and function of the cephalopod orthologs may provide clues. Recent genome sequencing projects have provided blueprints for the full complement of coleoid cephalopod ADARs. Previous results from our laboratory have shown that squid express an ADAR2 homolog, with two splice variants named sqADAR2a and sqADAR2b and that these messages are extensively edited. Based on octopus and squid genomes, transcriptomes, and cDNA cloning, we discovered that two additional ADAR homologs are expressed in coleoids. The first is orthologous to vertebrate ADAR1. Unlike other ADAR1s, however, it contains a novel N-terminal domain of 641 aa that is predicted to be disordered, contains 67 phosphorylation motifs, and has an amino acid composition that is unusually high in serines and basic amino acids. mRNAs encoding sqADAR1 are themselves extensively edited. A third ADAR-like enzyme, sqADAR/D-like, which is not orthologous to any of the vertebrate isoforms, is also present. Messages encoding sqADAR/D-like are not edited. Studies using recombinant sqADARs suggest that only sqADAR1 and sqADAR2 are active adenosine deaminases, both on perfect duplex dsRNA and on a squid potassium channel mRNA substrate known to be edited in vivo. sqADAR/D-like shows no activity on these substrates. Overall, these results reveal some unique features in sqADARs that may contribute to the high-level RNA recoding observed in cephalopods.
Collapse
Affiliation(s)
| | - Gjendine Voss
- The Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Caroline B. Albertin
- The Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Noa Liscovitch-Brauer
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
| | | |
Collapse
|
34
|
Marx V. Welcome to the nursery. Nat Methods 2023:10.1038/s41592-023-01902-2. [PMID: 37202538 DOI: 10.1038/s41592-023-01902-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
Primack AS, Cazet JF, Little HM, Mühlbauer S, Cox BD, David CN, Farrell JA, Juliano CE. Differentiation trajectories of the Hydra nervous system reveal transcriptional regulators of neuronal fate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.531610. [PMID: 36993575 PMCID: PMC10055148 DOI: 10.1101/2023.03.15.531610] [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: 04/27/2023]
Abstract
The small freshwater cnidarian polyp Hydra vulgaris uses adult stem cells (interstitial stem cells) to continually replace neurons throughout its life. This feature, combined with the ability to image the entire nervous system (Badhiwala et al., 2021; Dupre & Yuste, 2017) and availability of gene knockdown techniques (Juliano, Reich, et al., 2014; Lohmann et al., 1999; Vogg et al., 2022), makes Hydra a tractable model for studying nervous system development and regeneration at the whole-organism level. In this study, we use single-cell RNA sequencing and trajectory inference to provide a comprehensive molecular description of the adult nervous system. This includes the most detailed transcriptional characterization of the adult Hydra nervous system to date. We identified eleven unique neuron subtypes together with the transcriptional changes that occur as the interstitial stem cells differentiate into each subtype. Towards the goal of building gene regulatory networks to describe Hydra neuron differentiation, we identified 48 transcription factors expressed specifically in the Hydra nervous system, including many that are conserved regulators of neurogenesis in bilaterians. We also performed ATAC-seq on sorted neurons to uncover previously unidentified putative regulatory regions near neuron-specific genes. Finally, we provide evidence to support the existence of transdifferentiation between mature neuron subtypes and we identify previously unknown transition states in these pathways. All together, we provide a comprehensive transcriptional description of an entire adult nervous system, including differentiation and transdifferentiation pathways, which provides a significant advance towards understanding mechanisms that underlie nervous system regeneration.
Collapse
Affiliation(s)
- Abby S Primack
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616
| | - Jack F Cazet
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616
| | - Hannah Morris Little
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616
| | - Susanne Mühlbauer
- Department of Plant Biochemistry, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Ben D Cox
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616
| | - Charles N David
- Department of Biology, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany
| | - Jeffrey A Farrell
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20814, USA
| | - Celina E Juliano
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616
| |
Collapse
|
37
|
Kang G, Allard CAH, Valencia-Montoya WA, van Giesen L, Kim JJ, Kilian PB, Bai X, Bellono NW, Hibbs RE. Sensory specializations drive octopus and squid behaviour. Nature 2023; 616:378-383. [PMID: 37045917 PMCID: PMC10262778 DOI: 10.1038/s41586-023-05808-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 02/08/2023] [Indexed: 04/14/2023]
Abstract
The evolution of new traits enables expansion into new ecological and behavioural niches. Nonetheless, demonstrated connections between divergence in protein structure, function and lineage-specific behaviours remain rare. Here we show that both octopus and squid use cephalopod-specific chemotactile receptors (CRs) to sense their respective marine environments, but structural adaptations in these receptors support the sensation of specific molecules suited to distinct physiological roles. We find that squid express ancient CRs that more closely resemble related nicotinic acetylcholine receptors, whereas octopuses exhibit a more recent expansion in CRs consistent with their elaborated 'taste by touch' sensory system. Using a combination of genetic profiling, physiology and behavioural analyses, we identify the founding member of squid CRs that detects soluble bitter molecules that are relevant in ambush predation. We present the cryo-electron microscopy structure of a squid CR and compare this with octopus CRs1 and nicotinic receptors2. These analyses demonstrate an evolutionary transition from an ancestral aromatic 'cage' that coordinates soluble neurotransmitters or tastants to a more recent octopus CR hydrophobic binding pocket that traps insoluble molecules to mediate contact-dependent chemosensation. Thus, our study provides a foundation for understanding how adaptation of protein structure drives the diversification of organismal traits and behaviour.
Collapse
Affiliation(s)
- Guipeun Kang
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Corey A H Allard
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Wendy A Valencia-Montoya
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Lena van Giesen
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Jeong Joo Kim
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Peter B Kilian
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Xiaochen Bai
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nicholas W Bellono
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
| | - Ryan E Hibbs
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Neurobiology, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
38
|
Allard CAH, Kang G, Kim JJ, Valencia-Montoya WA, Hibbs RE, Bellono NW. Structural basis of sensory receptor evolution in octopus. Nature 2023; 616:373-377. [PMID: 37045920 PMCID: PMC10228259 DOI: 10.1038/s41586-023-05822-1] [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: 09/02/2022] [Accepted: 02/10/2023] [Indexed: 04/14/2023]
Abstract
Chemotactile receptors (CRs) are a cephalopod-specific innovation that allow octopuses to explore the seafloor via 'taste by touch'1. CRs diverged from nicotinic acetylcholine receptors to mediate contact-dependent chemosensation of insoluble molecules that do not readily diffuse in marine environments. Here we exploit octopus CRs to probe the structural basis of sensory receptor evolution. We present the cryo-electron microscopy structure of an octopus CR and compare it with nicotinic receptors to determine features that enable environmental sensation versus neurotransmission. Evolutionary, structural and biophysical analyses show that the channel architecture involved in cation permeation and signal transduction is conserved. By contrast, the orthosteric ligand-binding site is subject to diversifying selection, thereby mediating the detection of new molecules. Serendipitous findings in the cryo-electron microscopy structure reveal that the octopus CR ligand-binding pocket is exceptionally hydrophobic, enabling sensation of greasy compounds versus the small polar molecules detected by canonical neurotransmitter receptors. These discoveries provide a structural framework for understanding connections between evolutionary adaptations at the atomic level and the emergence of new organismal behaviour.
Collapse
Affiliation(s)
- Corey A H Allard
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Guipeun Kang
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jeong Joo Kim
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wendy A Valencia-Montoya
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Ryan E Hibbs
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Neurobiology, University of California, San Diego, La Jolla, CA, USA.
| | - Nicholas W Bellono
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
39
|
Zhang P, Zhu Y, Guo Q, Li J, Zhan X, Yu H, Xie N, Tan H, Lundholm N, Garcia-Cuetos L, Martin MD, Subirats MA, Su YH, Ruiz-Trillo I, Martindale MQ, Yu JK, Gilbert MTP, Zhang G, Li Q. On the origin and evolution of RNA editing in metazoans. Cell Rep 2023; 42:112112. [PMID: 36795564 PMCID: PMC9989829 DOI: 10.1016/j.celrep.2023.112112] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/28/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
Extensive adenosine-to-inosine (A-to-I) editing of nuclear-transcribed mRNAs is the hallmark of metazoan transcriptional regulation. Here, by profiling the RNA editomes of 22 species that cover major groups of Holozoa, we provide substantial evidence supporting A-to-I mRNA editing as a regulatory innovation originating in the last common ancestor of extant metazoans. This ancient biochemistry process is preserved in most extant metazoan phyla and primarily targets endogenous double-stranded RNA (dsRNA) formed by evolutionarily young repeats. We also find intermolecular pairing of sense-antisense transcripts as an important mechanism for forming dsRNA substrates for A-to-I editing in some but not all lineages. Likewise, recoding editing is rarely shared across lineages but preferentially targets genes involved in neural and cytoskeleton systems in bilaterians. We conclude that metazoan A-to-I editing might first emerge as a safeguard mechanism against repeat-derived dsRNA and was later co-opted into diverse biological processes due to its mutagenic nature.
Collapse
Affiliation(s)
- Pei Zhang
- BGI-Shenzhen, Shenzhen 518083, China; Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Qunfei Guo
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji Li
- BGI Research-Wuhan, BGI, Wuhan 430074, China
| | | | - Hao Yu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Nianxia Xie
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Nina Lundholm
- Natural History Museum of Denmark, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Lydia Garcia-Cuetos
- Natural History Museum of Denmark, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; Center for Theoretical Evolutionary Genomics, Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | | | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Iñaki Ruiz-Trillo
- Institute of Evolutionary Biology, UPF-CSIC Barcelona, 08003 Barcelona, Spain; ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Catalonia, Spain; Departament de Genètica, Microbiologia i Estadística, Facultat de Bilogia, Universitat de Barcelona (UB), 08028 Barcelona, Spain
| | - Mark Q Martindale
- The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan; Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan 26242, Taiwan
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Guojie Zhang
- Center of Evolutionary and Organismal Biology, & Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Qiye Li
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
40
|
Rosenthal JJC, Eisenberg E. Extensive Recoding of the Neural Proteome in Cephalopods by RNA Editing. Annu Rev Anim Biosci 2023; 11:57-75. [PMID: 36790891 DOI: 10.1146/annurev-animal-060322-114534] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The coleoid cephalopods have the largest brains, and display the most complex behaviors, of all invertebrates. The molecular and cellular mechanisms that underlie these remarkable advancements remain largely unexplored. Early molecular cloning studies of squid ion channel transcripts uncovered an unusually large number of A→I RNA editing sites that recoded codons. Further cloning of other neural transcripts showed a similar pattern. The advent of deep-sequencing technologies and the associated bioinformatics allowed the mapping of RNA editing events across the entire neural transcriptomes of various cephalopods. The results were remarkable: They contained orders of magnitude more recoding editing sites than any other taxon. Although RNA editing sites are abundant in most multicellular metazoans, they rarely recode. In cephalopods, the majority of neural transcripts are recoded. Recent studies have focused on whether these events are adaptive, as well as other noncanonical aspects of cephalopod RNA editing.
Collapse
Affiliation(s)
- Joshua J C Rosenthal
- The Eugene Bell Center, The Marine Biological Laboratory, Woods Hole, Massachusetts, USA;
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
41
|
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.
Collapse
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.
| |
Collapse
|
42
|
Song J, Li B, Zeng L, Ye Z, Wu W, Hu B. A Mini-Review on Reflectins, from Biochemical Properties to Bio-Inspired Applications. Int J Mol Sci 2022; 23:ijms232415679. [PMID: 36555320 PMCID: PMC9779258 DOI: 10.3390/ijms232415679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/23/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Some cephalopods (squids, octopuses, and cuttlefishes) produce dynamic structural colors, for camouflage or communication. The key to this remarkable capability is one group of specialized cells called iridocytes, which contain aligned membrane-enclosed platelets of high-reflective reflectins and work as intracellular Bragg reflectors. These reflectins have unusual amino acid compositions and sequential properties, which endows them with functional characteristics: an extremely high reflective index among natural proteins and the ability to answer various environmental stimuli. Based on their unique material composition and responsive self-organization properties, the material community has developed an impressive array of reflectin- or iridocyte-inspired optical systems with distinct tunable reflectance according to a series of internal and external factors. More recently, scientists have made creative attempts to engineer mammalian cells to explore the function potentials of reflectin proteins as well as their working mechanism in the cellular environment. Progress in wide scientific areas (biophysics, genomics, gene editing, etc.) brings in new opportunities to better understand reflectins and new approaches to fully utilize them. The work introduced the composition features, biochemical properties, the latest developments, future considerations of reflectins, and their inspiration applications to give newcomers a comprehensive understanding and mutually exchanged knowledge from different communities (e.g., biology and material).
Collapse
Affiliation(s)
- Junyi Song
- Correspondence: (J.S.); (B.H.); Tel.: +86-18969697729 (J.S.); +86-13308492461 (B.H.)
| | | | | | | | | | - Biru Hu
- Correspondence: (J.S.); (B.H.); Tel.: +86-18969697729 (J.S.); +86-13308492461 (B.H.)
| |
Collapse
|
43
|
The role of post-transcriptional modifications during development. Biol Futur 2022:10.1007/s42977-022-00142-3. [PMID: 36481986 DOI: 10.1007/s42977-022-00142-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
AbstractWhile the existence of post-transcriptional modifications of RNA nucleotides has been known for decades, in most RNA species the exact positions of these modifications and their physiological function have been elusive until recently. Technological advances, such as high-throughput next-generation sequencing (NGS) methods and nanopore-based mapping technologies, have made it possible to map the position of these modifications with single nucleotide accuracy, and genetic screens have uncovered the “writer”, “reader” and “eraser” proteins that help to install, interpret and remove such modifications, respectively. These discoveries led to intensive research programmes with the aim of uncovering the roles of these modifications during diverse biological processes. In this review, we assess novel discoveries related to the role of post-transcriptional modifications during animal development, highlighting how these discoveries can affect multiple aspects of development from fertilization to differentiation in many species.
Collapse
|
44
|
Zolotarov G, Fromm B, Legnini I, Ayoub S, Polese G, Maselli V, Chabot PJ, Vinther J, Styfhals R, Seuntjens E, Di Cosmo A, Peterson KJ, Rajewsky N. MicroRNAs are deeply linked to the emergence of the complex octopus brain. SCIENCE ADVANCES 2022; 8:eadd9938. [PMID: 36427315 PMCID: PMC9699675 DOI: 10.1126/sciadv.add9938] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/27/2022] [Indexed: 05/25/2023]
Abstract
Soft-bodied cephalopods such as octopuses are exceptionally intelligent invertebrates with a highly complex nervous system that evolved independently from vertebrates. Because of elevated RNA editing in their nervous tissues, we hypothesized that RNA regulation may play a major role in the cognitive success of this group. We thus profiled messenger RNAs and small RNAs in three cephalopod species including 18 tissues of the Octopus vulgaris. We show that the major RNA innovation of soft-bodied cephalopods is an expansion of the microRNA (miRNA) gene repertoire. These evolutionarily novel miRNAs were primarily expressed in adult neuronal tissues and during the development and had conserved and thus likely functional target sites. The only comparable miRNA expansions happened, notably, in vertebrates. Thus, we propose that miRNAs are intimately linked to the evolution of complex animal brains.
Collapse
Affiliation(s)
- Grygoriy Zolotarov
- Laboratory of Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Bastian Fromm
- UiT The Arctic University of Norway, Tromsø, Norway
- SciLifeLab, Stockholm University, Stockholm, Sweden
| | - Ivano Legnini
- Laboratory of Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
| | - Salah Ayoub
- Laboratory of Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
| | - Gianluca Polese
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Valeria Maselli
- Department of Biology, University of Naples Federico II, Naples, Italy
| | | | - Jakob Vinther
- School of Earth Sciences, University of Bristol, Bristol, UK
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Ruth Styfhals
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Anna Di Cosmo
- Department of Biology, University of Naples Federico II, Naples, Italy
| | | | - Nikolaus Rajewsky
- Laboratory of Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
| |
Collapse
|
45
|
Macchi F, Edsinger E, Sadler KC. Epigenetic machinery is functionally conserved in cephalopods. BMC Biol 2022; 20:202. [PMID: 36104784 PMCID: PMC9476566 DOI: 10.1186/s12915-022-01404-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 09/07/2022] [Indexed: 11/29/2022] Open
Abstract
Background Epigenetic regulatory mechanisms are divergent across the animal kingdom, yet these mechanisms are not well studied in non-model organisms. Unique features of cephalopods make them attractive for investigating behavioral, sensory, developmental, and regenerative processes, and recent studies have elucidated novel features of genome organization and gene and transposon regulation in these animals. However, it is not known how epigenetics regulates these interesting cephalopod features. We combined bioinformatic and molecular analysis of Octopus bimaculoides to investigate the presence and pattern of DNA methylation and examined the presence of DNA methylation and 3 histone post-translational modifications across tissues of three cephalopod species. Results We report a dynamic expression profile of the genes encoding conserved epigenetic regulators, including DNA methylation maintenance factors in octopus tissues. Levels of 5-methyl-cytosine in multiple tissues of octopus, squid, and bobtail squid were lower compared to vertebrates. Whole genome bisulfite sequencing of two regions of the brain and reduced representation bisulfite sequencing from a hatchling of O. bimaculoides revealed that less than 10% of CpGs are methylated in all samples, with a distinct pattern of 5-methyl-cytosine genome distribution characterized by enrichment in the bodies of a subset of 14,000 genes and absence from transposons. Hypermethylated genes have distinct functions and, strikingly, many showed similar expression levels across tissues while hypomethylated genes were silenced or expressed at low levels. Histone marks H3K27me3, H3K9me3, and H3K4me3 were detected at different levels across tissues of all species. Conclusions Our results show that the DNA methylation and histone modification epigenetic machinery is conserved in cephalopods, and that, in octopus, 5-methyl-cytosine does not decorate transposable elements, but is enriched on the gene bodies of highly expressed genes and could cooperate with the histone code to regulate tissue-specific gene expression. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01404-1.
Collapse
|
46
|
Feng Y, Neme R, Beh LY, Chen X, Braun J, Lu MW, Landweber LF. Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes. eLife 2022; 11:82979. [PMID: 36421078 PMCID: PMC9797194 DOI: 10.7554/elife.82979] [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: 08/25/2022] [Accepted: 11/03/2022] [Indexed: 11/25/2022] Open
Abstract
Ciliates are microbial eukaryotes that undergo extensive programmed genome rearrangement, a natural genome editing process that converts long germline chromosomes into smaller gene-rich somatic chromosomes. Three well-studied ciliates include Oxytricha trifallax, Tetrahymena thermophila, and Paramecium tetraurelia, but only the Oxytricha lineage has a massively scrambled genome, whose assembly during development requires hundreds of thousands of precisely programmed DNA joining events, representing the most complex genome dynamics of any known organism. Here we study the emergence of such complex genomes by examining the origin and evolution of discontinuous and scrambled genes in the Oxytricha lineage. This study compares six genomes from three species, the germline and somatic genomes for Euplotes woodruffi, Tetmemena sp., and the model ciliate O. trifallax. We sequenced, assembled, and annotated the germline and somatic genomes of E. woodruffi, which provides an outgroup, and the germline genome of Tetmemena sp. We find that the germline genome of Tetmemena is as massively scrambled and interrupted as Oxytricha's: 13.6% of its gene loci require programmed translocations and/or inversions, with some genes requiring hundreds of precise gene editing events during development. This study revealed that the earlier diverged spirotrich, E. woodruffi, also has a scrambled genome, but only roughly half as many loci (7.3%) are scrambled. Furthermore, its scrambled genes are less complex, together supporting the position of Euplotes as a possible evolutionary intermediate in this lineage, in the process of accumulating complex evolutionary genome rearrangements, all of which require extensive repair to assemble functional coding regions. Comparative analysis also reveals that scrambled loci are often associated with local duplications, supporting a gradual model for the origin of complex, scrambled genomes via many small events of DNA duplication and decay.
Collapse
Affiliation(s)
- Yi Feng
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Rafik Neme
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia UniversityNew YorkUnited States,Department of Chemistry and Biology, Universidad del NorteBarranquillaColombia
| | - Leslie Y Beh
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Xiao Chen
- Pacific BiosciencesMenlo ParkUnited States
| | - Jasper Braun
- Department of Mathematics and Statistics, University of South FloridaTampaUnited States
| | - Michael W Lu
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Laura F Landweber
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia UniversityNew YorkUnited States
| |
Collapse
|