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Parey E, Ortega-Martinez O, Delroisse J, Piovani L, Czarkwiani A, Dylus D, Arya S, Dupont S, Thorndyke M, Larsson T, Johannesson K, Buckley KM, Martinez P, Oliveri P, Marlétaz F. The brittle star genome illuminates the genetic basis of animal appendage regeneration. Nat Ecol Evol 2024; 8:1505-1521. [PMID: 39030276 PMCID: PMC11310086 DOI: 10.1038/s41559-024-02456-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/29/2024] [Indexed: 07/21/2024]
Abstract
Species within nearly all extant animal lineages are capable of regenerating body parts. However, it remains unclear whether the gene expression programme controlling regeneration is evolutionarily conserved. Brittle stars are a species-rich class of echinoderms with outstanding regenerative abilities, but investigations into the genetic bases of regeneration in this group have been hindered by the limited genomic resources. Here we report a chromosome-scale genome assembly for the brittle star Amphiura filiformis. We show that the brittle star genome is the most rearranged among echinoderms sequenced so far, featuring a reorganized Hox cluster reminiscent of the rearrangements observed in sea urchins. In addition, we performed an extensive profiling of gene expression during brittle star adult arm regeneration and identified sequential waves of gene expression governing wound healing, proliferation and differentiation. We conducted comparative transcriptomic analyses with other invertebrate and vertebrate models for appendage regeneration and uncovered hundreds of genes with conserved expression dynamics, particularly during the proliferative phase of regeneration. Our findings emphasize the crucial importance of echinoderms to detect long-range expression conservation between vertebrates and classical invertebrate regeneration model systems.
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Affiliation(s)
- Elise Parey
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - Olga Ortega-Martinez
- Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Jérôme Delroisse
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Laura Piovani
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Anna Czarkwiani
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Technische Universität Dresden, Center for Regenerative Therapies Dresden (CRTD), Dresden, Germany
| | - David Dylus
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Roche Pharmaceutical Research and Early Development (pRED), Cardiovascular and Metabolism, Immunology, Infectious Disease, and Ophthalmology (CMI2O), F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Srishti Arya
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- MRC Laboratory of Medical Sciences, Imperial College London, London, UK
| | - Samuel Dupont
- Department of Biology and Environmental Science, University of Gothenburg, Kristineberg Marine Research Station, Fiskebäckskil, Sweden
- IAEA Marine Environment Laboratories, Radioecology Laboratory, Quai Antoine 1er, Monaco
| | - Michael Thorndyke
- Department of Biology and Environmental Science, University of Gothenburg, Kristineberg Marine Research Station, Fiskebäckskil, Sweden
| | - Tomas Larsson
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kerstin Johannesson
- Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | | | - Pedro Martinez
- Departament de Genètica, Microbiologia, i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Paola Oliveri
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - Ferdinand Marlétaz
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
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2
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Wei Z, Zhang X, Chen Y, Liu H, Wang S, Zhang M, Ma H, Yu K, Wang L. A new strategy based on a cascade amplification strategy biosensor for on-site eDNA detection and outbreak warning of crown-of-thorns starfish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172258. [PMID: 38583618 DOI: 10.1016/j.scitotenv.2024.172258] [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: 02/26/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
Population outbreaks of the crown-of-thorns starfish (COTS) seriously threaten the sustainability of coral reef ecosystems. However, traditional ecological monitoring techniques cannot provide early warning before the outbreaks, thus preventing timely intervention. Therefore, there is an urgent need for a more accurate and faster technology to predict the outbreaks of COTS. In this work, we developed an electrochemical biosensor based on a programmed catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR) cyclic amplification strategy for sensitive and selective detection of COTS environmental DNA (eDNA) in water bodies. This biosensor exhibited excellent electrochemical characteristics, including a low limit of detection (LOD = 18.4 fM), low limit of quantification (LOQ = 41.1 fM), and wide linear range (50 fM - 10 nM). The biosensing technology successfully allowed the detection of COTS eDNA in the aquarium environment, and the results also demonstrated a significant correlation between eDNA concentration and COTS number (r = 0.990; P < 0.001). The reliability and accuracy of the biosensor results have been further validated through comparison with digital droplet PCR (ddPCR). Moreover, the applicability and accuracy of the biosensor were reconfirmed in field tests at the COTS outbreak site in the South China Sea, which has shown potential application in dynamically monitoring the larvae before the COTS outbreak. Therefore, this efficient electrochemical biosensing technology offers a new solution for on-site monitoring and early warning of the COTS outbreak.
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Affiliation(s)
- Zongwu Wei
- School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Xuzhe Zhang
- School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Yingzhan Chen
- School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Hongjie Liu
- School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Shaopeng Wang
- School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Man Zhang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Honglin Ma
- Sansha Track Ocean Coral Reef Conservation Research Institute Co. Ltd., Qionghai 571499, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning 530004, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
| | - Liwei Wang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning 530004, China.
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3
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Morin M, Jönsson M, Wang CK, Craik DJ, Degnan SM, Degnan BM. Seasonal tissue-specific gene expression in wild crown-of-thorns starfish reveals reproductive and stress-related transcriptional systems. PLoS Biol 2024; 22:e3002620. [PMID: 38743647 PMCID: PMC11093393 DOI: 10.1371/journal.pbio.3002620] [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: 12/18/2023] [Accepted: 04/10/2024] [Indexed: 05/16/2024] Open
Abstract
Animals are influenced by the season, yet we know little about the changes that occur in most species throughout the year. This is particularly true in tropical marine animals that experience relatively small annual temperature and daylight changes. Like many coral reef inhabitants, the crown-of-thorns starfish (COTS), well known as a notorious consumer of corals and destroyer of coral reefs, reproduces exclusively in the summer. By comparing gene expression in 7 somatic tissues procured from wild COTS sampled on the Great Barrier Reef, we identified more than 2,000 protein-coding genes that change significantly between summer and winter. COTS genes that appear to mediate conspecific communication, including both signalling factors released into the surrounding sea water and cell surface receptors, are up-regulated in external secretory and sensory tissues in the summer, often in a sex-specific manner. Sexually dimorphic gene expression appears to be underpinned by sex- and season-specific transcription factors (TFs) and gene regulatory programs. There are over 100 TFs that are seasonally expressed, 87% of which are significantly up-regulated in the summer. Six nuclear receptors are up-regulated in all tissues in the summer, suggesting that systemic seasonal changes are hormonally controlled, as in vertebrates. Unexpectedly, there is a suite of stress-related chaperone proteins and TFs, including HIFa, ATF3, C/EBP, CREB, and NF-κB, that are uniquely and widely co-expressed in gravid females. The up-regulation of these stress proteins in the summer suggests the demands of oogenesis in this highly fecund starfish affects protein stability and turnover in somatic cells. Together, these circannual changes in gene expression provide novel insights into seasonal changes in this coral reef pest and have the potential to identify vulnerabilities for targeted biocontrol.
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Affiliation(s)
- Marie Morin
- Centre for Marine Science, School of the Environment, The University of Queensland, Brisbane, Australia
| | - Mathias Jönsson
- Centre for Marine Science, School of the Environment, The University of Queensland, Brisbane, Australia
| | - Conan K. Wang
- Institute for Molecular Bioscience, ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Australia
| | - Sandie M. Degnan
- Centre for Marine Science, School of the Environment, The University of Queensland, Brisbane, Australia
| | - Bernard M. Degnan
- Centre for Marine Science, School of the Environment, The University of Queensland, Brisbane, Australia
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4
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Webb M, Clements M, Selvakumaraswamy P, McLaren E, Byrne M. Chemosensory behaviour of juvenile crown-of-thorns sea star ( Acanthaster sp.), attraction to algal and coral food and avoidance of adult conspecifics. Proc Biol Sci 2024; 291:20240623. [PMID: 38807518 DOI: 10.1098/rspb.2024.0623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/15/2024] [Indexed: 05/30/2024] Open
Abstract
Intraspecific and habitat-mediated responses to chemical cues play key roles in structuring populations of marine species. We investigated the behaviour of herbivorous-stage juvenile crown-of-thorns sea stars (COTS; Acanthaster sp.) in flow-through choice chambers to determine if chemical cues from their habitat influence movement and their transition to become coral predators. Juveniles at the diet transition stage were exposed to cues from their nursery habitat (coral rubble-crustose coralline algae (CCA)), live coral and adult COTS to determine if waterborne cues influence movement. In response to CCA and coral as sole cues, juveniles moved towards the cue source and when these cues were presented in combination, they exhibited a preference for coral. Juveniles moved away from adult COTS cues. Exposure to food cues (coral, CCA) in the presence of adult cues resulted in variable responses. Our results suggest a feedback mechanism whereby juvenile behaviour is mediated by adult chemical cues. Cues from the adult population may deter juveniles from the switch to corallivory. As outbreaks wane, juveniles released from competition may serve as a proximate source of outbreaks, supporting the juveniles-in-waiting hypothesis. The accumulation of juveniles within the reef infrastructure is an underappreciated potential source of COTS outbreaks that devastate coral reefs.
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Affiliation(s)
- M Webb
- School of Life and Environmental Sciences, The University of Sydney , Sydney, New South Wales, Australia
| | - M Clements
- School of Life and Environmental Sciences, The University of Sydney , Sydney, New South Wales, Australia
| | - P Selvakumaraswamy
- School of Life and Environmental Sciences, The University of Sydney , Sydney, New South Wales, Australia
| | - E McLaren
- School of Life and Environmental Sciences, The University of Sydney , Sydney, New South Wales, Australia
| | - M Byrne
- School of Life and Environmental Sciences, The University of Sydney , Sydney, New South Wales, Australia
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5
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Matthews SA, Williamson DH, Beeden R, Emslie MJ, Abom RTM, Beard D, Bonin M, Bray P, Campili AR, Ceccarelli DM, Fernandes L, Fletcher CS, Godoy D, Hemingson CR, Jonker MJ, Lang BJ, Morris S, Mosquera E, Phillips GL, Sinclair-Taylor TH, Taylor S, Tracey D, Wilmes JC, Quincey R. Protecting Great Barrier Reef resilience through effective management of crown-of-thorns starfish outbreaks. PLoS One 2024; 19:e0298073. [PMID: 38656948 PMCID: PMC11042723 DOI: 10.1371/journal.pone.0298073] [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: 10/11/2023] [Accepted: 01/18/2024] [Indexed: 04/26/2024] Open
Abstract
Resilience-based management is essential to protect ecosystems in the Anthropocene. Unlike large-scale climate threats to Great Barrier Reef (GBR) corals, outbreaks of coral-eating crown-of-thorns starfish (COTS; Acanthaster cf. solaris) can be directly managed through targeted culling. Here, we evaluate the outcomes of a decade of strategic COTS management in suppressing outbreaks and protecting corals during the 4th COTS outbreak wave at reef and regional scales (sectors). We compare COTS density and coral cover dynamics during the 3rd and 4th outbreak waves. During the 4th outbreak wave, sectors that received limited to no culling had sustained COTS outbreaks causing significant coral losses. In contrast, in sectors that received timely and sufficient cull effort, coral cover increased substantially, and outbreaks were suppressed with COTS densities up to six-fold lower than in the 3rd outbreak wave. In the Townsville sector for example, despite exposure to comparable disturbance regimes during the 4th outbreak wave, effective outbreak suppression coincided with relative increases in sector-wide coral cover (44%), versus significant coral cover declines (37%) during the 3rd outbreak wave. Importantly, these estimated increases span entire sectors, not just reefs with active COTS control. Outbreaking reefs with higher levels of culling had net increases in coral cover, while the rate of coral loss was more than halved on reefs with lower levels of cull effort. Our results also indicate that outbreak wave progression to adjoining sectors has been delayed, probably via suppression of COTS larval supply. Our findings provide compelling evidence that proactive, targeted, and sustained COTS management can effectively suppress COTS outbreaks and deliver coral growth and recovery benefits at reef and sector-wide scales. The clear coral protection outcomes demonstrate the value of targeted manual culling as both a scalable intervention to mitigate COTS outbreaks, and a potent resilience-based management tool to "buy time" for coral reefs, protecting reef ecosystem functions and biodiversity as the climate changes.
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Affiliation(s)
| | | | - Roger Beeden
- Great Barrier Reef Marine Park Authority, Townsville, QLD, Australia
| | | | | | | | - Mary Bonin
- Great Barrier Reef Foundation, Brisbane City, QLD, Australia
| | - Peran Bray
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | | | | | - Leanne Fernandes
- Great Barrier Reef Marine Park Authority, Townsville, QLD, Australia
| | | | - Dan Godoy
- Blue Planet Marine, Canberra, ACT, Australia
| | - Christopher R. Hemingson
- The University of Texas at Austin, Marine Science Institute, Port Aransas, Texas, United States of America
| | | | - Bethan J. Lang
- Great Barrier Reef Marine Park Authority, Townsville, QLD, Australia
- The University of New South Wales, Sydney, NSW, Australia
- ARC Centre of Excellence, James Cook University, Townsville, QLD, Australia
| | | | | | - Gareth L. Phillips
- Association of Marine Park Tourism Operators Ltd, Cairns, QLD, Australia
| | | | - Sascha Taylor
- Queensland Department of Environment and Science, Queensland Parks and Wildlife Service and Partnerships (Marine Parks), Brisbane, Queensland, Australia
| | - Dieter Tracey
- Great Barrier Reef Marine Park Authority, Townsville, QLD, Australia
| | | | - Richard Quincey
- Great Barrier Reef Marine Park Authority, Townsville, QLD, Australia
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6
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Popovic I, Bergeron LA, Bozec YM, Waldvogel AM, Howitt SM, Damjanovic K, Patel F, Cabrera MG, Wörheide G, Uthicke S, Riginos C. High germline mutation rates, but not extreme population outbreaks, influence genetic diversity in a keystone coral predator. PLoS Genet 2024; 20:e1011129. [PMID: 38346089 PMCID: PMC10861045 DOI: 10.1371/journal.pgen.1011129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/08/2024] [Indexed: 02/15/2024] Open
Abstract
Lewontin's paradox, the observation that levels of genetic diversity (π) do not scale linearly with census population size (Nc) variation, is an evolutionary conundrum. The most extreme mismatches between π and Nc are found for highly abundant marine invertebrates. Yet, the influences of new mutations on π relative to extrinsic processes such as Nc fluctuations are unknown. Here, we provide the first germline mutation rate (μ) estimate for a marine invertebrate in corallivorous crown-of-thorns sea stars (Acanthaster cf. solaris). We use high-coverage whole-genome sequencing of 14 parent-offspring trios alongside empirical estimates of Nc in Australia's Great Barrier Reef to jointly examine the determinants of π in populations undergoing extreme Nc fluctuations. The A. cf. solaris mean μ was 9.13 x 10-09 mutations per-site per-generation (95% CI: 6.51 x 10-09 to 1.18 x 10-08), exceeding estimates for other invertebrates and showing greater concordance with vertebrate mutation rates. Lower-than-expected Ne (~70,000-180,000) and low Ne/Nc values (0.0047-0.048) indicated weak influences of population outbreaks on long-term π. Our findings are consistent with elevated μ evolving in response to reduced Ne and generation time length, with important implications for explaining high mutational loads and the determinants of genetic diversity in marine invertebrate taxa.
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Affiliation(s)
- Iva Popovic
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
| | - Lucie A. Bergeron
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yves-Marie Bozec
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
| | | | - Samantha M. Howitt
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
| | | | - Frances Patel
- Australian Institute of Marine Science, Townsville, Australia
| | | | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB)–Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
| | - Sven Uthicke
- Australian Institute of Marine Science, Townsville, Australia
| | - Cynthia Riginos
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
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7
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Wang Y, Wang Y, Yang Y, Ni G, Li Y, Chen M. Chromosome-level genome assembly of the northern Pacific seastar Asterias amurensis. Sci Data 2023; 10:767. [PMID: 37925473 PMCID: PMC10625585 DOI: 10.1038/s41597-023-02688-w] [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: 07/06/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
Asterias amurensis has attracted widespread concern because of its population outbreaks, which has impacted fisheries and aquaculture, as well as disrupting local ecosystems. A high-quality reference genome is necessary to better investigate mechanisms of outbreak and adaptive changes. Combining PacBio HiFi and Hi-C sequencing data, we generated a chromosome-level A. amurensis genome with a size of 491.53 Mb. The contig N50 and scaffold N50 were 8.05 and 23.75 Mb, respectively. The result of BUSCO analysis revealed a completeness score of 98.85%. A total of 16,531 protein-coding genes were predicted in the genome, of which 94.63% were functionally annotated. The high-quality genome assembly resulting from this study will provide a valuable genetic resource for future research on the mechanism of population outbreaks and invasion ecology.
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Affiliation(s)
- Yanlin Wang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yixin Wang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yujia Yang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Gang Ni
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yulong Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Muyan Chen
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
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8
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Doll PC, Uthicke S, Caballes CF, Patel F, Gomez Cabrera MDC, Lang BJ, Pratchett MS. Induction of larval settlement in crown-of-thorns starfish is not mediated by conspecific cues. Sci Rep 2023; 13:17119. [PMID: 37816798 PMCID: PMC10564929 DOI: 10.1038/s41598-023-44422-x] [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: 08/11/2023] [Accepted: 10/08/2023] [Indexed: 10/12/2023] Open
Abstract
Population irruptions of crown-of-thorns starfish (COTS; Acanthaster spp.) remain a major cause of coral reef degradation throughout the Pacific and Indian Oceans and are inherently modulated by larval settlement and recruitment success. Gregarious larval settlement, as exhibited by many other ecologically important marine invertebrates, can catalyse population growth and replenishment. However, whether conspecific cues induce or influence the settlement of COTS larvae remains a critical information gap. This experimental study examined the induction of COTS settlement in response to a range of conspecific cues associated with early- and late-stage herbivorous juveniles, corallivorous juveniles and adults. Competent COTS larvae were generally not induced to settle by the presence of conspecifics or cues associated with conspecifics, while the settlement success of COTS in the presence of coralline algae was not inhibited or enhanced by adding conspecific conditioned seawater. Rather than being reinforced by gregarious settlement, the recruitment of COTS populations appears dependent on associative settlement cues (i.e., coralline algae and/or associated microbial communities) signalling suitable benthic habitat.
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Affiliation(s)
- Peter C Doll
- Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia.
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia.
| | - Sven Uthicke
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
| | - Ciemon F Caballes
- Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
- University of Guam - Marine Laboratory, Mangilao, GU, 96923, USA
| | - Frances Patel
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
| | | | - Bethan J Lang
- Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Morgan S Pratchett
- Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
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9
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Hillberg AK, Smith MK, Lausen BS, Suwansa-ard S, Johnston R, Mitu SA, MacDonald LE, Zhao M, Motti CA, Wang T, Elizur A, Nakashima K, Satoh N, Cummins SF. Crown-of-thorns starfish spines secrete defence proteins. PeerJ 2023; 11:e15689. [PMID: 37637177 PMCID: PMC10448888 DOI: 10.7717/peerj.15689] [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: 02/24/2023] [Accepted: 06/14/2023] [Indexed: 08/29/2023] Open
Abstract
Background The crown-of-thorns starfish (COTS; Acanthaster species) is a slow-moving corallivore protected by an extensive array of long, sharp toxic spines. Envenomation can result in nausea, numbness, vomiting, joint aches and sometimes paralysis. Small molecule saponins and the plancitoxin proteins have been implicated in COTS toxicity. Methods Brine shrimp lethality assays were used to confirm the secretion of spine toxin biomolecules. Histological analysis, followed by spine-derived proteomics helped to explain the source and identity of proteins, while quantitative RNA-sequencing and phylogeny confirmed target gene expression and relative conservation, respectively. Results We demonstrate the lethality of COTS spine secreted biomolecules on brine shrimp, including significant toxicity using aboral spine semi-purifications of >10 kDa (p > 0.05, 9.82 µg/ml), supporting the presence of secreted proteins as toxins. Ultrastructure observations of the COTS aboral spine showed the presence of pores that could facilitate the distribution of secreted proteins. Subsequent purification and mass spectrometry analysis of spine-derived proteins identified numerous secretory proteins, including plancitoxins, as well as those with relatively high gene expression in spines, including phospholipase A2, protease inhibitor 16-like protein, ependymin-related proteins and those uncharacterized. Some secretory proteins (e.g., vitellogenin and deleted in malignant brain tumor protein 1) were not highly expressed in spine tissue, yet the spine may serve as a storage or release site. This study contributes to our understanding of the COTS through functional, ultrastructural and proteomic analysis of aboral spines.
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Affiliation(s)
- Adam K. Hillberg
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD, Australia
| | - Meaghan K. Smith
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD, Australia
| | - Blake S. Lausen
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD, Australia
| | - Saowaros Suwansa-ard
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD, Australia
| | - Ryan Johnston
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD, Australia
| | - Shahida A. Mitu
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD, Australia
| | - Leah E. MacDonald
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD, Australia
| | - Min Zhao
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD, Australia
| | - Cherie A. Motti
- Australian Institute of Marine Science, Townsville, Australia
| | - Tianfang Wang
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD, Australia
| | - Abigail Elizur
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD, Australia
| | - Keisuke Nakashima
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Scott F. Cummins
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD, Australia
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10
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Liu J, Zhou Y, Pu Y, Zhang H. A chromosome-level genome assembly of a deep-sea starfish (Zoroaster cf. ophiactis). Sci Data 2023; 10:506. [PMID: 37528102 PMCID: PMC10394057 DOI: 10.1038/s41597-023-02397-4] [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: 02/03/2023] [Accepted: 07/18/2023] [Indexed: 08/03/2023] Open
Abstract
Understanding of adaptation and evolution of organisms in the deep sea requires more genomic resources. Zoroaster cf. ophiactis is a sea star in the family Zoroasteridae occurring exclusively in the deep sea. In this study, a chromosome-level genome assembly for Z. cf. ophiactis was generated by combining Nanopore long-read, Illumina short-read, and Hi-C sequencing data. The final assembly was 1,002.0 Mb in length, with a contig N50 of 376 Kb and a scaffold N50 of 40.4 Mb, and included 22 pseudo-chromosomes, covering 92.3% of the assembly. Completeness analysis evaluated with BUSCO revealed that 95.91% of the metazoan conserved genes were complete. Additionally, 39,426 protein-coding genes were annotated for this assembly. This chromosome-level genome assembly represents the first high-quality genome for the deep-sea Asteroidea, and will provide a valuable resource for future studies on evolution and adaptation of deep-sea echinoderms.
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Affiliation(s)
- Jun Liu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Yang Zhou
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Yujin Pu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haibin Zhang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.
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11
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Wang Q, Cao T, Wang Y, Li X, Wang Y. Genome-wide identification and comparative analysis of Dmrt genes in echinoderms. Sci Rep 2023; 13:7664. [PMID: 37169947 PMCID: PMC10175285 DOI: 10.1038/s41598-023-34819-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 05/08/2023] [Indexed: 05/13/2023] Open
Abstract
The Dmrt (Doublesex-mab3-related transcription factor) gene family is a class of crucial transcription factors characterized by one or several conserved DM (Doublesex/Mab-3) domains. Dmrt family genes can participate in various physiological developmental processes, especially in sex determination/differentiation. Echinoderms are extremely important research objects in various fields, such as sex determination/differentiation and neuroscience. However, to date, the genome-wide characterization and analysis of Dmrt genes in echinoderms have not been investigated. In this study, the identification and analysis of Dmrt genes in 11 representative echinoderms were performed using bioinformatics methods. A total of 43 Dmrt genes have been found in the studied echinoderms, and the number of Dmrt genes in different species ranges from 2 to 5. The phylogenetic tree showed that all Dmrt genes from echinoderms can be subdivided into 5 classes, the Dmrt2-like class, Dmrt3-like class, Dmrt4/5-like class, Dsx-like class, and a novel Dmrt (starfish-specific) class. Furthermore, selective pressure assessment suggested that the Dmrt genes underwent purifying selection pressure. In general, this study provides a molecular basis for echinoderm Dmrt genes and may serve as a reference for in-depth phylogenomics.
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Affiliation(s)
- Quanchao Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Key Laboratory of Ecological Warning, Protection and Restoration for Bohai Sea, Ministry of Natural Resources, Qingdao, 266061, China
| | - Tiangui Cao
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Yanxia Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Xiaojing Li
- Yantai Vocational College, Yantai, 264670, China
| | - Yue Wang
- Yantai Vocational College, Yantai, 264670, China.
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12
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Chen T, Ren C, Wong NK, Yan A, Sun C, Fan D, Luo P, Jiang X, Zhang L, Ruan Y, Li J, Wu X, Huo D, Huang J, Li X, Wu F, E Z, Cheng C, Zhang X, Wang Y, Hu C. The Holothuria leucospilota genome elucidates sacrificial organ expulsion and bioadhesive trap enriched with amyloid-patterned proteins. Proc Natl Acad Sci U S A 2023; 120:e2213512120. [PMID: 37036994 PMCID: PMC10120082 DOI: 10.1073/pnas.2213512120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 02/04/2023] [Indexed: 04/12/2023] Open
Abstract
Some tropical sea cucumbers of the family Holothuriidae can efficiently repel or even fatally ensnare predators by sacrificially ejecting a bioadhesive matrix termed the Cuvierian organ (CO), so named by the French zoologist Georges Cuvier who first described it in 1831. Still, the precise mechanisms for how adhesiveness genetically arose in CO and how sea cucumbers perceive and transduce danger signals for CO expulsion during defense have remained unclear. Here, we report the first high-quality, chromosome-level genome assembly of Holothuria leucospilota, an ecologically significant sea cucumber with prototypical CO. The H. leucospilota genome reveals characteristic long-repeat signatures in CO-specific outer-layer proteins, analogous to fibrous proteins of disparate species origins, including spider spidroin and silkworm fibroin. Intriguingly, several CO-specific proteins occur with amyloid-like patterns featuring extensive intramolecular cross-β structures readily stainable by amyloid indicator dyes. Distinct proteins within the CO connective tissue and outer surface cooperate to give the expelled matrix its apparent tenacity and adhesiveness, respectively. Genomic evidence offers further hints that H. leucospilota directly transduces predator-induced mechanical pressure onto the CO surface through mediation by transient receptor potential channels, which culminates in acetylcholine-triggered CO expulsion in part or in entirety. Evolutionarily, innovative events in two distinct regions of the H. leucospilota genome have apparently spurred CO's differentiation from the respiratory tree to a lethal defensive organ against predators.
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Affiliation(s)
- Ting Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Chunhua Ren
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Nai-Kei Wong
- Clinical Pharmacology Section, Department of Pharmacology, Shantou University Medical College, Shantou515041, China
| | - Aifen Yan
- School of Medicine, Foshan University, Foshan528225, China
| | - Caiyun Sun
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou510275, China
- Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou510275, China
| | - Dingding Fan
- EasyATGC Limited Liability Company, Shenzhen518081, China
| | - Peng Luo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Xiao Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Lvping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Yao Ruan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Jiaxi Li
- School of Medicine, Foshan University, Foshan528225, China
| | - Xiaofen Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Da Huo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Jiasheng Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Xiaomin Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Feifei Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Zixuan E
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Chuhang Cheng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning530007, China
| | - Xin Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Yanhong Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Chaoqun Hu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning530007, China
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13
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Losilla M, Gallant JR. Molecular evolution of the ependymin-related gene epdl2 in African weakly electric fish. G3 (BETHESDA, MD.) 2023; 13:6931758. [PMID: 36529459 PMCID: PMC9997568 DOI: 10.1093/g3journal/jkac331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/01/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022]
Abstract
Gene duplication and subsequent molecular evolution can give rise to taxon-specific gene specializations. In previous work, we found evidence that African weakly electric fish (Mormyridae) may have as many as three copies of the epdl2 gene, and the expression of two epdl2 genes is correlated with electric signal divergence. Epdl2 belongs to the ependymin-related family (EPDR), a functionally diverse family of secretory glycoproteins. In this study, we first describe vertebrate EPDR evolution and then present a detailed evolutionary history of epdl2 in Mormyridae with emphasis on the speciose genus Paramormyrops. Using Sanger sequencing, we confirm three apparently functional epdl2 genes in Paramormyrops kingsleyae. Next, we developed a nanopore-based amplicon sequencing strategy and bioinformatics pipeline to obtain and classify full-length epdl2 gene sequences (N = 34) across Mormyridae. Our phylogenetic analysis proposes three or four epdl2 paralogs dating from early Paramormyrops evolution. Finally, we conducted selection tests which detected positive selection around the duplication events and identified ten sites likely targeted by selection in the resulting paralogs. These sites' locations in our modeled 3D protein structure involve four sites in ligand binding and six sites in homodimer formation. Together, these findings strongly imply an evolutionary mechanism whereby epdl2 genes underwent selection-driven functional specialization after tandem duplications in the rapidly speciating Paramormyrops. Considering previous evidence, we propose that epdl2 may contribute to electric signal diversification in mormyrids, an important aspect of species recognition during mating.
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Affiliation(s)
- Mauricio Losilla
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA.,Graduate Program in Ecology, Evolution and Behavior, Michigan State University, East Lansing, MI 48824, USA
| | - Jason R Gallant
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA.,Graduate Program in Ecology, Evolution and Behavior, Michigan State University, East Lansing, MI 48824, USA
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14
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Structure and proteomic analysis of the crown-of-thorns starfish (Acanthaster sp.) radial nerve cord. Sci Rep 2023; 13:3349. [PMID: 36849815 PMCID: PMC9971248 DOI: 10.1038/s41598-023-30425-1] [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: 09/27/2022] [Accepted: 02/22/2023] [Indexed: 03/01/2023] Open
Abstract
The nervous system of the Asteroidea (starfish or seastar) consists of radial nerve cords (RNCs) that interconnect with a ring nerve. Despite its relative simplicity, it facilitates the movement of multiple arms and numerous tube feet, as well as regeneration of damaged limbs. Here, we investigated the RNC ultrastructure and its molecular components within the of Pacific crown-of-thorns starfish (COTS; Acanthaster sp.), a well-known coral predator that in high-density outbreaks has major ecological impacts on coral reefs. We describe the presence of an array of unique small bulbous bulbs (40-100 μm diameter) that project from the ectoneural region of the adult RNC. Each comprise large secretory-like cells and prominent cilia. In contrast, juvenile COTS and its congener Acanthaster brevispinus lack these features, both of which are non-corallivorous. Proteomic analysis of the RNC (and isolated neural bulbs) provides the first comprehensive echinoderm protein database for neural tissue, including numerous secreted proteins associated with signalling, transport and defence. The neural bulbs contained several neuropeptides (e.g., bombyxin-type, starfish myorelaxant peptide, secretogranin 7B2-like, Ap15a-like, and ApNp35) and Deleted in Malignant Brain Tumor 1-like proteins. In summary, this study provides a new insight into the novel traits of COTS, a major pest on coral reefs, and a proteomics resource that can be used to develop (bio)control strategies and understand molecular mechanisms of regeneration.
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15
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Mendoza-Porras O, Nguyen TV, Shah RM, Thomas-Hall P, Bastin L, Deaker DJ, Motti CA, Byrne M, Beale DJ. Biochemical metabolomic profiling of the Crown-of-Thorns Starfish (Acanthaster): New insight into its biology for improved pest management. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 861:160525. [PMID: 36574554 DOI: 10.1016/j.scitotenv.2022.160525] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/20/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
The Crown-of-Thorns Starfish (COTS), Acanthaster species, is a voracious coral predator that destroys coral reefs when in outbreak status. The baseline metabolite and lipid biomolecules of 10 COTS tissues, including eggs from gravid females, were investigated in this study to provide insight into their biology and identify avenues for control. Targeted and untargeted metabolite- and lipidomics-based mass spectrometry approaches were used to obtain tissue-specific metabolite and lipid profiles. Across all COTS tissues, 410 metabolites and 367 lipids were identified. Most abundant were amino acids and peptides (18.7%) and wax esters (17%). There were 262 metabolites and 192 lipids identified in COTS eggs. Wax esters were more abundant in the eggs (30%) followed by triacylglycerols (TG), amino acids, and peptides. The diversity of asterosaponins in eggs (34) was higher than in tissues (2). Several asterosaponins known to modulate sperm acrosome reaction were putatively identified, including glycoside B, asterosaponin-4 (Co-Aris III), and regularoside B (asterosaponin A). The saponins saponin A, thornasteroside A, hillaside B, and non-saponins dictyol J and axinellamine B which have been shown to possess defensive properties, were found in abundance in gonads, skin, and radial nerve tissues. Inosine and 2-hexyldecanoic acid are the most abundant metabolites in tissues and eggs. As a secondary metabolite of purine degradation, inosine plays an important role in purine biosynthesis, while 2-hexyldecanoic acid is known to suppress side-chain crystallization during the synthesis of amphiphilic macromolecules (i.e., phospholipids). These significant spatial changes in metabolite, lipid, and asterosaponin profiles enabled unique insights into key biological tissue-specific processes that could be manipulated to better control COTS populations. Our findings highlight COTS as a novel source of molecules with therapeutic and cosmetic properties (ceramides, sphingolipids, carnosine, and inosine). These outcomes will be highly relevant for the development of strategies for COTS management including chemotaxis-based biocontrol and exploitation of COTS carcasses for the extraction of commercial molecules.
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Affiliation(s)
- Omar Mendoza-Porras
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Queensland Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Thao V Nguyen
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Rohan M Shah
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Peter Thomas-Hall
- Australian Institute of Marine Science (AIMS), Townsville, QLD 4810, Australia
| | - Lee Bastin
- Australian Institute of Marine Science (AIMS), Townsville, QLD 4810, Australia
| | - Dione J Deaker
- Marine Studies Institute, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Cherie A Motti
- Australian Institute of Marine Science (AIMS), Townsville, QLD 4810, Australia
| | - Maria Byrne
- Marine Studies Institute, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Ecosciences Precinct, Dutton Park, QLD 4102, Australia.
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16
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A Proteomic Analysis for the Red Seaweed Asparagopsis taxiformis. BIOLOGY 2023; 12:biology12020167. [PMID: 36829446 PMCID: PMC9952816 DOI: 10.3390/biology12020167] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/22/2023]
Abstract
The red seaweed Asparagopsis taxiformis is a promising ruminant feed additive with anti-methanogenic properties that could contribute to global climate change solutions. Genomics has provided a strong foundation for in-depth molecular investigations, including proteomics. Here, we investigated the proteome of A. taxiformis (Lineage 6) in both sporophyte and gametophyte stages, using soluble and insoluble extraction methods. We identified 741 unique non-redundant proteins using a genome-derived database and 2007 using a transcriptome-derived database, which included numerous proteins predicted to be of fungal origin. We further investigated the genome-derived proteins to focus on seaweed-specific proteins. Ontology analysis indicated a relatively large proportion of ion-binding proteins (i.e., iron, zinc, manganese, potassium and copper), which may play a role in seaweed heavy metal tolerance. In addition, we identified 58 stress-related proteins (e.g., heat shock and vanadium-dependent haloperoxidases) and 44 photosynthesis-related proteins (e.g., phycobilisomes, photosystem I, photosystem II and ATPase), which were in general more abundantly identified from female gametophytes. Forty proteins were predicted to be secreted, including ten rhodophyte collagen-alpha-like proteins (RCAPs), which displayed overall high gene expression levels. These findings provide a comprehensive overview of expressed proteins in A. taxiformis, highlighting the potential for targeted protein extraction and functional characterisation for future biodiscovery.
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17
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Shao G, He T, Mu Y, Mu P, Ao J, Lin X, Ruan L, Wang Y, Gao Y, Liu D, Zhang L, Chen X. The genome of a hadal sea cucumber reveals novel adaptive strategies to deep-sea environments. iScience 2022; 25:105545. [PMID: 36444293 PMCID: PMC9700323 DOI: 10.1016/j.isci.2022.105545] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/18/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
How organisms cope with coldness and high pressure in the hadal zone remains poorly understood. Here, we sequenced and assembled the genome of hadal sea cucumber Paelopatides sp. Yap with high quality and explored its potential mechanisms for deep-sea adaptation. First, the expansion of ACOX1 for rate-limiting enzyme in the DHA synthesis pathway, increased DHA content in the phospholipid bilayer, and positive selection of EPT1 may maintain cell membrane fluidity. Second, three genes for translation initiation factors and two for ribosomal proteins underwent expansion, and three ribosomal protein genes were positively selected, which may ameliorate the protein synthesis inhibition or ribosome dissociation in the hadal zone. Third, expansion and positive selection of genes associated with stalled replication fork recovery and DNA repair suggest improvements in DNA protection. This is the first genome sequence of a hadal invertebrate. Our results provide insights into the genetic adaptations used by invertebrate in deep oceans.
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Affiliation(s)
- Guangming Shao
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Tianliang He
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yinnan Mu
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Pengfei Mu
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Jingqun Ao
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xihuang Lin
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian 361005, China
| | - Lingwei Ruan
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian 361005, China
| | - YuGuang Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian 361005, China
| | - Yuan Gao
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Dinggao Liu
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Liangsheng Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xinhua Chen
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong 519000, China
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18
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Jönsson M, Morin M, Wang CK, Craik DJ, Degnan SM, Degnan BM. Sex-specific expression of pheromones and other signals in gravid starfish. BMC Biol 2022; 20:288. [PMID: 36528687 PMCID: PMC9759900 DOI: 10.1186/s12915-022-01491-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Many echinoderms form seasonal aggregations prior to spawning. In some fecund species, a spawning event can lead to population outbreaks with detrimental ecosystem impacts. For instance, outbreaks of crown-of-thorns starfish (COTS), a corallivore, can destroy coral reefs. Here, we examine the gene expression in gravid male and female COTS prior to spawning in the wild, to identify genome-encoded factors that may regulate aggregation and spawning. This study is informed by a previously identified exoproteome that attracts conspecifics. To capture the natural gene expression profiles, we isolated RNAs from gravid female and male COTS immediately after they were removed from the Great Barrier Reef. RESULTS: Sexually dimorphic gene expression is present in all seven somatic tissues and organs that we surveyed and in the gonads. Approximately 40% of the exoproteome transcripts are differentially expressed between sexes. Males uniquely upregulate an additional 68 secreted factors in their testes. A suite of neuropeptides in sensory organs, coelomocytes and gonads is differentially expressed between sexes, including the relaxin-like gonad-stimulating peptide and gonadotropin-releasing hormones. Female sensory tentacles-chemosensory organs at the distal tips of the starfish arms-uniquely upregulate diverse receptors and signalling molecules, including chemosensory G-protein-coupled receptors and several neuropeptides, including kisspeptin, SALMFamide and orexin. CONCLUSIONS Analysis of 103 tissue/organ transcriptomes from 13 wild COTS has revealed genes that are consistently differentially expressed between gravid females and males and that all tissues surveyed are sexually dimorphic at the molecular level. This finding is consistent with female and male COTS using sex-specific pheromones to regulate reproductive aggregations and synchronised spawning events. These pheromones appear to be received primarily by the sensory tentacles, which express a range of receptors and signalling molecules in a sex-specific manner. Furthermore, coelomocytes and gonads differentially express signalling and regulatory factors that control gametogenesis and spawning in other echinoderms.
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Affiliation(s)
- Mathias Jönsson
- Centre for Marine Science, School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Marie Morin
- Centre for Marine Science, School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sandie M Degnan
- Centre for Marine Science, School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Bernard M Degnan
- Centre for Marine Science, School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.
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19
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Santella L, Chun JT. Structural actin dynamics during oocyte maturation and fertilization. Biochem Biophys Res Commun 2022; 633:13-16. [DOI: 10.1016/j.bbrc.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/06/2022]
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20
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Zhou P, Li J, Huang J, Li F, Zhang Q, Zhang M. Genome Survey Sequencing and Genetic Background Characterization of Ilex chinensis Sims (Aquifoliaceae) Based on Next-Generation Sequencing. PLANTS (BASEL, SWITZERLAND) 2022; 11:3322. [PMID: 36501361 PMCID: PMC9740704 DOI: 10.3390/plants11233322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Ilex chinensis Sims. is an evergreen arbor species with high ornamental and medicinal value that is widely distributed in China. However, there is a lack of molecular and genomic data for this plant, which severely restricts the development of its relevant research. To obtain the whole reference genome, we first conducted a genome survey of I. chinensis by next-generation sequencing (NGS) to perform de novo whole-genome sequencing. As a result, our estimates using k-mer and flow cytometric analysis suggested the genome size of I. chinensis to be around 618-655 Mb, with the GC content, heterozygous rate, and repeat sequence rate of 37.52%, 1.1%, and 38%, respectively. A total of 334,649 microsatellite motifs were detected from the I. chinensis genome data, which will provide basic molecular markers for germplasm characterization, genetic diversity, and QTL mapping studies for I. chinensis. In summary, the I. chinensis genome is complex with high heterozygosity and few repeated sequences. Overall, this is the first report on the genome features of I. chinensis, and the information may lay a strong groundwork for future whole-genome sequencing and molecular breeding studies of this species.
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Affiliation(s)
- Peng Zhou
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing 211153, China
| | - Jiao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Jing Huang
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing 211153, China
| | - Fei Li
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing 211153, China
| | - Qiang Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Min Zhang
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing 211153, China
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21
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Macfarlane FR, Lorenzi T, Painter KJ. The Impact of Phenotypic Heterogeneity on Chemotactic Self-Organisation. Bull Math Biol 2022; 84:143. [PMID: 36319913 PMCID: PMC9626439 DOI: 10.1007/s11538-022-01099-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
Abstract
The capacity to aggregate through chemosensitive movement forms a paradigm of self-organisation, with examples spanning cellular and animal systems. A basic mechanism assumes a phenotypically homogeneous population that secretes its own attractant, with the well known system introduced more than five decades ago by Keller and Segel proving resolutely popular in modelling studies. The typical assumption of population phenotypic homogeneity, however, often lies at odds with the heterogeneity of natural systems, where populations may comprise distinct phenotypes that vary according to their chemotactic ability, attractant secretion, etc. To initiate an understanding into how this diversity can impact on autoaggregation, we propose a simple extension to the classical Keller and Segel model, in which the population is divided into two distinct phenotypes: those performing chemotaxis and those producing attractant. Using a combination of linear stability analysis and numerical simulations, we demonstrate that switching between these phenotypic states alters the capacity of a population to self-aggregate. Further, we show that switching based on the local environment (population density or chemoattractant level) leads to diverse patterning and provides a route through which a population can effectively curb the size and density of an aggregate. We discuss the results in the context of real world examples of chemotactic aggregation, as well as theoretical aspects of the model such as global existence and blow-up of solutions.
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Affiliation(s)
- Fiona R Macfarlane
- School of Mathematics and Statistics, University of St Andrews, St Andrews, Scotland.
| | - Tommaso Lorenzi
- Department of Mathematical Sciences "G. L. Lagrange", Politecnico di Torino, Turin, Italy
| | - Kevin J Painter
- Inter-university Department of Regional and Urban Studies and Planning, Politecnico di Torino, Turin, Italy
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22
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De novo genome assembly and annotation of Holothuria scabra (Jaeger, 1833) from nanopore sequencing reads. Genes Genomics 2022; 44:1487-1498. [DOI: 10.1007/s13258-022-01322-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/29/2022] [Indexed: 11/04/2022]
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23
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Ketchum RN, Davidson PL, Smith EG, Wray GA, Burt JA, Ryan JF, Reitzel AM. A Chromosome-level Genome Assembly of the Highly Heterozygous Sea Urchin Echinometra sp. EZ Reveals Adaptation in the Regulatory Regions of Stress Response Genes. Genome Biol Evol 2022; 14:evac144. [PMID: 36161313 PMCID: PMC9557091 DOI: 10.1093/gbe/evac144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2022] [Indexed: 11/14/2022] Open
Abstract
Echinometra is the most widespread genus of sea urchin and has been the focus of a wide range of studies in ecology, speciation, and reproduction. However, available genetic data for this genus are generally limited to a few select loci. Here, we present a chromosome-level genome assembly based on 10x Genomics, PacBio, and Hi-C sequencing for Echinometra sp. EZ from the Persian/Arabian Gulf. The genome is assembled into 210 scaffolds totaling 817.8 Mb with an N50 of 39.5 Mb. From this assembly, we determined that the E. sp. EZ genome consists of 2n = 42 chromosomes. BUSCO analysis showed that 95.3% of BUSCO genes were complete. Ab initio and transcript-informed gene modeling and annotation identified 29,405 genes, including a conserved Hox cluster. E. sp. EZ can be found in high-temperature and high-salinity environments, and we therefore compared E. sp. EZ gene families and transcription factors associated with environmental stress response ("defensome") with other echinoid species with similar high-quality genomic resources. While the number of defensome genes was broadly similar for all species, we identified strong signatures of positive selection in E. sp. EZ noncoding elements near genes involved in environmental response pathways as well as losses of transcription factors important for environmental response. These data provide key insights into the biology of E. sp. EZ as well as the diversification of Echinometra more widely and will serve as a useful tool for the community to explore questions in this taxonomic group and beyond.
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Affiliation(s)
- Remi N Ketchum
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
- Whitney Laboratory for Marine Bioscience, University of Florida, Marineland, Florida, USA
| | | | - Edward G Smith
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Gregory A Wray
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - John A Burt
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, Marineland, Florida, USA
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
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24
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Mashanov V, Machado DJ, Reid R, Brouwer C, Kofsky J, Janies DA. Twinkle twinkle brittle star: the draft genome of Ophioderma brevispinum (Echinodermata: Ophiuroidea) as a resource for regeneration research. BMC Genomics 2022; 23:574. [PMID: 35953768 PMCID: PMC9367165 DOI: 10.1186/s12864-022-08750-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 07/08/2022] [Indexed: 12/13/2022] Open
Abstract
Background Echinoderms are established models in experimental and developmental biology, however genomic resources are still lacking for many species. Here, we present the draft genome of Ophioderma brevispinum, an emerging model organism in the field of regenerative biology. This new genomic resource provides a reference for experimental studies of regenerative mechanisms. Results We report a de novo nuclear genome assembly for the brittle star O. brevispinum and annotation facilitated by the transcriptome assembly. The final assembly is 2.68 Gb in length and contains 146,703 predicted protein-coding gene models. We also report a mitochondrial genome for this species, which is 15,831 bp in length, and contains 13 protein-coding, 22 tRNAs, and 2 rRNAs genes, respectively. In addition, 29 genes of the Notch signaling pathway are identified to illustrate the practical utility of the assembly for studies of regeneration. Conclusions The sequenced and annotated genome of O. brevispinum presented here provides the first such resource for an ophiuroid model species. Considering the remarkable regenerative capacity of this species, this genome will be an essential resource in future research efforts on molecular mechanisms regulating regeneration. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-022-08750-y).
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Affiliation(s)
- Vladimir Mashanov
- Wake Forest Institute for Regenerative Medicine, 391 Technology Way, Winston-Salem, 27101, NC, USA. .,University of North Florida, Department of Biology, 1 UNF Drive, Jacksonville, 32224, FL, USA.
| | - Denis Jacob Machado
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, 9201 University City Blvd, Charlotte, 28223, NC, USA
| | - Robert Reid
- University of North Carolina at Charlotte, College of Computing and Informatics, North Carolina Research Campus, 150 Research Campus Drive, Kannapolis, 28081, NC, USA
| | - Cory Brouwer
- University of North Carolina at Charlotte, College of Computing and Informatics, North Carolina Research Campus, 150 Research Campus Drive, Kannapolis, 28081, NC, USA
| | - Janice Kofsky
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, 9201 University City Blvd, Charlotte, 28223, NC, USA
| | - Daniel A Janies
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, 9201 University City Blvd, Charlotte, 28223, NC, USA
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25
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Paramonov AS, Shulepko MA, Makhonin AM, Bychkov ML, Kulbatskii DS, Chernikov AM, Myshkin MY, Shabelnikov SV, Shenkarev ZO, Kirpichnikov MP, Lyukmanova EN. New Three-Finger Protein from Starfish Asteria rubens Shares Structure and Pharmacology with Human Brain Neuromodulator Lynx2. Mar Drugs 2022; 20:md20080503. [PMID: 36005506 PMCID: PMC9410279 DOI: 10.3390/md20080503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Three-finger proteins (TFPs) are small proteins with characteristic three-finger β-structural fold stabilized by the system of conserved disulfide bonds. These proteins have been found in organisms from different taxonomic groups and perform various important regulatory functions or act as components of snake venoms. Recently, four TFPs (Lystars 1–4) with unknown function were identified in the coelomic fluid proteome of starfish A. rubens. Here we analyzed the genomes of A. rubens and A. planci starfishes and predicted additional five and six proteins containing three-finger domains, respectively. One of them, named Lystar5, is expressed in A. rubens coelomocytes and has sequence homology to the human brain neuromodulator Lynx2. The three-finger structure of Lystar5 close to the structure of Lynx2 was confirmed by NMR. Similar to Lynx2, Lystar5 negatively modulated α4β2 nicotinic acetylcholine receptors (nAChRs) expressed in X. laevis oocytes. Incubation with Lystar5 decreased the expression of acetylcholine esterase and α4 and α7 nAChR subunits in the hippocampal neurons. In summary, for the first time we reported modulator of the cholinergic system in starfish.
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Affiliation(s)
- Alexander S. Paramonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
| | - Mikhail A. Shulepko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
| | - Alexey M. Makhonin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
- AI Centre, National Research University Higher School of Economics, Myasnitskaya Str. 20, 101000 Moscow, Russia
| | - Maxim L. Bychkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
| | - Dmitrii S. Kulbatskii
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
| | - Andrey M. Chernikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
- Interdisciplinary Scientific and Educational School of Moscow University “Molecular Technologies of the Living Systems and Synthetic Biology”, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory, 119234 Moscow, Russia
| | - Mikhail Yu. Myshkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
| | - Sergey V. Shabelnikov
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Prospect 4, 194064 St. Petersburg, Russia;
| | - Zakhar O. Shenkarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
- Moscow Institute of Physics and Technology, State University, Institutskiy Per. 9, 141701 Moscow, Russia
| | - Mikhail P. Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
- Interdisciplinary Scientific and Educational School of Moscow University “Molecular Technologies of the Living Systems and Synthetic Biology”, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory, 119234 Moscow, Russia
| | - Ekaterina N. Lyukmanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
- Interdisciplinary Scientific and Educational School of Moscow University “Molecular Technologies of the Living Systems and Synthetic Biology”, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory, 119234 Moscow, Russia
- Moscow Institute of Physics and Technology, State University, Institutskiy Per. 9, 141701 Moscow, Russia
- Correspondence:
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26
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Oulhen N, Byrne M, Duffin P, Gomez-Chiarri M, Hewson I, Hodin J, Konar B, Lipp EK, Miner BG, Newton AL, Schiebelhut LM, Smolowitz R, Wahltinez SJ, Wessel GM, Work TM, Zaki HA, Wares JP. A Review of Asteroid Biology in the Context of Sea Star Wasting: Possible Causes and Consequences. THE BIOLOGICAL BULLETIN 2022; 243:50-75. [PMID: 36108034 PMCID: PMC10642522 DOI: 10.1086/719928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
AbstractSea star wasting-marked in a variety of sea star species as varying degrees of skin lesions followed by disintegration-recently caused one of the largest marine die-offs ever recorded on the west coast of North America, killing billions of sea stars. Despite the important ramifications this mortality had for coastal benthic ecosystems, such as increased abundance of prey, little is known about the causes of the disease or the mechanisms of its progression. Although there have been studies indicating a range of causal mechanisms, including viruses and environmental effects, the broad spatial and depth range of affected populations leaves many questions remaining about either infectious or non-infectious mechanisms. Wasting appears to start with degradation of mutable connective tissue in the body wall, leading to disintegration of the epidermis. Here, we briefly review basic sea star biology in the context of sea star wasting and present our current knowledge and hypotheses related to the symptoms, the microbiome, the viruses, and the associated environmental stressors. We also highlight throughout the article knowledge gaps and the data needed to better understand sea star wasting mechanistically, its causes, and potential management.
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Affiliation(s)
- Nathalie Oulhen
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Maria Byrne
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Paige Duffin
- Department of Genetics, University of Georgia, Athens, Georgia
| | - Marta Gomez-Chiarri
- Department of Fisheries, Animal, and Veterinary Science, University of Rhode Island, Kingston, Rhode Island
| | - Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, New York
| | - Jason Hodin
- Friday Harbor Labs, University of Washington, Friday Harbor, Washington
| | - Brenda Konar
- College of Fisheries and Ocean Sciences, University of Alaska, Fairbanks, Alaska
| | - Erin K. Lipp
- Department of Environmental Health Science, University of Georgia, Athens, Georgia
| | - Benjamin G. Miner
- Department of Biology, Western Washington University, Bellingham, Washington
| | | | - Lauren M. Schiebelhut
- Department of Life and Environmental Sciences, University of California, Merced, California
| | - Roxanna Smolowitz
- Department of Biology and Marine Biology, Roger Williams University, Bristol, Rhode Island
| | - Sarah J. Wahltinez
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida
| | - Gary M. Wessel
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Thierry M. Work
- US Geological Survey, National Wildlife Health Center, Honolulu Field Station, Honolulu, Hawaii
| | - Hossam A. Zaki
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - John P. Wares
- Department of Genetics, University of Georgia, Athens, Georgia
- Odum School of Ecology, University of Georgia, Athens, Georgia
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27
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Biosynthesis of saponin defensive compounds in sea cucumbers. Nat Chem Biol 2022; 18:774-781. [PMID: 35761075 PMCID: PMC9236903 DOI: 10.1038/s41589-022-01054-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 05/09/2022] [Indexed: 12/03/2022]
Abstract
Soft-bodied slow-moving sea creatures such as sea stars and sea cucumbers lack an adaptive immune system and have instead evolved the ability to make specialized protective chemicals (glycosylated steroids and triterpenes) as part of their innate immune system. This raises the intriguing question of how these biosynthetic pathways have evolved. Sea star saponins are steroidal, while those of the sea cucumber are triterpenoid. Sterol biosynthesis in animals involves cyclization of 2,3-oxidosqualene to lanosterol by the oxidosqualene cyclase (OSC) enzyme lanosterol synthase (LSS). Here we show that sea cucumbers lack LSS and instead have two divergent OSCs that produce triterpene saponins and that are likely to have evolved from an ancestral LSS by gene duplication and neofunctionalization. We further show that sea cucumbers make alternate sterols that confer protection against self-poisoning by their own saponins. Collectively, these events have enabled sea cucumbers to evolve the ability to produce saponins and saponin-resistant sterols concomitantly. ![]()
Sea stars and sea cucumbers biosynthesize protective glycosylated steroids and triterpenes via divergent oxidosqualene cyclases (OSCs) that produce these distinct saponins in different species as well as in different tissues of a single species.
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28
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Evans TG, Bible JM, Maynard A, Griffith KR, Sanford E, Kültz D. Proteomic changes associated with predator-induced morphological defenses in oysters. Mol Ecol 2022; 31:4254-4270. [PMID: 35754098 DOI: 10.1111/mec.16580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/03/2022] [Accepted: 06/20/2022] [Indexed: 11/27/2022]
Abstract
Inducible prey defenses occur when organisms undergo plastic changes in phenotype to reduce predation risk. When predation pressure varies persistently over space or time, such as when predator and prey co-occur over only part of their biogeographic ranges, prey populations can become locally adapted in their inducible defenses. In California estuaries, native Olympia oyster (Ostrea lurida) populations have evolved disparate phenotypic responses to an invasive predator, the Atlantic oyster drill (Urosalpinx cinerea). In this study, oysters from an estuary with drills, and oysters from an estuary without drills, were reared for two generations in a laboratory common garden, and subsequently exposed to cues from Atlantic drills. Comparative proteomics was then used to investigate molecular mechanisms underlying conserved and divergent aspects of their inducible defenses. Both populations developed smaller, thicker, and harder shells after drill exposure, and these changes in shell phenotype were associated with up-regulation of calcium transport proteins that could influence biomineralization. Inducible defenses evolve in part because defended phenotypes incur fitness costs when predation risk is low. Immune proteins were down-regulated by both oyster populations after exposure to drills, implying a trade-off between biomineralization and immune function. Following drill exposure, oysters from the population that co-occurs with drills grew smaller shells than oysters inhabiting the estuary not yet invaded by the predator. Variation in the response to drills between populations was associated with isoform-specific protein expression. This trend suggests that a stronger inducible defense response evolved in oysters that co-occur with drills through modification of an existing mechanism.
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Affiliation(s)
- Tyler G Evans
- Department of Biological Sciences, California State University East Bay, Hayward, CA 94542, USA
| | - Jillian M Bible
- Department of Environmental Science and Studies, Washington College, Chestertown, MD 21620, USA
| | - Ashley Maynard
- Department of Biological Sciences, California State University East Bay, Hayward, CA 94542, USA
| | - Kaylee R Griffith
- Department of Evolution and Ecology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA 94923, USA
| | - Eric Sanford
- Department of Evolution and Ecology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA 94923, USA
| | - Dietmar Kültz
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA
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29
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Yaguchi S, Wada H. Marine genomics, transcriptomics, and beyond in developmental, cell, and evolutionary biology. Dev Growth Differ 2022; 64:196-197. [PMID: 35665922 DOI: 10.1111/dgd.12792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Shunsuke Yaguchi
- Shimoda Marine Research Center, University of Tsukuba, Tsukuba, Japan
| | - Hiroshi Wada
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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30
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Suraweera CD, Banjara S, Hinds MG, Kvansakul M. Metazoans and Intrinsic Apoptosis: An Evolutionary Analysis of the Bcl-2 Family. Int J Mol Sci 2022; 23:ijms23073691. [PMID: 35409052 PMCID: PMC8998228 DOI: 10.3390/ijms23073691] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 01/12/2023] Open
Abstract
The B-cell lymphoma-2 (Bcl-2) family is a group of genes regulating intrinsic apoptosis, a process controlling events such as development, homeostasis and the innate and adaptive immune responses in metazoans. In higher organisms, Bcl-2 proteins coordinate intrinsic apoptosis through their regulation of the integrity of the mitochondrial outer membrane; this function appears to have originated in the basal metazoans. Bcl-2 genes predate the cnidarian-bilaterian split and have been identified in porifera, placozoans and cnidarians but not ctenophores and some nematodes. The Bcl-2 family is composed of two groups of proteins, one with an α-helical Bcl-2 fold that has been identified in porifera, placozoans, cnidarians, and almost all higher bilaterians. The second group of proteins, the BH3-only group, has little sequence conservation and less well-defined structures and is found in cnidarians and most bilaterians, but not porifera or placozoans. Here we examine the evolutionary relationships between Bcl-2 proteins. We show that the structures of the Bcl-2-fold proteins are highly conserved over evolutionary time. Some metazoans such as the urochordate Oikopleura dioica have lost all Bcl-2 family members. This gene loss indicates that Bcl-2 regulated apoptosis is not an absolute requirement in metazoans, a finding mirrored in recent gene deletion studies in mice. Sequence analysis suggests that at least some Bcl-2 proteins lack the ability to bind BH3-only antagonists and therefore potentially have other non-apoptotic functions. By examining the foundations of the Bcl-2 regulated apoptosis, functional relationships may be clarified that allow us to understand the role of specific Bcl-2 proteins in evolution and disease.
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Affiliation(s)
- Chathura D. Suraweera
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia; (C.D.S.); (S.B.)
| | - Suresh Banjara
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia; (C.D.S.); (S.B.)
| | - Mark G. Hinds
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3052, Australia
- Correspondence: (M.G.H.); (M.K.)
| | - Marc Kvansakul
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia; (C.D.S.); (S.B.)
- Correspondence: (M.G.H.); (M.K.)
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31
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Zhang L, He J, Tan P, Gong Z, Qian S, Miao Y, Zhang HY, Tu G, Chen Q, Zhong Q, Han G, He J, Wang M. The genome of an apodid holothuroid (Chiridota heheva) provides insights into its adaptation to a deep-sea reducing environment. Commun Biol 2022; 5:224. [PMID: 35273345 PMCID: PMC8913654 DOI: 10.1038/s42003-022-03176-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 02/16/2022] [Indexed: 11/09/2022] Open
Abstract
Cold seeps and hydrothermal vents are deep-sea reducing environments that are characterized by lacking oxygen and photosynthesis-derived nutrients. Most animals acquire nutrition in cold seeps or hydrothermal vents by maintaining epi- or endosymbiotic relationship with chemoautotrophic microorganisms. Although several seep- and vent-dwelling animals hosting symbiotic microbes have been well-studied, the genomic basis of adaptation to deep-sea reducing environment in nonsymbiotic animals is still lacking. Here, we report a high-quality genome of Chiridota heheva Pawson & Vance, 2004, which thrives by extracting organic components from sediment detritus and suspended material, as a reference for nonsymbiotic animal's adaptation to deep-sea reducing environments. The expansion of the aerolysin-like protein family in C. heheva compared with other echinoderms might be involved in the disintegration of microbes during digestion. Moreover, several hypoxia-related genes (Pyruvate Kinase M2, PKM2; Phospholysine Phosphohistidine Inorganic Pyrophosphate Phosphatase, LHPP; Poly(A)-specific Ribonuclease Subunit PAN2, PAN2; and Ribosomal RNA Processing 9, RRP9) were subject to positive selection in the genome of C. heheva, which contributes to their adaptation to hypoxic environments.
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Affiliation(s)
- Long Zhang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Jian He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Peipei Tan
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Zhen Gong
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shiyu Qian
- School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Yuanyuan Miao
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Han-Yu Zhang
- Hainan Key Laboratory of Marine Georesource and Prospecting, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Guangxian Tu
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Qi Chen
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Qiqi Zhong
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Guanzhu Han
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jianguo He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China. .,Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China. .,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Maoming, 525435, China.
| | - Muhua Wang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China. .,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Maoming, 525435, China.
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Crown of thorns starfish life-history traits contribute to outbreaks, a continuing concern for coral reefs. Emerg Top Life Sci 2022; 6:67-79. [PMID: 35225331 PMCID: PMC9023020 DOI: 10.1042/etls20210239] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/22/2022] [Accepted: 02/03/2022] [Indexed: 11/24/2022]
Abstract
Crown of thorns starfish (COTS, Acanthaster sp.) are notorious for their destructive consumption of coral that decimates tropical reefs, an attribute unique among tropical marine invertebrates. Their populations can rapidly increase from 0–1 COTS ha−1 to more than 10–1000 COTS ha−1 in short order causing a drastic change to benthic communities and reducing the functional and species diversity of coral reef ecosystems. Population outbreaks were first identified to be a significant threat to coral reefs in the 1960s. Since then, they have become one of the leading causes of coral loss along with coral bleaching. Decades of research and significant investment in Australia and elsewhere, particularly Japan, have been directed towards identifying, understanding, and managing the potential causes of outbreaks and designing population control methods. Despite this, the drivers of outbreaks remain elusive. What is becoming increasingly clear is that the success of COTS is tied to their inherent biological traits, especially in early life. Survival of larval and juvenile COTS is likely to be enhanced by their dietary flexibility and resilience to variable food conditions as well as their phenotypically plastic growth dynamics, all magnified by the extreme reproductive potential of COTS. These traits enable COTS to capitalise on anthropogenic disturbances to reef systems as well as endure less favourable conditions.
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Somatostatin-type and allatostatin-C-type neuropeptides are paralogous and have opposing myoregulatory roles in an echinoderm. Proc Natl Acad Sci U S A 2022; 119:2113589119. [PMID: 35145030 PMCID: PMC8851493 DOI: 10.1073/pnas.2113589119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2021] [Indexed: 12/25/2022] Open
Abstract
Somatostatin (SS) and allatostatin-C (ASTC) are related neuropeptide hormones that act as inhibitory regulators of physiological processes in chordates (e.g., humans) and protostome invertebrates (e.g., insects), respectively. We have discovered that echinoderms (e.g., starfish) uniquely have both SS-type and ASTC-type neuropeptides, which act as inhibitory and excitatory regulators of muscle activity, respectively. Our findings suggest that SS-type and ASTC-type neuropeptides evolved by duplication of a common ancestral encoding gene. Then, one of the neuropeptides was lost in protostomes and chordates, probably because of their functional redundancy as inhibitory regulators. Conversely, the unique retention of both neuropeptide types in echinoderms may be explained by evolution of an excitatory role for ASTC-type neuropeptides mediated by yet-to-be-determined signaling mechanisms. Somatostatin (SS) and allatostatin-C (ASTC) are inhibitory neuropeptides in chordates and protostomes, respectively, which hitherto were identified as orthologs. However, echinoderms have two SS/ASTC-type neuropeptides (SS1 and SS2), and here, our analysis of sequence data indicates that SS1 is an ortholog of ASTC and SS2 is an ortholog of SS. The occurrence of both SS-type and ASTC-type neuropeptides in echinoderms provides a unique context to compare their physiological roles. Investigation of the expression and actions of the ASTC-type neuropeptide ArSS1 in the starfish Asterias rubens revealed that it causes muscle contraction (myoexcitation), contrasting with myoinhibitory effects of the SS-type neuropeptide ArSS2. Our findings suggest that SS-type and ASTC-type neuropeptides are paralogous and originated by gene duplication in a common ancestor of the Bilateria, with only one type being retained in chordates (SS) and protostomes (ASTC) but with both types being retained in echinoderms. Loss of ASTC-type and SS-type neuropeptides in chordates and protostomes, respectively, may have been due to their functional redundancy as inhibitory regulators of physiological processes. Conversely, the retention of both neuropeptide types in echinoderms may be a consequence of the evolution of a myoexcitatory role for ASTC-type neuropeptides mediated by as yet unknown signaling mechanisms.
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Pratchett MS, Caballes CF, Cvitanovic C, Raymundo ML, Babcock RC, Bonin MC, Bozec YM, Burn D, Byrne M, Castro-Sanguino C, Chen CCM, Condie SA, Cowan ZL, Deaker DJ, Desbiens A, Devantier LM, Doherty PJ, Doll PC, Doyle JR, Dworjanyn SA, Fabricius KE, Haywood MDE, Hock K, Hoggett AK, Høj L, Keesing JK, Kenchington RA, Lang BJ, Ling SD, Matthews SA, McCallum HI, Mellin C, Mos B, Motti CA, Mumby PJ, Stump RJW, Uthicke S, Vail L, Wolfe K, Wilson SK. Knowledge Gaps in the Biology, Ecology, and Management of the Pacific Crown-of-Thorns Sea Star Acanthaster sp. on Australia's Great Barrier Reef. THE BIOLOGICAL BULLETIN 2021; 241:330-346. [PMID: 35015620 DOI: 10.1086/717026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
AbstractCrown-of-thorns sea stars (Acanthaster sp.) are among the most studied coral reef organisms, owing to their propensity to undergo major population irruptions, which contribute to significant coral loss and reef degradation throughout the Indo-Pacific. However, there are still important knowledge gaps pertaining to the biology, ecology, and management of Acanthaster sp. Renewed efforts to advance understanding and management of Pacific crown-of-thorns sea stars (Acanthaster sp.) on Australia's Great Barrier Reef require explicit consideration of relevant and tractable knowledge gaps. Drawing on established horizon scanning methodologies, this study identified contemporary knowledge gaps by asking active and/or established crown-of-thorns sea star researchers to pose critical research questions that they believe should be addressed to improve the understanding and management of crown-of-thorns sea stars on the Great Barrier Reef. A total of 38 participants proposed 246 independent research questions, organized into 7 themes: feeding ecology, demography, distribution and abundance, predation, settlement, management, and environmental change. Questions were further assigned to 48 specific topics nested within the 7 themes. During this process, redundant questions were removed, which reduced the total number of distinct research questions to 172. Research questions posed were mostly related to themes of demography (46 questions) and management (48 questions). The dominant topics, meanwhile, were the incidence of population irruptions (16 questions), feeding ecology of larval sea stars (15 questions), effects of elevated water temperature on crown-of-thorns sea stars (13 questions), and predation on juveniles (12 questions). While the breadth of questions suggests that there is considerable research needed to improve understanding and management of crown-of-thorns sea stars on the Great Barrier Reef, the predominance of certain themes and topics suggests a major focus for new research while also providing a roadmap to guide future research efforts.
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Hart MW, Guerra VI, Allen JD, Byrne M. Cloning and Selfing Affect Population Genetic Variation in Simulations of Outcrossing, Sexual Sea Stars. THE BIOLOGICAL BULLETIN 2021; 241:286-302. [PMID: 35015625 DOI: 10.1086/717293] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
AbstractMany sea stars are well known for facultative or obligate asexual reproduction in both the adult and larval life-cycle stages. Some species and lineages are also capable of facultative or obligate hermaphroditic reproduction with self-fertilization. However, models of population genetic variation and empirical analyses of genetic data typically assume only sexual reproduction and outcrossing. A recent reanalysis of previously published empirical data (microsatellite genotypes) from two studies of one of the most well-known sea star species (the crown-of-thorns sea star; Acanthaster sp.) concluded that cloning and self-fertilization in that species are rare and contribute little to patterns of population genetic variation. Here we reconsider that conclusion by simulating the contribution of cloning and selfing to genetic variation in a series of models of sea star demography. Simulated variation in two simple models (analogous to previous analyses of empirical data) was consistent with high rates of cloning or selfing or both. More realistic scenarios that characterize population flux in sea stars of ecological significance, including outbreaks of crown-of-thorns sea stars that devastate coral reefs, invasions by Asterias amurensis, and epizootics of sea star wasting disease that kill Pisaster ochraceus, also showed significant but smaller effects of cloning and selfing on variation within subpopulations and differentiation between subpopulations. Future models or analyses of genetic variation in similar study systems might benefit from simulation modeling to characterize possible contributions of cloning or selfing to genetic variation in population samples or to understand the limits on inferring the effects of cloning or selfing in nature.
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Deaker DJ, Balogh R, Dworjanyn SA, Mos B, Byrne M. Echidnas of the Sea: The Defensive Behavior of Juvenile and Adult Crown-of-Thorns Sea Stars. THE BIOLOGICAL BULLETIN 2021; 241:259-270. [PMID: 35015617 DOI: 10.1086/716777] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
AbstractCrown-of-thorns sea stars are one of the most ecologically important tropical marine invertebrates, with boom-bust population dynamics that influence the community structure of coral reefs. Although predation is likely to influence the development of population outbreaks, little is known about the defensive behavior of crown-of-thorns sea stars. Righting behavior after being overturned, a key defensive response in echinoderms, was investigated for the newly settled herbivorous juvenile, the corallivorous juvenile, and adult stages of crown-of-thorns sea stars. The average righting time of the newly settled juveniles (0.3-1.0-mm diameter) was 2.74 minutes. For the coral-eating juveniles (15-55-mm diameter), the righting time (mean = 6.24 min) was faster in larger juveniles, and the mean righting time of the adults was 6.28 minutes. During righting and in response to being lifted off of the substrate, the juveniles and adults exhibited an arm curling response, during which their arms closed over their oral side, often forming a spine ball, a feature not known for other asteroids. The righting and curling responses of the corallivorous juveniles were influenced by the presence of a natural enemy, a coral guard crab, which caused the juveniles to spend more time with their arms curled. These behaviors indicate that crown-of-thorns sea stars use their spines to protect the soft tissue of their oral side. The highly defended morphology and behavioral adaptations of crown-of-thorns sea stars are likely to have evolved as antipredator mechanisms. This points to the potential importance of predators in regulating their populations, which may have decreased in recent times due to fishing, a factor that may contribute to outbreaks.
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Abstract
Dispersed populations often need to organize into groups. Chemical attractants provide one means of directing individuals into an aggregate, but whether these structures emerge can depend on various factors, such as there being a sufficiently large population or the response to the attractant being sufficiently sensitive. In an aquatic environment, fluid flow may heavily impact on population distribution and many aquatic organisms adopt a rheotaxis response when exposed to a current, orienting and swimming according to the flow field. Consequently, flow-induced transport could be substantially different for the population members and any aggregating signal they secrete. With the aim of investigating how flows and rheotaxis responses impact on an aquatic population's ability to form and maintain an aggregated profile, we develop and analyse a mathematical model that incorporates these factors. Through a systematic analysis into the effect of introducing rheotactic behaviour under various forms of environmental flow, we demonstrate that each of flow and rheotaxis can act beneficially or detrimentally on the ability to form and maintain a cluster. Synthesizing these findings, we test a hypothesis that density-dependent rheotaxis may be optimal for group formation and maintenance, in which individuals increase their rheotactic effort as they approach an aggregated state.
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Affiliation(s)
- K J Painter
- Dipartimento Interateneo di Scienze, Progetto e Politiche del Territorio (DIST), Politecnico di Torino, Viale Pier Andrea Mattioli, 39 10125 Torino, Italy
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38
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Sania RE, Cardoso JCR, Louro B, Marquet N, Canário AVM. A new subfamily of ionotropic glutamate receptors unique to the echinoderms with putative sensory role. Mol Ecol 2021; 30:6642-6658. [PMID: 34601781 DOI: 10.1111/mec.16206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 11/29/2022]
Abstract
Chemosensation is a critical signalling process in animals and especially important in sea cucumbers, a group of ecologically and economically important marine echinoderms (class Holothuroidea), which lack audio and visual organs and rely on chemical sensing for survival, feeding and reproduction. The ionotropic receptors are a recently identified family of chemosensory receptors in insects and other protostomes, related to the ionotropic glutamate receptor family (iGluR), a large family of membrane receptors in metazoan. Here we characterize the echinoderm iGluR subunits and consider their possible role in chemical communication in sea cucumbers. Sequence similarity searches revealed that sea cucumbers have in general a higher number of iGluR subunits when compared to other echinoderms. Phylogenetic analysis and sequence comparisons revealed GluH as a specific iGluR subfamily present in all echinoderms. Homologues of the vertebrate GluA (aka α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid, AMPA), GluK (aka kainate) and GluD (aka delta) were also identified. The GluN (aka N-methyl-d-aspartate, NMDA) as well as the invertebrate deuterostome subfamily GluF (aka phi) are absent in echinoderms. The echinoderm GluH subfamily shares conserved structural protein organization with vertebrate iGluRs and the ligand binding domain (LBD) is the most conserved region; genome analysis indicates evolution via lineage and species-specific tandem gene duplications. GluH genes (named Grih) are the most highly expressed iGluRs subunit genes in tissues in the sea cucumber Holothuria arguinesis, with Griha1, Griha2 and Griha5 exclusively expressed in tentacles, making them candidates to have a chemosensory role in this species. The multiple GluH subunits may provide alternative receptor assembly combinations, thus expanding the functional possibilities and widening the range of compounds detected during aggregation and spawning in echinoderms.
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Affiliation(s)
- Rubaiyat E Sania
- CCMAR/CIMAR LA, Centro de Ciências do Mar do Algarve, Universidade do Algarve, Faro, Portugal
| | - João C R Cardoso
- CCMAR/CIMAR LA, Centro de Ciências do Mar do Algarve, Universidade do Algarve, Faro, Portugal
| | - Bruno Louro
- CCMAR/CIMAR LA, Centro de Ciências do Mar do Algarve, Universidade do Algarve, Faro, Portugal
| | - Nathalie Marquet
- CCMAR/CIMAR LA, Centro de Ciências do Mar do Algarve, Universidade do Algarve, Faro, Portugal
| | - Adelino V M Canário
- CCMAR/CIMAR LA, Centro de Ciências do Mar do Algarve, Universidade do Algarve, Faro, Portugal
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Powell D, Groβe-Wilde E, Krokene P, Roy A, Chakraborty A, Löfstedt C, Vogel H, Andersson MN, Schlyter F. A highly-contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus, provides insight into a major forest pest. Commun Biol 2021; 4:1059. [PMID: 34504275 PMCID: PMC8429705 DOI: 10.1038/s42003-021-02602-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/25/2021] [Indexed: 02/08/2023] Open
Abstract
Conifer-feeding bark beetles are important herbivores and decomposers in forest ecosystems. These species complete their life cycle in nutritionally poor substrates and some can kill enormous numbers of trees during population outbreaks. The Eurasian spruce bark beetle (Ips typographus) can destroy >100 million m3 of spruce in a single year. We report a 236.8 Mb I. typographus genome assembly using PacBio long-read sequencing. The final phased assembly has a contig N50 of 6.65 Mb in 272 contigs and is predicted to contain 23,923 protein-coding genes. We reveal expanded gene families associated with plant cell wall degradation, including pectinases, aspartyl proteases, and glycosyl hydrolases. This genome sequence from the genus Ips provides timely resources to address questions about the evolutionary biology of the true weevils (Curculionidae), one of the most species-rich animal families. In forests of today, increasingly stressed by global warming, this draft genome may assist in developing pest control strategies to mitigate outbreaks.
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Affiliation(s)
- Daniel Powell
- Czech University of Life Sciences Prague, Faculty of Forestry and Wood Sciences, Excellent Team for Mitigation (ETM), Kamýcká 129, Praha 6, Suchdol, Czech Republic
- Department of Biology, Lund University, Lund, Sweden
- Global Change Ecology Research Group, School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Ewald Groβe-Wilde
- Czech University of Life Sciences Prague, Faculty of Forestry and Wood Sciences, Excellent Team for Mitigation (ETM), Kamýcká 129, Praha 6, Suchdol, Czech Republic
| | - Paal Krokene
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Amit Roy
- Czech University of Life Sciences Prague, Faculty of Forestry and Wood Sciences, Excellent Team for Mitigation (ETM), Kamýcká 129, Praha 6, Suchdol, Czech Republic
| | - Amrita Chakraborty
- Czech University of Life Sciences Prague, Faculty of Forestry and Wood Sciences, EVA 4.0 Unit, Kamýcká 129, Praha 6, Suchdol, Czech Republic
| | | | - Heiko Vogel
- Entomology Department, Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | - Fredrik Schlyter
- Czech University of Life Sciences Prague, Faculty of Forestry and Wood Sciences, Excellent Team for Mitigation (ETM), Kamýcká 129, Praha 6, Suchdol, Czech Republic
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
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40
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Carter HF, Thompson JR, Elphick MR, Oliveri P. The Development and Neuronal Complexity of Bipinnaria Larvae of the Sea Star Asterias rubens. Integr Comp Biol 2021; 61:337-351. [PMID: 34048552 PMCID: PMC8427176 DOI: 10.1093/icb/icab103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Free-swimming planktonic larvae are a key stage in the development of many marine phyla, and studies of these organisms have contributed to our understanding of major genetic and evolutionary processes. Although transitory, these larvae often attain a remarkable degree of tissue complexity, with well-defined musculature and nervous systems. Among the best studied are larvae belonging to the phylum Echinodermata, but with work largely focused on the pluteus larvae of sea urchins (class Echinoidea). The greatest diversity of larval strategies among echinoderms is found in the class Asteroidea (sea stars), organisms that are rapidly emerging as experimental systems for genetic and developmental studies. However, the bipinnaria larvae of sea stars have only been studied in detail in a small number of species and although they have been relatively well described neuro-anatomically, they are poorly understood neurochemically. Here, we have analyzed embryonic development and bipinnaria larval anatomy in the common North Atlantic sea star Asterias rubens, using a variety of staining methods in combination with confocal microscopy. Importantly, the chemical complexity of the nervous system of bipinnaria larvae was revealed through use of a diverse set of antibodies, with identification of at least three centers of differing neurochemical signature within the previously described nervous system: the anterior apical organ, oral region, and ciliary bands. Furthermore, the anatomy of the musculature and sites of cell division in bipinnaria larvae was analyzed. Comparisons of developmental progression and molecular anatomy across the Echinodermata provided a basis for hypotheses on the shared evolutionary and developmental processes that have shaped this group of animals. We conclude that bipinnaria larvae appear to be remarkably conserved across ∼200 million years of evolutionary time and may represent a strong evolutionary and/or developmental constraint on species utilizing this larval strategy.
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Affiliation(s)
- Hugh F Carter
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
- Department of Life Sciences, Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK
| | - Jeffrey R Thompson
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
- UCL Centre for Life’s Origins and Evolution (CLOE), University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Maurice R Elphick
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Paola Oliveri
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
- UCL Centre for Life’s Origins and Evolution (CLOE), University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
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41
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Yuasa H, Kajitani R, Nakamura Y, Takahashi K, Okuno M, Kobayashi F, Shinoda T, Toyoda A, Suzuki Y, Thongtham N, Forsman Z, Bronstein O, Seveso D, Montalbetti E, Taquet C, Eyal G, Yasuda N, Itoh T. Elucidation of the speciation history of three sister species of crown-of-thorns starfish (Acanthaster spp.) based on genomic analysis. DNA Res 2021; 28:6350483. [PMID: 34387305 DOI: 10.1093/dnares/dsab012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Indexed: 11/14/2022] Open
Abstract
The crown-of-thorns starfish (COTS) is a coral predator that is widely distributed in Indo-Pacific Oceans. A previous phylogenetic study using partial mitochondrial sequences suggested that COTS had diverged into four distinct species, but a nuclear genome-based analysis to confirm this was not conducted. To address this, COTS species nuclear genome sequences were analysed here, sequencing Northern Indian Ocean (NIO) and Red Sea (RS) species genomes for the first time, followed by a comparative analysis with the Pacific Ocean (PO) species. Phylogenetic analysis and ADMIXTURE analysis revealed clear divergences between the three COTS species. Furthermore, within the PO species, the phylogenetic position of the Hawaiian sample was further away from the other Pacific-derived samples than expected based on the mitochondrial data, suggesting that it may be a PO subspecies. The pairwise sequentially Markovian coalescent model showed that the trajectories of the population size diverged by region during the Mid-Pleistocene transition when the sea-level was dramatically decreased, strongly suggesting that the three COTS species experienced allopatric speciation. Analysis of the orthologues indicated that there were remarkable genes with species-specific positive selection in the genomes of the PO and RS species, which suggested that there may be local adaptations in the COTS species.
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Affiliation(s)
- Hideaki Yuasa
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Rei Kajitani
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Yuta Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Kazuki Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Miki Okuno
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Fumiya Kobayashi
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Takahiro Shinoda
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima City, Shizuoka 411-8540, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba 272-8562, Japan
| | | | - Zac Forsman
- Hawai'i Institute of Marine Biology, School of Ocean & Earth Sciences & Technology, University of Hawai'i at Mānoa, Coconut Island, Kāne'ohe, HI, USA
| | - Omri Bronstein
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv 6997801, Israel.,The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Davide Seveso
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, 20126 Milan, Italy.,Marine Research and High Education Center (MaRHE Center), 12030 Faafu Magoodhoo, Republic of Maldives
| | - Enrico Montalbetti
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, 20126 Milan, Italy.,Marine Research and High Education Center (MaRHE Center), 12030 Faafu Magoodhoo, Republic of Maldives
| | | | - Gal Eyal
- ARC Centre of Excellence for Coral Reef Studies, School of Biological Sciences, University of Queensland, St. Lucia, QLD 4072, Australia.,The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Nina Yasuda
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki 889-2192, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
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42
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Tassia MG, David KT, Townsend JP, Halanych KM. TIAMMAt: Leveraging biodiversity to revise protein domain models, evidence from innate immunity. Mol Biol Evol 2021; 38:5806-5818. [PMID: 34459919 PMCID: PMC8662601 DOI: 10.1093/molbev/msab258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Sequence annotation is fundamental for studying the evolution of protein families, particularly when working with nonmodel species. Given the rapid, ever-increasing number of species receiving high-quality genome sequencing, accurate domain modeling that is representative of species diversity is crucial for understanding protein family sequence evolution and their inferred function(s). Here, we describe a bioinformatic tool called Taxon-Informed Adjustment of Markov Model Attributes (TIAMMAt) which revises domain profile hidden Markov models (HMMs) by incorporating homologous domain sequences from underrepresented and nonmodel species. Using innate immunity pathways as a case study, we show that revising profile HMM parameters to directly account for variation in homologs among underrepresented species provides valuable insight into the evolution of protein families. Following adjustment by TIAMMAt, domain profile HMMs exhibit changes in their per-site amino acid state emission probabilities and insertion/deletion probabilities while maintaining the overall structure of the consensus sequence. Our results show that domain revision can heavily impact evolutionary interpretations for some families (i.e., NLR’s NACHT domain), whereas impact on other domains (e.g., rel homology domain and interferon regulatory factor domains) is minimal due to high levels of sequence conservation across the sampled phylogenetic depth (i.e., Metazoa). Importantly, TIAMMAt revises target domain models to reflect homologous sequence variation using the taxonomic distribution under consideration by the user. TIAMMAt’s flexibility to revise any subset of the Pfam database using a user-defined taxonomic pool will make it a valuable tool for future protein evolution studies, particularly when incorporating (or focusing) on nonmodel species.
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Affiliation(s)
- Michael G Tassia
- Department of Biological Sciences, Auburn University, Auburn, Alabama
| | - Kyle T David
- Department of Biological Sciences, Auburn University, Auburn, Alabama
| | - James P Townsend
- Whitman Center, Marine Biological Laboratory, Woods Hole, Massachusetts.,Department of Biology, Providence College, Providence, Rhode Island
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43
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Christiansen H, Heindler FM, Hellemans B, Jossart Q, Pasotti F, Robert H, Verheye M, Danis B, Kochzius M, Leliaert F, Moreau C, Patel T, Van de Putte AP, Vanreusel A, Volckaert FAM, Schön I. Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. BMC Genomics 2021; 22:625. [PMID: 34418978 PMCID: PMC8380342 DOI: 10.1186/s12864-021-07917-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/26/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. RESULTS In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. CONCLUSIONS Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.
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Affiliation(s)
- Henrik Christiansen
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.
| | - Franz M Heindler
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Quentin Jossart
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | - Henri Robert
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Marie Verheye
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Bruno Danis
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Marc Kochzius
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Frederik Leliaert
- Marine Biology Research Group, Ghent University, Ghent, Belgium.,Meise Botanic Garden, Meise, Belgium
| | - Camille Moreau
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Université de Bourgogne Franche-Comté (UBFC) UMR CNRS 6282 Biogéosciences, Dijon, France
| | - Tasnim Patel
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Anton P Van de Putte
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.,OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ann Vanreusel
- Marine Biology Research Group, Ghent University, Ghent, Belgium
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Isa Schön
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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44
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Beatman TR, Buckley KM, Cary GA, Hinman VF, Ettensohn CA. A nomenclature for echinoderm genes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6350312. [PMID: 34386815 PMCID: PMC8361234 DOI: 10.1093/database/baab052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/02/2021] [Accepted: 08/02/2021] [Indexed: 12/16/2022]
Abstract
Echinoderm embryos and larvae are prominent experimental model systems for studying developmental mechanisms. High-quality, assembled, annotated genome sequences are now available for several echinoderm species, including representatives from most classes. The increased availability of these data necessitates the development of a nomenclature that assigns universally interpretable gene symbols to echinoderm genes to facilitate cross-species comparisons of gene functions, both within echinoderms and across other phyla. This paper describes the implementation of an improved set of echinoderm gene nomenclature guidelines that both communicates meaningful orthology information in protein-coding gene symbols and names and establishes continuity with nomenclatures developed for major vertebrate model organisms, including humans. Differences between the echinoderm gene nomenclature guidelines and vertebrate guidelines are examined and explained. This nomenclature incorporates novel solutions to allow for several types of orthologous relationships, including the single echinoderm genes with multiple vertebrate co-orthologs that result from whole-genome-duplication events. The current version of the Echinoderm Gene Nomenclature Guidelines can be found at https://www.echinobase.org/gene/static/geneNomenclature.jsp Database URL https://www.echinobase.org/
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Affiliation(s)
- Thomas R Beatman
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.,Echinobase, #646 Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA 15213, USA
| | - Katherine M Buckley
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences, Auburn, AL 36849, USA
| | - Gregory A Cary
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Veronica F Hinman
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.,Echinobase, #646 Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA 15213, USA
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.,Echinobase, #646 Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA 15213, USA
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45
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Veenstra JA. Ambulacrarian insulin-related peptides and their putative receptors suggest how insulin and similar peptides may have evolved from insulin-like growth factor. PeerJ 2021; 9:e11799. [PMID: 34316411 PMCID: PMC8286064 DOI: 10.7717/peerj.11799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/25/2021] [Indexed: 01/23/2023] Open
Abstract
Background Some insulin/IGF-related peptides (irps) stimulate a receptor tyrosine kinase (RTK) that transfers the extracellular hormonal signal into an intracellular response. Other irps, such as relaxin, do not use an RTK, but a G-protein coupled receptor (GPCR). This is unusual since evolutionarily related hormones typically either use the same or paralogous receptors. In arthropods three different irps, i.e. arthropod IGF, gonadulin and Drosophila insulin-like peptide 7 (dilp7), likely evolved from a gene triplication, as in several species genes encoding these three peptides are located next to one another on the same chromosomal fragment. These arthropod irps have homologs in vertebrates, suggesting that the initial gene triplication was perhaps already present in the last common ancestor of deuterostomes and protostomes. It would be interesting to know whether this is indeed so and how insulin might be related to this trio of irps. Methodology Genes encoding irps as well as their putative receptors were identified in genomes and transcriptomes from echinoderms and hemichordates. Results A similar triplet of genes coding for irps also occurs in some ambulacrarians. Two of these are orthologs of arthropod IGF and dilp7 and the third is likely a gonadulin ortholog. In echinoderms, two novel irps emerged, gonad stimulating substance (GSS) and multinsulin, likely from gene duplications of the IGF and dilp7-like genes respectively. The structures of GSS diverged considerably from IGF, which would suggest they use different receptors from IGF, but no novel irp receptors evolved. If IGF and GSS use different receptors, and the evolution of GSS from a gene duplication of IGF is not associated with the appearance of a novel receptor, while irps are known to use two different types of receptors, the ancestor of GSS and IGF might have acted on both types of receptors while one or both of its descendants act on only one. There are three ambulacrarian GPCRs that have amino acid sequences suggestive of being irp GPCRs, two of these are orthologs of the gonadulin and dilp7 receptors. This suggests that the third might be an IGF receptor, and that by deduction, GSS only acts on the RTK. The evolution of GSS from IGF may represent a pattern, where IGF gene duplications lead to novel genes coding for shorter peptides that activate an RTK. It is likely this is how insulin and the insect neuroendocrine irps evolved independently from IGF. Conclusion The local gene triplication described from arthropods that yielded three genes encoding irps was already present in the last common ancestor of protostomes and deuterostomes. It seems plausible that irps, such as those produced by neuroendocrine cells in the brain of insects and echinoderm GSS evolved independently from IGF and, thus, are not true orthologs, but the result of convergent evolution.
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Affiliation(s)
- Jan A Veenstra
- INCIA UMR 5287 CNRS, Université de Bordeaux, Pessac, Gironde, France
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46
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Wolff A, Hinman V. The Use of Larval Sea Stars and Sea Urchins in the Discovery of Shared Mechanisms of Metazoan Whole-Body Regeneration. Genes (Basel) 2021; 12:1063. [PMID: 34356079 PMCID: PMC8303351 DOI: 10.3390/genes12071063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 02/07/2023] Open
Abstract
The ability to regenerate is scattered among the metazoan tree of life. Further still, regenerative capacity varies widely within these specific organisms. Numerous organisms, all with different regenerative capabilities, have been studied at length and key similarities and disparities in how regeneration occurs have been identified. In order to get a better grasp on understanding regeneration as a whole, we must search for new models that are capable of extensive regeneration, as well as those that have been under sampled in the literature. As invertebrate deuterostomes, echinoderms fit both of these requirements. Multiple members regenerate various tissue types at all life stages, including examples of whole-body regeneration. Interrogations in two highly studied echinoderms, the sea urchin and the sea star, have provided knowledge of tissue and whole-body regeneration at various life stages. Work has begun to examine regeneration in echinoderm larvae, a potential new system for understanding regenerative mechanisms in a basal deuterostome. Here, we review the ways these two animals' larvae have been utilized as a model of regeneration.
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Affiliation(s)
- Andrew Wolff
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA;
| | - Veronica Hinman
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
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47
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Pereira RC, Sudatti DB, Moreira TSG, Ventura CRR. Chemical defense in developmental stages and adult of the sea star Echinaster ( Othilia) brasiliensis. PeerJ 2021; 9:e11503. [PMID: 34178443 PMCID: PMC8216172 DOI: 10.7717/peerj.11503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 05/03/2021] [Indexed: 11/25/2022] Open
Abstract
To date, evidence regarding the performance of secondary metabolites from larval stages of sea stars as an anti-predation defense relates only to a few species/specimens from a few geographic ranges. Unfortunately, this hinders a comprehensive global understanding of this inter-specific predator-prey interaction. Here, we present laboratory experimental evidence of chemical defense action in the early developmental stages and adults of the sea star Echinaster (Othilia) brasiliensis from Brazil against sympatric and allopatric invertebrate consumers. Blastulae, early and late brachiolarias of E. (O.) brasiliensis were not consumed by the sympatric and allopatric crabs Mithraculus forceps. Blastulae were also avoided by the sympatric and allopatric individuals of the anemone Anemonia sargassensis, but not the larval stages. Extracts from embryos (blastula) and brachiolarias of E. (O.) brasiliensis from one sampled population (João Fernandes beach) significantly inhibited the consumption by sympatric M. forceps, but not by allopatric crabs and A. sargassensi anemone. In this same site, extracts from adults E. (O.) brasiliensis significantly inhibited the consumption by sympatric and allopatric specimens of the crab in a range of concentrations. Whereas equivalent extract concentrations of E. (O.) brasiliensis from other population (Itaipu beach)inhibited the predation by allopatric M. forceps, while sympatric individuals of this crab avoided the only the higher level tested. Then, early stages and adult specimens of E. (O.) brasiliensis can be chemically defended against consumers, but this action is quite variable, depending on the type (anemone or crab) and the origin of the consumer (sympatric or allopatric).
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Affiliation(s)
- Renato Crespo Pereira
- Department of Marine Biology, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Daniela Bueno Sudatti
- Department of Marine Biology, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Thaise S G Moreira
- Department of Marine Biology, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Carlos Renato R Ventura
- Invertebrate Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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48
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Klein AH, Motti CA, Hillberg AK, Ventura T, Thomas-Hall P, Armstrong T, Barker T, Whatmore P, Cummins SF. Development and Interrogation of a Transcriptomic Resource for the Giant Triton Snail (Charonia tritonis). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:501-515. [PMID: 34191212 PMCID: PMC8270824 DOI: 10.1007/s10126-021-10042-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/03/2021] [Indexed: 06/01/2023]
Abstract
Gastropod molluscs are among the most abundant species that inhabit coral reef ecosystems. Many are specialist predators, along with the giant triton snail Charonia tritonis (Linnaeus, 1758) whose diet consists of Acanthaster planci (crown-of-thorns starfish), a corallivore known to consume enormous quantities of reef-building coral. C. tritonis are considered vulnerable due to overexploitation, and a decline in their populations is believed to have contributed to recurring A. planci population outbreaks. Aquaculture is considered one approach that could help restore natural populations of C. tritonis and mitigate coral loss; however, numerous questions remain unanswered regarding their life cycle, including the molecular factors that regulate their reproduction and development. In this study, we have established a reference C. tritonis transcriptome derived from developmental stages (embryo and veliger) and adult tissues. This was used to identify genes associated with cell signalling, such as neuropeptides and G protein-coupled receptors (GPCRs), involved in endocrine and olfactory signalling. A comparison of developmental stages showed that several neuropeptide precursors are exclusively expressed in post-hatch veligers and functional analysis found that FFamide stimulated a significant (20.3%) increase in larval heart rate. GPCRs unique to veligers, and a diversity of rhodopsin-like GPCRs located within adult cephalic tentacles, all represent candidate olfactory receptors. In addition, the cytochrome P450 superfamily, which participates in the biosynthesis and degradation of steroid hormones and lipids, was also found to be expanded with at least 91 genes annotated, mostly in gill tissue. These findings further progress our understanding of C. tritonis with possible application in developing aquaculture methods.
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Affiliation(s)
- A H Klein
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - C A Motti
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville, QLD, 4810, Australia
| | - A K Hillberg
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - T Ventura
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - P Thomas-Hall
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville, QLD, 4810, Australia
| | - T Armstrong
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville, QLD, 4810, Australia
| | - T Barker
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville, QLD, 4810, Australia
| | - P Whatmore
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
- eResearch Office, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - S F Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.
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49
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Ballard KR, Klein AH, Hayes RA, Wang T, Cummins SF. The protein and volatile components of trail mucus in the Common Garden Snail, Cornu aspersum. PLoS One 2021; 16:e0251565. [PMID: 34043643 PMCID: PMC8158898 DOI: 10.1371/journal.pone.0251565] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/28/2021] [Indexed: 11/19/2022] Open
Abstract
The Common or Brown Garden Snail, Cornu aspersum, is an invasive land snail that has successfully colonized a diverse range of global environments. Like other invasive land snails, it is a significant pest of a variety of agricultural crops, including citrus, grapes and canola. Cornu aspersum secretes a mucus trail when mobile that facilitates locomotion. The involvement of the trail in conspecific chemical communication has also been postulated. Our study found that anterior tentacle contact with conspecific mucus elicited a significant increase in heart rate from 46.9 to 51 beats per minute. In order to gain a better understanding of the constituents of the trail mucus and the role it may play in snail communication, the protein and volatile components of mucus trails were investigated. Using two different protein extraction methods, mass spectrometry analysis yielded 175 different proteins, 29 of which had no significant similarity to any entries in the non-redundant protein sequence database. Of the mucus proteins, 22 contain features consistent with secreted proteins, including a perlucin-like protein. The eight most abundant volatiles detected using gas chromatography were recorded (including propanoic acid and limonene) and their potential role as putative pheromones are discussed. In summary, this study has provided an avenue for further research pertaining to the role of trail mucus in snail communication and provides a useful repository for land snail trail mucus components. This may be utilized for further research regarding snail attraction and dispersal, which may be applied in the fields of agriculture, ecology and human health.
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Affiliation(s)
- Kaylene R. Ballard
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
| | - Anne H. Klein
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
| | - Richard A. Hayes
- Forest Industries Research Centre, Forest Research Institute, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
| | - Tianfang Wang
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
| | - Scott F. Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
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50
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Sassa M, Takagi T, Kinjo A, Yoshioka Y, Zayasu Y, Shinzato C, Kanda S, Murakami-Sugihara N, Shirai K, Inoue K. Divalent metal transporter-related protein restricts animals to marine habitats. Commun Biol 2021; 4:463. [PMID: 33846549 PMCID: PMC8041893 DOI: 10.1038/s42003-021-01984-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 03/12/2021] [Indexed: 12/30/2022] Open
Abstract
Utilization and regulation of metals from seawater by marine organisms are important physiological processes. To better understand metal regulation, we searched the crown-of-thorns starfish genome for the divalent metal transporter (DMT) gene, a membrane protein responsible for uptake of divalent cations. We found two DMT-like sequences. One is an ortholog of vertebrate DMT, but the other is an unknown protein, which we named DMT-related protein (DMTRP). Functional analysis using a yeast expression system demonstrated that DMT transports various metals, like known DMTs, but DMTRP does not. In contrast, DMTRP reduced the intracellular concentration of some metals, especially zinc, suggesting its involvement in negative regulation of metal uptake. Phylogenetic distribution of the DMTRP gene in various metazoans, including sponges, protostomes, and deuterostomes, indicates that it originated early in metazoan evolution. However, the DMTRP gene is only retained in marine species, and its loss seems to have occurred independently in ecdysozoan and vertebrate lineages from which major freshwater and land animals appeared. DMTRP may be an evolutionary and ecological limitation, restricting organisms that possess it to marine habitats, whereas its loss may have allowed other organisms to invade freshwater and terrestrial habitats. Mieko Sassa et al. report a novel divalent metal transporter protein (DMTRP) in the crown-of-thorns starfish genome and determine that all organisms with a DMTRP gene are located in marine habitats. They also show in a functional yeast system that DMTRP can prevent uptake of certain metals, bringing insight into the evolution of metal regulation for marine organisms.
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Affiliation(s)
- Mieko Sassa
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan. .,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan.
| | - Toshiyuki Takagi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Azusa Kinjo
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Yuki Yoshioka
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Yuna Zayasu
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Shinji Kanda
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | | | - Kotaro Shirai
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Koji Inoue
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
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