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Addamo AM, Modrell MS, Taviani M, Machordom A. Unravelling the relationships among Madrepora Linnaeus, 1758, Oculina Lamark, 1816 and Cladocora Ehrenberg, 1834 (Cnidaria: Anthozoa: Scleractinia). INVERTEBR SYST 2024; 38:IS23027. [PMID: 38744497 DOI: 10.1071/is23027] [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: 06/08/2023] [Accepted: 03/18/2024] [Indexed: 05/16/2024]
Abstract
Despite the widespread use of integrative taxonomic approaches, many scleractinian coral genera and species remain grouped in polyphyletic families, classified as incertae sedis or simply understudied. Oculinidae Gray, 1847 represents a family for which many taxonomic questions remain unresolved, particularly those related to some of the current genera, such as Oculina Lamark, 1816 or recently removed genera, including Cladocora Ehrenberg, 1834 and Madrepora Linnaeus, 1758. Cladocora is currently assigned to the family Cladocoridae Milne Edwards & Haime, 1857 and a new family, Bathyporidae Kitahara, Capel, Zilberberg & Cairns, 2024, was recently raised to accommodate Madrepora . However, the name Bathyporidae is not valid because this was not formed on the basis of a type genus name. To resolve taxonomic questions related to these three genera, the evolutionary relationships are explored through phylogenetic analyses of 18 molecular markers. The results of these analyses support a close relationship between the species Oculina patagonica and Cladocora caespitosa , indicating that these may belong to the same family (and possibly genus), and highlighting the need for detailed revisions of Oculina and Cladocora . By contrast, a distant relationship is found between these two species and Madrepora oculata , with the overall evidence supporting the placement of Madrepora in the resurrected family Madreporidae Ehrenberg, 1834. This study advances our knowledge of coral systematics and highlights the need for a comprehensive review of the genera Oculina , Cladocora and Madrepora .
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Affiliation(s)
- Anna M Addamo
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), E-28006 Madrid, Spain; and European Commission, Joint Research Centre (JRC), I-21027 Ispra, Italy; and Climate Change Research Centre (CCRC), University of Insubria, I-21100 Varese, Italy; and Present address: Faculty of Biosciences and Aquaculture, Nord University, NO-8049 Bodø, Norway
| | - Melinda S Modrell
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), E-28006 Madrid, Spain
| | - Marco Taviani
- Istituto di Scienze Marine, Consiglio Nazionale delle Ricerche (ISMAR-CNR), I-40129 Bologna, Italy; and Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Annie Machordom
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), E-28006 Madrid, Spain
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Vaga CF, Seiblitz IGL, Stolarski J, Capel KCC, Quattrini AM, Cairns SD, Huang D, Quek RZB, Kitahara MV. 300 million years apart: the extreme case of macromorphological skeletal convergence between deltocyathids and a turbinoliid coral (Anthozoa, Scleractinia). INVERTEBR SYST 2024; 38:IS23053. [PMID: 38744500 DOI: 10.1071/is23053] [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: 11/03/2023] [Accepted: 03/18/2024] [Indexed: 05/16/2024]
Abstract
The integration of morphological and molecular lines of evidence has enabled the family Deltocyathidae to be erected to accommodate Deltocyathus species that were previously ascribed to the family Caryophylliidae. However, although displaying the same morphological characteristics as other species of Deltocyathus , molecular data suggested that D. magnificus was phylogenetically distant from Deltocyathidae, falling within the family Turbinoliidae instead. To elucidate the enigmatic evolutionary history of this species and skeletal microstructural features, the phylogenetic relationships of Deltocyathidae and Turbinoliidae were investigated using nuclear ultraconserved and exon loci and complete mitochondrial genomes. Both nuclear and mitochondrial phylogenomic reconstructions confirmed the position of D. magnificus within turbinolids. Furthermore, a novel mitochondrial gene order was uncovered for Deltocyathidae species. This gene order was not present in Turbinoliidae or in D. magnificus that both have the scleractinian canonical gene order, further indicating the taxonomic utility of mitochondrial gene order. D. magnificus is therefore formally moved to the family Turbinoliidae and accommodated in a new genus (Dennantotrochus Kitahara, Vaga & Stolarski, gen. nov.). Surprisingly, turbinolids and deltocyathids do not differ in microstructural organisation of the skeleton that consists of densely packed, individualised rapid accretion deposits and thickening deposits composed of fibres perpendicular to the skeleton surface. Therefore, although both families are clearly evolutionarily divergent, macromorphological features indicate a case of skeletal convergence while these may still share conservative biomineralisation mechanisms. ZooBank: urn:lsid:zoobank.org:pub:5F1C0E25-3CC6-4D1F-B1F0-CD9D0014678E.
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Affiliation(s)
- C F Vaga
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA; and Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - I G L Seiblitz
- Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - J Stolarski
- Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, PL-00-818 Warsaw, Poland
| | - K C C Capel
- Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Invertebrate Department, National Museum of Rio de Janeiro, Federal University of Rio de Janeiro, 20940-040, Rio de Janeiro, Brazil
| | - A M Quattrini
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA
| | - S D Cairns
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA
| | - D Huang
- Lee Kong Chian Natural History Museum, National University of Singapore, Conservatory Drive, Singapore 117377, Singapore; and Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - R Z B Quek
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; and Yale-NUS College, National University of Singapore, Singapore 138527, Singapore
| | - M V Kitahara
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA; and Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
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Capel KCC, Zilberberg C, Carpes RM, Morrison CL, Vaga CF, Quattrini AM, Zb Quek R, Huang D, Cairns SD, Kitahara MV. How long have we been mistaken? Multi-tools shedding light into the systematics of the widespread deep-water genus Madrepora Linnaeus, 1758 (Scleractinia). Mol Phylogenet Evol 2024; 191:107994. [PMID: 38113961 DOI: 10.1016/j.ympev.2023.107994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/02/2023] [Accepted: 12/12/2023] [Indexed: 12/21/2023]
Abstract
Deep-water coral reefs are found worldwide and harbor biodiversity levels that are comparable to their shallow-water counterparts. However, the genetic diversity and population structure of deep-water species remain poorly explored, and historical taxonomical issues still need to be resolved. Here we used microsatellite markers as well as ultraconserved elements (UCE) and exons to shed light on the population structure, genetic diversity, and phylogenetic position of the genus Madrepora, which contains M. oculata, one of the most widespread scleractinian species. Population structure of 107 samples from three Southwestern Atlantic sedimentary basins revealed the occurrence of a cryptic species, herein named M. piresae sp. nov. (authored by Kitahara, Capel and Zilberberg), which can be found in sympatry with M. oculata. Phylogeny reconstructions based on 134 UCEs and exon regions corroborated the population genetic data, with the recovery of two well-supported groups, and reinforced the polyphyly of the family Oculinidae. In order to better accommodate the genus Madrepora, while reducing taxonomical confusion associated with the name Madreporidae, we propose the monogeneric family Bathyporidae fam. nov. (authored by Kitahara, Capel, Zilberberg and Cairns). Our findings advance the knowledge on the widespread deep-water genus Madrepora, resolve a long-standing question regarding the phylogenetic position of the genus, and highlight the need of a worldwide review of the genus.
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Affiliation(s)
- Kátia C C Capel
- Center for Marine Biology, University of São Paulo, São Sebastião, São Paulo, Brazil; Instituto Coral Vivo, Rua dos Coqueiros, 87, 45807-000 Santa Cruz Cabrália, BA, Brazil.
| | - Carla Zilberberg
- Instituto Coral Vivo, Rua dos Coqueiros, 87, 45807-000 Santa Cruz Cabrália, BA, Brazil; Department of Zoology, Institute of Biodiversity and Sustainability - Nupem, Federal University of Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Raphael M Carpes
- Department of Zoology, Institute of Biodiversity and Sustainability - Nupem, Federal University of Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Cheryl L Morrison
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research Laboratory, Kearneysville, United States
| | - Claudia F Vaga
- Center for Marine Biology, University of São Paulo, São Sebastião, São Paulo, Brazil; Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil; Department of Invertebrate Zoology, Smithsonian Institution, Washington DC, United States
| | - Andrea M Quattrini
- Department of Invertebrate Zoology, Smithsonian Institution, Washington DC, United States
| | - Randolph Zb Quek
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore; Lee Kong Chian Natural History Museum, National University of Singapore, Singapore
| | - Stephen D Cairns
- Department of Invertebrate Zoology, Smithsonian Institution, Washington DC, United States
| | - Marcelo V Kitahara
- Center for Marine Biology, University of São Paulo, São Sebastião, São Paulo, Brazil; Instituto Coral Vivo, Rua dos Coqueiros, 87, 45807-000 Santa Cruz Cabrália, BA, Brazil; Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil; Department of Invertebrate Zoology, Smithsonian Institution, Washington DC, United States.
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Randolph Quek ZB, Jain SS, Richards ZT, Arrigoni R, Benzoni F, Hoeksema BW, Carvajal JI, Wilson NG, Baird AH, Kitahara MV, Seiblitz IGL, Vaga CF, Huang D. A hybrid-capture approach to reconstruct the phylogeny of Scleractinia (Cnidaria: Hexacorallia). Mol Phylogenet Evol 2023:107867. [PMID: 37348770 DOI: 10.1016/j.ympev.2023.107867] [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: 02/26/2023] [Revised: 05/28/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023]
Abstract
A well-supported evolutionary tree representing most major lineages of scleractinian corals is in sight with the development and application of phylogenomic approaches. Specifically, hybrid-capture techniques are shedding light on the evolution and systematics of corals. Here, we reconstructed a broad phylogeny of Scleractinia to test previous phylogenetic hypotheses inferred from a few molecular markers, in particular, the relationships among major scleractinian families and genera, and to identify clades that require further research. We analysed 449 nuclear loci from 422 corals, comprising 266 species spanning 26 families, combining data across whole genomes, transcriptomes, hybrid capture and low-coverage sequencing to reconstruct the largest phylogenomic tree of scleractinians to date. Due to the large number of loci and data completeness (<38% missing data), node supports were high across shallow and deep nodes with incongruences observed in only a few shallow nodes. The "Robust" and "Complex" clades were recovered unequivocally, and our analyses confirmed that Micrabaciidae Vaughan, 1905 is sister to the "Robust" clade, transforming our understanding of the "Basal" clade. Several families remain polyphyletic in our phylogeny, including Deltocyathiidae Kitahara, Cairns, Stolarski & Miller, 2012, Caryophylliidae Dana, 1846, and Coscinaraeidae Benzoni, Arrigoni, Stefani & Stolarski, 2012, and we hereby formally proposed the family name Pachyseridae Benzoni & Hoeksema to accommodate Pachyseris Milne Edwards & Haime, 1849, which is phylogenetically distinct from Agariciidae Gray, 1847. Results also revealed species misidentifications and inconsistencies within morphologically complex clades, such as Acropora Oken, 1815 and Platygyra Ehrenberg, 1834, underscoring the need for reference skeletal material and topotypes, as well as the importance of detailed taxonomic work. The approach and findings here provide much promise for further stabilising the topology of the scleractinian tree of life and advancing our understanding of coral evolution.
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Affiliation(s)
- Z B Randolph Quek
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Yale-NUS College, National University of Singapore, Singapore 138527, Singapore.
| | - Sudhanshi S Jain
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Zoe T Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia 6102, Australia; Collections and Research, Western Australian Museum, Welshpool, Western Australia 6106, Australia
| | - Roberto Arrigoni
- Department of Biology and Evolution of Marine Organisms, Genoa Marine Centre, Stazione Zoologica Anton Dohrn-National Institute of Marine Biology, Ecology and Biotechnology, 16126 Genoa, Italy
| | - Francesca Benzoni
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Bert W Hoeksema
- Taxonomy, Systematics and Geodiversity Group, Naturalis Biodiversity Center, 2300 RA Leiden, The Netherlands; Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9700 CC Groningen, The Netherlands
| | - Jose I Carvajal
- Collections and Research, Western Australian Museum, Welshpool, Western Australia 6106, Australia
| | - Nerida G Wilson
- Collections and Research, Western Australian Museum, Welshpool, Western Australia 6106, Australia; School of Biological Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Andrew H Baird
- College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia
| | - Marcelo V Kitahara
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560, United States of America
| | - Isabela G L Seiblitz
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - Claudia F Vaga
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Lee Kong Chian Natural History Museum, National University of Singapore, Singapore 117377, Singapore; Tropical Marine Science Institute, National University of Singapore, Singapore 119227, Singapore; Centre for Nature-based Climate Solutions, National University of Singapore, Singapore 117558, Singapore.
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Quattrini AM, Snyder KE, Purow-Ruderman R, Seiblitz IGL, Hoang J, Floerke N, Ramos NI, Wirshing HH, Rodriguez E, McFadden CS. Mito-nuclear discordance within Anthozoa, with notes on unique properties of their mitochondrial genomes. Sci Rep 2023; 13:7443. [PMID: 37156831 PMCID: PMC10167242 DOI: 10.1038/s41598-023-34059-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/24/2023] [Indexed: 05/10/2023] Open
Abstract
Whole mitochondrial genomes are often used in phylogenetic reconstruction. However, discordant patterns in species relationships between mitochondrial and nuclear phylogenies are commonly observed. Within Anthozoa (Phylum Cnidaria), mitochondrial (mt)-nuclear discordance has not yet been examined using a large and comparable dataset. Here, we used data obtained from target-capture enrichment sequencing to assemble and annotate mt genomes and reconstruct phylogenies for comparisons to phylogenies inferred from hundreds of nuclear loci obtained from the same samples. The datasets comprised 108 hexacorals and 94 octocorals representing all orders and > 50% of extant families. Results indicated rampant discordance between datasets at every taxonomic level. This discordance is not attributable to substitution saturation, but rather likely caused by introgressive hybridization and unique properties of mt genomes, including slow rates of evolution driven by strong purifying selection and substitution rate variation. Strong purifying selection across the mt genomes caution their use in analyses that rely on assumptions of neutrality. Furthermore, unique properties of the mt genomes were noted, including genome rearrangements and the presence of nad5 introns. Specifically, we note the presence of the homing endonuclease in ceriantharians. This large dataset of mitochondrial genomes further demonstrates the utility of off-target reads generated from target-capture data for mt genome assembly and adds to the growing knowledge of anthozoan evolution.
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Affiliation(s)
- Andrea M Quattrini
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC, 20560, USA.
| | - Karen E Snyder
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | | | - Isabela G L Seiblitz
- Centre for Marine Biology, University of São Paulo, São Sebastião, 11612-109, Brazil
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, 05508-900, Brazil
| | - Johnson Hoang
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | - Natasha Floerke
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | - Nina I Ramos
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Herman H Wirshing
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Estefanía Rodriguez
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
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Vaga CF, Seiblitz IGL, Capel KCC, Kitahara MV. The mitochondrial genomes of Crispatotrochus rubescens and Crispatotrochus rugosus (Hexacorallia; Scleractinia): new insights on the phylogeny of the family Caryophylliidae. Mol Biol Rep 2022; 49:12269-12273. [PMID: 36264418 DOI: 10.1007/s11033-022-08029-1] [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: 08/24/2022] [Accepted: 10/12/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Caryophylliidae is one of the most diverse scleractinian families, however it was recovered as polyphyletic in multiple molecular studies. Recently, the mitochondrial gene order was proposed as a character for a taxonomic revision of the family. Here we describe the first mitogenome of the caryophylliid genus Crispatotrochus, whose phylogenetic position remains uncertain. METHODS AND RESULTS The complete mitochondrial genomes of Crispatotrochus rubescens and Crispatotrochus rugosus were sequenced, assembled, and annotated. The two mitogenomes are identical and circular, have a length of 16,536 bp, a GC content of 35.9%, and contain 13 protein-coding genes, 2 ribosomal RNAs and 2 transfer RNAs. Both species have a transposition of a three gene block - cob, nad2, and nad6 - similarly to a group of caryophylliid genera that were recovered as monophyletic, including the type genus (Caryophyllia) of the family. The phylogenetic analyses recovered Crispatotrochus within the clade that presents the gene rearrangement and specifically as sister taxa of the genus Caryophyllia, a result consistent with previous studies and the similar gross morphology of the two genera. CONCLUSIONS We determined the mitochondrial genomes of the genus Crispatotrochus to investigate their relations within Scleractinia. Results from this study provide insights on the phylogenetic position of the genus and corroborate that the mitochondrial gene order could be used as taxonomic character for the family Caryophylliidae.
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Affiliation(s)
- C F Vaga
- Centre for Marine Biology, University of Sao Paulo, Sao Sebastiao, 11612-109, Brazil. .,Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil.
| | - I G L Seiblitz
- Centre for Marine Biology, University of Sao Paulo, Sao Sebastiao, 11612-109, Brazil.,Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil
| | - K C C Capel
- Centre for Marine Biology, University of Sao Paulo, Sao Sebastiao, 11612-109, Brazil.,Department of Marine Science, Federal University of Sao Paulo, Santos, 11070-100, Brazil
| | - M V Kitahara
- Centre for Marine Biology, University of Sao Paulo, Sao Sebastiao, 11612-109, Brazil.,Department of Invertebrate Zoology, Smithsonian Institution, National Museum of Natural History, MRC 163, PO Box 37012, Washington, DC, 20013-7012, USA
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