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Sandberg TOM, Yahalomi D, Bracha N, Haddas-Sasson M, Pupko T, Atkinson SD, Bartholomew JL, Zhang JY, Huchon D. Evolution of myxozoan mitochondrial genomes: insights from myxobolids. BMC Genomics 2024; 25:388. [PMID: 38649808 PMCID: PMC11034133 DOI: 10.1186/s12864-024-10254-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: 12/03/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Myxozoa is a class of cnidarian parasites that encompasses over 2,400 species. Phylogenetic relationships among myxozoans remain highly debated, owing to both a lack of informative morphological characters and a shortage of molecular markers. Mitochondrial (mt) genomes are a common marker in phylogeny and biogeography. However, only five complete myxozoan mt genomes have been sequenced: four belonging to two closely related genera, Enteromyxum and Kudoa, and one from the genus Myxobolus. Interestingly, while cytochrome oxidase genes could be identified in Enteromyxum and Kudoa, no such genes were found in Myxobolus squamalis, and another member of the Myxobolidae (Henneguya salminicola) was found to have lost its entire mt genome. To evaluate the utility of mt genomes to reconstruct myxozoan relationships and to understand if the loss of cytochrome oxidase genes is a characteristic of myxobolids, we sequenced the mt genome of five myxozoans (Myxobolus wulii, M. honghuensis, M. shantungensis, Thelohanellus kitauei and, Sphaeromyxa zaharoni) using Illumina and Oxford Nanopore platforms. RESULTS Unlike Enteromyxum, which possesses a partitioned mt genome, the five mt genomes were encoded on single circular chromosomes. An mt plasmid was found in M. wulii, as described previously in Kudoa iwatai. In all new myxozoan genomes, five protein-coding genes (cob, cox1, cox2, nad1, and nad5) and two rRNAs (rnl and rns) were recognized, but no tRNA. We found that Myxobolus and Thelohanellus species shared unidentified reading frames, supporting the view that these mt open reading frames are functional. Our phylogenetic reconstructions based on the five conserved mt genes agree with previously published trees based on the 18S rRNA gene. CONCLUSIONS Our results suggest that the loss of cytochrome oxidase genes is not a characteristic of all myxobolids, the ancestral myxozoan mt genome was likely encoded on a single circular chromosome, and mt plasmids exist in a few lineages. Our findings indicate that myxozoan mt sequences are poor markers for reconstructing myxozoan phylogenetic relationships because of their fast-evolutionary rates and the abundance of repeated elements, which complicates assembly.
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Affiliation(s)
| | - Dayana Yahalomi
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Noam Bracha
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Michal Haddas-Sasson
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Stephen D Atkinson
- Department of Microbiology, Oregon State University, 97331, Corvallis, OR, USA
| | - Jerri L Bartholomew
- Department of Microbiology, Oregon State University, 97331, Corvallis, OR, USA
| | - Jin Yong Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Dorothée Huchon
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel.
- The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, 6997801, Tel Aviv, Israel.
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Cruz BA, Cappelmann A, Chutjian H, Roman JC, Reid MA, Wright J, Gonzalez AD, Keyman T, Griffith KM, Appiah-Madson HJ, Distel DL, Hayes VE, Drewery J, Pettay DT, Staton JL, Brugler MR. Complete mitochondrial genomes of the black corals Alternatipathesmirabilis Opresko & Molodtsova, 2021 and Parantipatheslarix (Esper, 1788) (Cnidaria, Anthozoa, Hexacorallia, Antipatharia, Schizopathidae). Zookeys 2024; 1196:79-93. [PMID: 38560095 PMCID: PMC10980879 DOI: 10.3897/zookeys.1196.116837] [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: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 04/04/2024] Open
Abstract
We describe the complete mitogenomes of the black corals Alternatipathesmirabilis Opresko & Molodtsova, 2021 and Parantipatheslarix (Esper, 1790) (Cnidaria, Anthozoa, Hexacorallia, Antipatharia, Schizopathidae). The analysed specimens include the holotype of Alternatipathesmirabilis, collected from Derickson Seamount (North Pacific Ocean; Gulf of Alaska) at 4,685 m depth and a potential topotype of Parantipatheslarix, collected from Secca dei Candelieri (Mediterranean Sea; Tyrrhenian Sea; Salerno Gulf; Italy) at 131 m depth. We also assemble, annotate and make available nine additional black coral mitogenomes that were included in a recent phylogeny (Quattrini et al. 2023b), but not made easily accessible on GenBank. This is the first study to present and compare two mitogenomes from the same species of black coral (Stauropathesarctica (Lütken, 1871)) and, thus, place minimum boundaries on the expected level of intraspecific variation at the mitogenome level. We also compare interspecific variation at the mitogenome-level across five different specimens of Parantipathes Brook, 1889 (representing at least two different species) from the NE Atlantic and Mediterranean Sea.
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Affiliation(s)
- Brendan A. Cruz
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Anneau Cappelmann
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Hope Chutjian
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Jude C. Roman
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Mason A. Reid
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Jacob Wright
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Aydanni D. Gonzalez
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Taylor Keyman
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Kierstin M. Griffith
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Hannah J. Appiah-Madson
- Ocean Genome Legacy Center, Northeastern University, 430 Nahant Road, Nahant, MA 01908, USANortheastern UniversityNahantUnited States of America
| | - Daniel L. Distel
- Ocean Genome Legacy Center, Northeastern University, 430 Nahant Road, Nahant, MA 01908, USANortheastern UniversityNahantUnited States of America
| | - Vonda E. Hayes
- Department of Fisheries & Oceans Canada, Northwest Atlantic Fisheries Centre, 80 East White Hills Road, St. John’s, Newfoundland & Labrador, A1C 5X1, CanadaNorthwest Atlantic Fisheries CentreNewfoundland & LabradorCanada
| | - Jim Drewery
- Marine Directorate of Scottish Government, Marine Laboratory, 375 Victoria Road, Aberdeen AB11 9DB, Scotland, UKMarine Directorate of Scottish Government, Marine LaboratoryAberdeenUnited Kingdom
| | - D. Tye Pettay
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Joseph L. Staton
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Mercer R. Brugler
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USAAmerican Museum of Natural HistoryNew YorkUnited States of America
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC 20560, USANational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
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3
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Shizuru LEK, Montgomery AD, Wagner D, Freel EB, Toonen RJ. The complete mitochondrial genome of a species of Cirrhipathes de Blainville, 1830 from Kaua'i, Hawai'i (Hexacorallia: Antipatharia). Mitochondrial DNA B Resour 2024; 9:223-226. [PMID: 38313464 PMCID: PMC10836483 DOI: 10.1080/23802359.2024.2310130] [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: 01/23/2023] [Accepted: 01/20/2024] [Indexed: 02/06/2024] Open
Abstract
This study reports the first mitogenome from the antipatharian (black coral) genus Cirrhipathes (GenBank accession number ON653414). The 20,452 bp mitochondrial genome of Cirrhipathes cf. anguina LS-2022 consists of 13 protein-coding genes, two rRNA genes, and two tRNA genes (trnM and trnW). The mitogenome is typical of other antipatharian families, including an A + T biased (64.1%) base composition and cytochrome c oxidase subunit I (COX1) intron with embedded homing endonuclease gene (HEG). A phylogenetic tree based on complete mitogenome sequences of currently available antipatharians indicates Cirrhipathes cf. anguina LS-2022 is sister and closely related to Stichopathes sp. SCBUCN-8849. However, it seems unlikely that intergeneric taxa share 99.97% similarity across their complete mitogenomes, raising questions about the current taxonomy of this group. This study highlights the need for additional vouchered antipatharian species to be sequenced so phylogenetic relationships can be compared with accepted taxonomy.
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Affiliation(s)
- Leah E K Shizuru
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Anthony D Montgomery
- US Fish and Wildlife Service, Pacific Fish and Wildlife Office, Honolulu, HI, USA
| | | | - Evan B Freel
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
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4
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Jacobovitz MR, Hambleton EA, Guse A. Unlocking the Complex Cell Biology of Coral-Dinoflagellate Symbiosis: A Model Systems Approach. Annu Rev Genet 2023; 57:411-434. [PMID: 37722685 DOI: 10.1146/annurev-genet-072320-125436] [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] [Indexed: 09/20/2023]
Abstract
Symbiotic interactions occur in all domains of life, providing organisms with resources to adapt to new habitats. A prime example is the endosymbiosis between corals and photosynthetic dinoflagellates. Eukaryotic dinoflagellate symbionts reside inside coral cells and transfer essential nutrients to their hosts, driving the productivity of the most biodiverse marine ecosystem. Recent advances in molecular and genomic characterization have revealed symbiosis-specific genes and mechanisms shared among symbiotic cnidarians. In this review, we focus on the cellular and molecular processes that underpin the interaction between symbiont and host. We discuss symbiont acquisition via phagocytosis, modulation of host innate immunity, symbiont integration into host cell metabolism, and nutrient exchange as a fundamental aspect of stable symbiotic associations. We emphasize the importance of using model systems to dissect the cellular complexity of endosymbiosis, which ultimately serves as the basis for understanding its ecology and capacity to adapt in the face of climate change.
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Affiliation(s)
- Marie R Jacobovitz
- Cell Biology and Biophysics, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Elizabeth A Hambleton
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria;
| | - Annika Guse
- Faculty of Biology, Ludwig-Maximilians-Universität Munich, Munich, Germany;
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5
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Ling MK, Yap NWL, Iesa IB, Yip ZT, Huang D, Quek ZBR. Revisiting mitogenome evolution in Medusozoa with eight new mitochondrial genomes. iScience 2023; 26:108252. [PMID: 37965150 PMCID: PMC10641506 DOI: 10.1016/j.isci.2023.108252] [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: 04/10/2023] [Revised: 09/01/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Mitogenomics has improved our understanding of medusozoan phylogeny. However, sequenced medusozoan mitogenomes remain scarce, and Medusozoa phylogeny studies often analyze mitogenomic sequences without incorporating mitogenome rearrangements. To better understand medusozoan evolution, we analyzed Medusozoa mitogenome phylogeny by sequencing and assembling eight mitogenomes from three classes (Cubozoa, Hydrozoa, and Scyphozoa). We reconstructed the mitogenome phylogeny using these mitogenomes and 84 other existing cnidarian mitogenomes to study mitochondrial gene rearrangements. All reconstructed mitogenomes had 13 mitochondrial protein-coding genes and two ribosomal genes typical for Medusozoa. Non-cubozoan mitogenomes were all linear and had typical gene orders, while arrangement of genes in the fragmented Cubozoa (Morbakka sp.) mitogenome differed from other Cubozoa mitogenomes. Gene order comparisons and ancestral state reconstruction suggest minimal rearrangements within medusozoan classes except for Hydrozoa. Our findings support a staurozoan ancestral medusozoan gene order, expand the pool of available medusozoan mitogenomes, and enhance our understanding of medusozoan phylogenetic relationships.
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Affiliation(s)
- Min Kang Ling
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| | - Nicholas Wei Liang Yap
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
- St. John’s Island National Marine Laboratory, c/o Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
| | - Iffah Binte Iesa
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Singapore
| | - Zhi Ting Yip
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Singapore
| | - Zheng Bin Randolph Quek
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
- Yale-NUS College, National University of Singapore, Singapore 138527, Singapore
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6
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Mills CE, Westlake H, Hirano YM, Miranda LS. Description of a common stauromedusa on the Pacific Coast of the United States and Canada, Haliclystus sanjuanensis new species (Cnidaria: Staurozoa). PeerJ 2023; 11:e15944. [PMID: 37744232 PMCID: PMC10512941 DOI: 10.7717/peerj.15944] [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: 05/10/2023] [Accepted: 08/01/2023] [Indexed: 09/26/2023] Open
Abstract
Haliclystus "sanjuanensis" nomen nudum is the most common staurozoan on the west coast of the United States and Canada. This species was described in the M.S. Thesis by Gellermann (1926) and although that name has been in use nearly continuously since that time, no published description exists. Furthermore, the most popular operative name for this species has varied between several related species names over time, resulting in confusion. Herein, we provide a detailed description and synonymy of Haliclystus sanjuanensis n. sp., whose distribution is verified from Unalaska Island in the Aleutians (53.4° N, 166.8° W) in the northwest, to Santa Barbara County, California, just north of Point Conception (34.5° N, 120.5° W), in the south. Haliclystus sanjuanensis n. sp. is compared with the twelve other described species of Haliclystus and illustrations of both macroscopic and microscopic anatomy are provided. Haliclystus sanjuanensis n. sp. is unique among species of Haliclystus in the arrangement of the bright-white nematocyst spots in its calyx and the pattern of dark stripes running the length of the stalk and up the outside of the calyx.
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Affiliation(s)
- Claudia E. Mills
- Friday Harbor Laboratories and the Department of Biology, University of Washington, Friday Harbor, Washington, United States
| | - Hannah Westlake
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Yayoi M. Hirano
- Coastal Branch of Natural History Museum and Institute, Chiba, Katsuura, Chiba, Japan
| | - Lucília S. Miranda
- Department of Zoology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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7
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McCauley M, Goulet TL, Jackson CR, Loesgen S. Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations. Nat Commun 2023; 14:4899. [PMID: 37580316 PMCID: PMC10425419 DOI: 10.1038/s41467-023-39876-6] [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: 09/06/2022] [Accepted: 06/30/2023] [Indexed: 08/16/2023] Open
Abstract
Microorganisms play essential roles in the health and resilience of cnidarians. Understanding the factors influencing cnidarian microbiomes requires cross study comparisons, yet the plethora of protocols used hampers dataset integration. We unify 16S rRNA gene sequences from cnidarian microbiome studies under a single analysis pipeline. We reprocess 12,010 cnidarian microbiome samples from 186 studies, alongside 3,388 poriferan, 370 seawater samples, and 245 cultured Symbiodiniaceae, unifying ~6.5 billion sequence reads. Samples are partitioned by hypervariable region and sequencing platform to reduce sequencing variability. This systematic review uncovers an incredible diversity of 86 archaeal and bacterial phyla associated with Cnidaria, and highlights key bacteria hosted across host sub-phylum, depth, and microhabitat. Shallow (< 30 m) water Alcyonacea and Actinaria are characterized by highly shared and relatively abundant microbial communities, unlike Scleractinia and most deeper cnidarians. Utilizing the V4 region, we find that cnidarian microbial composition, richness, diversity, and structure are primarily influenced by host phylogeny, sampling depth, and ocean body, followed by microhabitat and sampling date. We identify host and geographical generalist and specific Endozoicomonas clades within Cnidaria and Porifera. This systematic review forms a framework for understanding factors governing cnidarian microbiomes and creates a baseline for assessing stress associated dysbiosis.
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Affiliation(s)
- M McCauley
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.
- Department of Biology, University of Mississippi, University, MS, USA.
- U.S. Geological Survey, Wetland and Aquatic Research Centre, Gainesville, FL, USA.
| | - T L Goulet
- Department of Biology, University of Mississippi, University, MS, USA
| | - C R Jackson
- Department of Biology, University of Mississippi, University, MS, USA
| | - S Loesgen
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
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8
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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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9
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Feng H, Lv S, Li R, Shi J, Wang J, Cao P. Mitochondrial genome comparison reveals the evolution of cnidarians. Ecol Evol 2023; 13:e10157. [PMID: 37325715 PMCID: PMC10261974 DOI: 10.1002/ece3.10157] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 04/18/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Abstract
Cnidarians are the most primitive metazoans, but their evolutionary relationships are poorly understood, although recent studies present several phylogenetic hypotheses. Here, we collected 266 complete cnidarian mitochondrial genomes and re-evaluated the phylogenetic relationships between the major lineages. We described the gene rearrangement patterns of Cnidaria. Anthozoans had significantly greater mitochondrial genome size and lower A + T content than medusozoans. Most of the protein-coding genes in anthozoans such as COX 13, ATP6, and CYTB displayed a faster rate of evolution based on selection analysis. There were 19 distinct patterns of mitochondrial gene order, including 16 unique gene orders in anthozoans and 3 mtDNA gene orders pattern in medusozoans, were identified among cnidarians. The gene order arrangement suggested that a linearized mtDNA structure may be more conducive to Medusozoan mtDNA stability. Based on phylogenetic analyses, the monophyly of the Anthozoa was strongly supported compared to previous mitochondrial genome-based analyses rather than octocorals forming a sister group relationship with medusozoans. In addition, Staurozoa were more closely related to Anthozoa than to Medusozoa. In conclusion, these results largely support the traditional phylogenetic view of the relationships of cnidarians and provide new insights into the evolutionary processes for studying the most ancient animal radiations.
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Affiliation(s)
- Hui Feng
- Marine Microorganism Ecological & Application LabZhejiang Ocean UniversityZhoushanChina
| | - Sitong Lv
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
| | - Rong Li
- Marine Microorganism Ecological & Application LabZhejiang Ocean UniversityZhoushanChina
| | - Jing Shi
- Marine Microorganism Ecological & Application LabZhejiang Ocean UniversityZhoushanChina
| | - Jianxing Wang
- Marine Microorganism Ecological & Application LabZhejiang Ocean UniversityZhoushanChina
| | - Pinglin Cao
- Marine Microorganism Ecological & Application LabZhejiang Ocean UniversityZhoushanChina
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10
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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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11
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Taite M, Fernández-Álvarez FÁ, Braid HE, Bush SL, Bolstad K, Drewery J, Mills S, Strugnell JM, Vecchione M, Villanueva R, Voight JR, Allcock AL. Genome skimming elucidates the evolutionary history of Octopoda. Mol Phylogenet Evol 2023; 182:107729. [PMID: 36773750 DOI: 10.1016/j.ympev.2023.107729] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 12/10/2022] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
Abstract
Phylogenies for Octopoda have, until now, been based on morphological characters or a few genes. Here we provide the complete mitogenomes and the nuclear 18S and 28S ribosomal genes of twenty Octopoda specimens, comprising 18 species of Cirrata and Incirrata, representing 13 genera and all five putative families of Cirrata (Cirroctopodidae, Cirroteuthidae, Grimpoteuthidae, Opisthoteuthidae and Stauroteuthidae) and six families of Incirrata (Amphitretidae, Argonautidae, Bathypolypodidae, Eledonidae, Enteroctopodidae, and Megaleledonidae) which were assembled using genome skimming. Phylogenetic trees were built using Maximum Likelihood and Bayesian Inference with several alignment matrices. All mitochondrial genomes had the 'typical' genome composition and gene order previously reported for octopodiforms, except Bathypolypus ergasticus, which appears to lack ND5, two tRNA genes that flank ND5 and two other tRNA genes. Argonautoidea was revealed as sister to Octopodidae by the mitochondrial protein-coding gene dataset, however, it was recovered as sister to all other incirrate octopods with strong support in an analysis using nuclear rRNA genes. Within Cirrata, our study supports two existing classifications suggesting neither is likely in conflict with the true evolutionary history of the suborder. Genome skimming is useful in the analysis of phylogenetic relationships within Octopoda; inclusion of both mitochondrial and nuclear data may be key.
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Affiliation(s)
- M Taite
- School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
| | - F Á Fernández-Álvarez
- School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland; Institut de Ciències del Mar (CSIC), Passeig Marítim 37-49, E-08003 Barcelona, Spain.
| | - H E Braid
- AUT Lab for Cephalopod Ecology & Systematics, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - S L Bush
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington DC 20560, USA.
| | - K Bolstad
- AUT Lab for Cephalopod Ecology & Systematics, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand.
| | - J Drewery
- Marine Scotland, Marine Laboratory, 375 Victoria Road, Aberdeen AB11 9DB, UK.
| | - S Mills
- National Institute of Water and Atmospheric Research, 301 Evans Bay Parade, Wellington, New Zealand.
| | - J M Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Qld, Australia.
| | - M Vecchione
- National Systematics Laboratory, Office of Science and Technology, NOAA Fisheries, Washington, DC, USA; Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, USA.
| | - R Villanueva
- Institut de Ciències del Mar (CSIC), Passeig Marítim 37-49, E-08003 Barcelona, Spain.
| | - J R Voight
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S DuSable Lake Shore Dr., Chicago, IL 60605, USA.
| | - A L Allcock
- School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland.
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12
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Aguilar-Camacho JM, Foreman K, Jaimes-Becerra A, Aharoni R, Gründer S, Moran Y. Functional analysis in a model sea anemone reveals phylogenetic complexity and a role in cnidocyte discharge of DEG/ENaC ion channels. Commun Biol 2023; 6:17. [PMID: 36609696 PMCID: PMC9822975 DOI: 10.1038/s42003-022-04399-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023] Open
Abstract
Ion channels of the DEG/ENaC family share a similar structure but serve strikingly diverse biological functions, such as Na+ reabsorption, mechanosensing, proton-sensing, chemosensing and cell-cell communication via neuropeptides. This functional diversity raises the question of the ancient function of DEG/ENaCs. Using an extensive phylogenetic analysis across many different animal groups, we found a surprising diversity of DEG/ENaCs already in Cnidaria (corals, sea anemones, hydroids and jellyfish). Using a combination of gene expression analysis, electrophysiological and functional studies combined with pharmacological inhibition as well as genetic knockout in the model cnidarian Nematostella vectensis, we reveal an unanticipated role for a proton-sensitive DEG/ENaC in discharge of N. vectensis cnidocytes, the stinging cells typifying all cnidarians. Our study supports the view that DEG/ENaCs are versatile channels that have been co-opted for diverse functions since their early occurrence in animals and that respond to simple and ancient stimuli, such as omnipresent protons.
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Affiliation(s)
- Jose Maria Aguilar-Camacho
- grid.9619.70000 0004 1937 0538Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel ,grid.40803.3f0000 0001 2173 6074Present Address: Department of Biological Sciences, North Carolina State University, Raleigh, NC USA
| | - Katharina Foreman
- grid.1957.a0000 0001 0728 696XInstitute of Physiology, RWTH Aachen University, Aachen, Germany
| | - Adrian Jaimes-Becerra
- grid.9619.70000 0004 1937 0538Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Reuven Aharoni
- grid.9619.70000 0004 1937 0538Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Stefan Gründer
- grid.1957.a0000 0001 0728 696XInstitute of Physiology, RWTH Aachen University, Aachen, Germany
| | - Yehu Moran
- grid.9619.70000 0004 1937 0538Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
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13
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Muffett K, Miglietta MP. Demystifying Cassiopea species identity in the Florida Keys: Cassiopea xamachana and Cassiopea andromeda coexist in shallow waters. PLoS One 2023; 18:e0283441. [PMID: 36989331 PMCID: PMC10058153 DOI: 10.1371/journal.pone.0283441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/09/2023] [Indexed: 03/30/2023] Open
Abstract
The phylogeny of the Upside-Down Jellyfish (Cassiopea spp.) has been revised multiple times in its history. This is especially true in the Florida Keys, where much of the Cassiopea stock for research and aquarium trade in the United States are collected. In August 2021, we collected 55 Cassiopea medusae at eight shallow water sites throughout the Florida Keys and sequenced COI, 16S, and 28S genes. Mitochondrial genes demonstrate that the shallow waters in Florida are inhabited by both Cassiopea xamachana and a non-native Cassiopea andromeda lineage, identified in multispecies assemblages at least thrice. While C. xamachana were present at all sites, the C. andromeda-mitotype individuals were present at only a minority of sites. While we cannot confirm hybridization or lack thereof between the C. xamanchana and C. andromeda lineages, these previously unknown multispecies assemblages are a likely root cause for the confusing and disputed COI-based species identities of Cassiopea in the Florida Keys. This also serves as a cautionary note to all Cassiopea researchers to barcode their individuals regardless of the location in which they were collected.
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Affiliation(s)
- Kaden Muffett
- Texas A&M University at Galveston, Galveston, Texas, United States of America
| | - Maria Pia Miglietta
- Texas A&M University at Galveston, Galveston, Texas, United States of America
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14
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Hogan RI, Hopkins K, Wheeler AJ, Yesson C, Allcock AL. Evolution of mitochondrial and nuclear genomes in Pennatulacea. Mol Phylogenet Evol 2023; 178:107630. [PMID: 36182053 DOI: 10.1016/j.ympev.2022.107630] [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: 02/16/2022] [Revised: 08/31/2022] [Accepted: 09/19/2022] [Indexed: 12/14/2022]
Abstract
We examine the phylogeny of sea pens using sequences of whole mitochondrial genomes and the nuclear ribosomal cluster generated through low coverage Illumina sequencing. Taxon sampling includes 30 species in 19 genera representing 13 families. Ancestral state reconstruction shows that most sea pen mitochondrial genomes have the ancestral gene order, and that Pennatulacea with diverse gene orders are found in a single clade. The monophyly of Pennatulidae and Protoptilidae are rejected by both the mitochondrial and nuclear dataset, while the mitochondrial dataset further rejects monophyly of Virgulariidae, and the nuclear dataset rejects monophyly of Kophobelemnidae. We show discordance between nuclear ribosomal gene cluster phylogenies and whole mitochondrial genome phylogenies and highlight key Pennatulacea taxa that could be included in cnidarian genome-wide studies to better resolve the sea pen tree of life. We further illustrate how well frequently sequenced markers capture the overall diversity of the mitochondrial genome and the nuclear ribosomal genes in sea pens.
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Affiliation(s)
- Raissa I Hogan
- School of Natural Sciencecs & Ryan Institute, University of Galway, University Road, Galway, Ireland
| | - Kevin Hopkins
- Institute of Zoology, Zoological Society of London, Regent's Park, London, UK
| | - Andrew J Wheeler
- School of Biological, Earth & Environmental Science, Irish Centre for Research in Applied Geosciences, University College Cork, Ireland
| | - Chris Yesson
- Institute of Zoology, Zoological Society of London, Regent's Park, London, UK
| | - A Louise Allcock
- School of Natural Sciencecs & Ryan Institute, University of Galway, University Road, Galway, Ireland.
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15
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Wang W, Cao B, Xu Z, Jia Z, Yu S, Tian P, Niu W, Xiao J. The complete mitochondrial genome of Montiporavietnamensis (Scleractinia, Acroporidae). Biodivers Data J 2022; 10:e91531. [PMID: 36761536 PMCID: PMC9848517 DOI: 10.3897/bdj.10.e91531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/02/2022] [Indexed: 11/12/2022] Open
Abstract
Montiporavietnamensis Veron, 2000 (Cnidaria, Anthozoa, Scleractinia, Acroporidae) is an uncommon, but distinctive species of stony coral. The complete mitochondrial genome of M.vietnamensis was sequenced in this study for the first time, based on 32 pairs of primers newly designed according to seven species in the family Acroporidae. The mitogenome of M.vietnamensis has a circular form and is 17,885 bp long, including 13 protein-coding genes (PCGs), 2 tRNA (tRNAMet, tRNATrp), 2 rRNA genes and a putative control-region. The base composition of the complete mitogenome was 24.8% A, 14.2% C, 24.2% G and 36.8% T, with a higher AT content (61.6%) than GC content (38.4%). Based on 13 protein-coding genes, a Maximum Likelihood phylogenetic analysis showed that M.vietnamensis is clustered in the genus Montipora which belongs to the family Acroporidae. More stony coral species should be sequenced for basic molecular information and to help confirm the taxonomic status and evolutionary relationships of Scleractinia in the future.
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Affiliation(s)
- Wei Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Bingbing Cao
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Ziqing Xu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Zhiyu Jia
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Shuangen Yu
- Key Laboratory of Mariculture of Ministry of Education, College of Fisheries, Ocean University of China, Qingdao, ChinaKey Laboratory of Mariculture of Ministry of Education, College of Fisheries, Ocean University of ChinaQingdaoChina
| | - Peng Tian
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Wentao Niu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Jiaguang Xiao
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
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16
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Adaptive Responses of the Sea Anemone Heteractis crispa to the Interaction of Acidification and Global Warming. Animals (Basel) 2022; 12:ani12172259. [PMID: 36077978 PMCID: PMC9454579 DOI: 10.3390/ani12172259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Ocean acidification and warming are two of the most important threats to the existence of marine organisms and are predicted to co-occur in oceans. The present work evaluated the effects of acidification (AC: 24 ± 0.1 °C and 900 μatm CO2), warming (WC: 30 ± 0.1 °C and 450 μatm CO2), and their combination (CC: 30 ± 0.1 °C and 900 μatm CO2) on the sea anemone, Heteractis crispa, from the aspects of photosynthetic apparatus (maximum quantum yield of photosystem II (PS II), chlorophyll level, and Symbiodiniaceae density) and sterol metabolism (cholesterol content and total sterol content). In a 15-day experiment, acidification alone had no apparent effect on the photosynthetic apparatus, but did affect sterol levels. Upregulation of their chlorophyll level is an important strategy for symbionts to adapt to high partial pressure of CO2 (pCO2). However, after warming stress, the benefits of high pCO2 had little effect on stress tolerance in H. crispa. Indeed, thermal stress was the dominant driver of the deteriorating health of H. crispa. Cholesterol and total sterol contents were significantly affected by all three stress conditions, although there was no significant change in the AC group on day 3. Thus, cholesterol or sterol levels could be used as important indicators to evaluate the impact of climate change on cnidarians. Our findings suggest that H. crispa might be relatively insensitive to the impact of ocean acidification, whereas increased temperature in the future ocean might impair viability of H. crispa.
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17
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Tian P, Jia Z, Cao B, Wang W, Xiao J, Niu W. Complete mitochondrial genome sequences of Physogyralichtensteini (Milne Edwards & Haime, 1851) and Plerogyrasinuosa (Dana, 1846) (Scleractinia, Plerogyridae): characterisation and phylogenetic analysis. Zookeys 2022; 1114:21-34. [PMID: 36761708 PMCID: PMC9848633 DOI: 10.3897/zookeys.1114.85028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/11/2022] [Indexed: 11/12/2022] Open
Abstract
In this study, the whole mitochondrial genomes of Physogyralichtensteini and Plerogyrasinuosa have been sequenced for the first time. The length of their assembled mitogenome sequences were 17,286 bp and 17,586 bp, respectively, both including 13 protein-coding genes, two tRNAs, and two rRNAs. Their mitogenomes offered no distinct structure and their gene order were the same as other typical scleractinians. Based on 13 protein-coding genes, a maximum likelihood phylogenetic analysis showed that Physogyralichtensteini and Plerogyrasinuosa are clustered in the family Plerogyridae, which belongs to the "Robust" clade. The 13 tandem mitogenome PCG sequences used in this research can provide important molecular information to clarify the evolutionary relationships amongst stony corals, especially at the family level. On the other hand, more advanced markers and more species need to be used in the future to confirm the evolutionary relationships of all the scleractinians.
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Affiliation(s)
- Peng Tian
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Zhiyu Jia
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Bingbing Cao
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Wei Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Jiaguang Xiao
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Wentao Niu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
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18
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Siro G, Pipite A, Christi K, Srinivasan S, Subramani R. Marine Actinomycetes Associated with Stony Corals: A Potential Hotspot for Specialized Metabolites. Microorganisms 2022; 10:microorganisms10071349. [PMID: 35889068 PMCID: PMC9319285 DOI: 10.3390/microorganisms10071349] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/29/2022] [Accepted: 07/02/2022] [Indexed: 02/05/2023] Open
Abstract
Microbial secondary metabolites are an important source of antibiotics currently available for combating drug-resistant pathogens. These important secondary metabolites are produced by various microorganisms, including Actinobacteria. Actinobacteria have a colossal genome with a wide array of genes that code for several bioactive metabolites and enzymes. Numerous studies have reported the isolation and screening of millions of strains of actinomycetes from various habitats for specialized metabolites worldwide. Looking at the extent of the importance of actinomycetes in various fields, corals are highlighted as a potential hotspot for untapped secondary metabolites and new bioactive metabolites. Unfortunately, knowledge about the diversity, distribution and biochemistry of marine actinomycetes compared to hard corals is limited. In this review, we aim to summarize the recent knowledge on the isolation, diversity, distribution and discovery of natural compounds from marine actinomycetes associated with hard corals. A total of 11 new species of actinomycetes, representing nine different families of actinomycetes, were recovered from hard corals during the period from 2007 to 2022. In addition, this study examined a total of 13 new compounds produced by five genera of actinomycetes reported from 2017 to 2022 with antibacterial, antifungal and cytotoxic activities. Coral-derived actinomycetes have different mechanisms of action against their competitors.
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Affiliation(s)
- Galana Siro
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Campus, Suva, Fiji; (G.S.); (K.C.); (R.S.)
| | - Atanas Pipite
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Campus, Suva, Fiji; (G.S.); (K.C.); (R.S.)
- Correspondence: (A.P.); or (S.S.)
| | - Ketan Christi
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Campus, Suva, Fiji; (G.S.); (K.C.); (R.S.)
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, Division of Environmental & Life Science, College of Natural Science, Seoul Women’s University, 623 Hwarangno, Nowon-gu, Seoul 01797, Korea
- Correspondence: (A.P.); or (S.S.)
| | - Ramesh Subramani
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Campus, Suva, Fiji; (G.S.); (K.C.); (R.S.)
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19
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A Missing Link between Retrotransposons and Retroviruses. mBio 2022; 13:e0018722. [PMID: 35289644 PMCID: PMC9040795 DOI: 10.1128/mbio.00187-22] [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] [Indexed: 11/22/2022] Open
Abstract
The origin and deep evolution of retroviruses remain largely unclear. It has been proposed that retroviruses might have originated from a Ty3/Gypsy retrotransposon, but all known Ty3/Gypsy retrotransposons are only distantly related to retroviruses. Retroviruses and some plant Athila/Tat elements (within Ty3/Gypsy retrotransposons) independently evolved a dual RNase H domain and an env/env-like gene. Here, we reported the discovery of a novel lineage of retrotransposons, designated Odin retrotransposons, in the genomes of eight sea anemones (order Actinaria) within the Cnidaria phylum. Odin retrotransposons exhibited unique genome features, encoding a dual RNase H domain (like retroviruses) but no env gene (like most Ty3/Gypsy retrotransposons). Phylogenetic analyses based on reverse transcriptase showed that Odin retrotransposons formed a sister group to lokiretroviruses, and lokiretroviruses and Odin retrotransposons together were sister to canonical retroviruses. Moreover, phylogenetic analyses based on RNase H and integrase also supported the hypothesis that Odin retrotransposons were sisters to lokiretroviruses. Lokiretroviruses and canonical retroviruses did not form a monophyletic group, indicating that lokiretroviruses and canonical retroviruses might represent two distinct virus families. Taken together, the discovery of Odin retrotransposons narrowed down the evolutionary gaps between retrotransposons and canonical retroviruses and lokiretroviruses.
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20
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Malkócs T, Viricel A, Becquet V, Evin L, Dubillot E, Pante E. Complex mitogenomic rearrangements within the Pectinidae (Mollusca: Bivalvia). BMC Ecol Evol 2022; 22:29. [PMID: 35272625 PMCID: PMC8915466 DOI: 10.1186/s12862-022-01976-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/18/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Scallops (Bivalvia: Pectinidae) present extraordinary variance in both mitochondrial genome size, structure and content, even when compared to the extreme diversity documented within Mollusca and Bivalvia. In pectinids, mitogenome rearrangements involve protein coding and rRNA genes along with tRNAs, and different genome organization patterns can be observed even at the level of Tribes. Existing pectinid phylogenies fail to resolve some relationships in the family, Chlamydinae being an especially problematic group. RESULTS In our study, we sequenced, annotated and characterized the mitochondrial genome of a member of Chlamydinae, Mimachlamys varia-a species of commercial interest and an effective bioindicator-revealing yet another novel gene arrangement in the Pectinidae. The phylogeny based on all mitochondrial protein coding and rRNA genes suggests the paraphyly of the Mimachlamys genus, further commending the taxonomic revision of the classification within the Chlamydinae subfamily. At the scale of the Pectinidae, we found that 15 sequence blocks are involved in mitogenome rearrangements, which behave as separate units. CONCLUSIONS Our study reveals incongruities between phylogenies based on mitochondrial protein-coding versus rRNA genes within the Pectinidae, suggesting that locus sampling affects phylogenetic inference at the scale of the family. We also conclude that the available taxon sampling does not allow for understanding of the mechanisms responsible for the high variability of mitogenome architecture observed in the Pectinidae, and that unraveling these processes will require denser taxon sampling.
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Affiliation(s)
- Tamás Malkócs
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 Rue Olympe de Gouges, 17042, La Rochelle Cedex 01, France. .,Pál Juhász-Nagy Doctoral School of Biology and Environmental Sciences, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary. .,Institute of Biology and Ecology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary. .,Institute of Aquatic Ecology, Centre for Ecological Research, 4026, Debrecen, Hungary.
| | - Amélia Viricel
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 Rue Olympe de Gouges, 17042, La Rochelle Cedex 01, France
| | - Vanessa Becquet
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 Rue Olympe de Gouges, 17042, La Rochelle Cedex 01, France
| | - Louise Evin
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 Rue Olympe de Gouges, 17042, La Rochelle Cedex 01, France
| | - Emmanuel Dubillot
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 Rue Olympe de Gouges, 17042, La Rochelle Cedex 01, France
| | - Eric Pante
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 Rue Olympe de Gouges, 17042, La Rochelle Cedex 01, France
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21
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Erofeeva TV, Grigorenko AP, Gusev FE, Kosevich IA, Rogaev EI. Studying of Molecular Regulation of Developmental Processes of Lower Metazoans Exemplified by Cnidaria Using High-Throughput Sequencing. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:269-293. [PMID: 35526848 DOI: 10.1134/s0006297922030075] [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: 10/28/2021] [Revised: 12/13/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
A unique set of features and characteristics of species of the Cnidaria phylum is the one reason that makes them a model for a various studies. The plasticity of a life cycle and the processes of cell differentiation and development of an integral multicellular organism associated with it are of a specific scientific interest. A new stage of development of molecular genetic methods, including methods for high-throughput genome, transcriptome, and epigenome sequencing, both at the level of the whole organism and at the level of individual cells, makes it possible to obtain a detailed picture of the development of these animals. This review examines some modern approaches and advances in the reconstruction of the processes of ontogenesis of cnidarians by studying the regulatory signal transduction pathways and their interactions.
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Affiliation(s)
- Taisia V Erofeeva
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anastasia P Grigorenko
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia.
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Fedor E Gusev
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Igor A Kosevich
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Evgeny I Rogaev
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
- Lomonosov Moscow State University, Moscow, 119234, Russia
- Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA 01545, USA
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22
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Cerri F, Saliu F, Maggioni D, Montano S, Seveso D, Lavorano S, Zoia L, Gosetti F, Lasagni M, Orlandi M, Taglialatela-Scafati O, Galli P. Cytotoxic Compounds from Alcyoniidae. An Overview of the Last 30 Years. Mar Drugs 2022; 20:md20020134. [PMID: 35200663 PMCID: PMC8874409 DOI: 10.3390/md20020134] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/29/2022] [Accepted: 02/10/2022] [Indexed: 11/30/2022] Open
Abstract
The octocoral family Alcyoniidae represents a rich source of bioactive substances with intriguing and unique structural features. This review aims to provide an updated overview of the compounds isolated from Alcyoniidae and displaying potential cytotoxic activity. In order to allow a better comparison among the bioactive compounds, we focused on molecules evaluated in vitro by using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay, by far the most widely used method to analyze cell proliferation and viability. Specifically, we surveyed the last thirty years of research, finding 153 papers reporting on 344 compounds with proven cytotoxicity. The data were organized in tables to provide a ranking of the most active compounds, to be exploited for the selection of the most promising candidates for further screening and pre-clinical evaluation as anti-cancer agents. Specifically, we found that (22S,24S)-24-methyl-22,25-epoxyfurost-5-ene-3β,20β-diol (16), 3β,11-dihydroxy-24-methylene-9,11-secocholestan-5-en-9-one (23), (24S)-ergostane-3β,5α,6β,25 tetraol (146), sinulerectadione (227), sinulerectol C (229), and cladieunicellin I (277) exhibited stronger cytotoxicity than their respective positive control and that their mechanism of action has not yet been further investigated.
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Affiliation(s)
- Federico Cerri
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, 20126 Milano, Italy;
| | - Francesco Saliu
- Department of Earth and Environmental Sciences DISAT, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (D.M.); (S.M.); (D.S.); (L.Z.); (F.G.); (M.L.); (M.O.); (P.G.)
- Correspondence: ; Tel.: +39-0264482813
| | - Davide Maggioni
- Department of Earth and Environmental Sciences DISAT, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (D.M.); (S.M.); (D.S.); (L.Z.); (F.G.); (M.L.); (M.O.); (P.G.)
- MaRHE Centre (Marine Research and High Education Center), Magoodhoo Island, Faafu Atoll 12030, Maldives
| | - Simone Montano
- Department of Earth and Environmental Sciences DISAT, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (D.M.); (S.M.); (D.S.); (L.Z.); (F.G.); (M.L.); (M.O.); (P.G.)
- MaRHE Centre (Marine Research and High Education Center), Magoodhoo Island, Faafu Atoll 12030, Maldives
| | - Davide Seveso
- Department of Earth and Environmental Sciences DISAT, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (D.M.); (S.M.); (D.S.); (L.Z.); (F.G.); (M.L.); (M.O.); (P.G.)
- MaRHE Centre (Marine Research and High Education Center), Magoodhoo Island, Faafu Atoll 12030, Maldives
| | - Silvia Lavorano
- Costa Edutainment SpA—Acquario di Genova, Area Porto Antico, Ponte Spinola, 16128 Genoa, Italy;
| | - Luca Zoia
- Department of Earth and Environmental Sciences DISAT, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (D.M.); (S.M.); (D.S.); (L.Z.); (F.G.); (M.L.); (M.O.); (P.G.)
| | - Fabio Gosetti
- Department of Earth and Environmental Sciences DISAT, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (D.M.); (S.M.); (D.S.); (L.Z.); (F.G.); (M.L.); (M.O.); (P.G.)
| | - Marina Lasagni
- Department of Earth and Environmental Sciences DISAT, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (D.M.); (S.M.); (D.S.); (L.Z.); (F.G.); (M.L.); (M.O.); (P.G.)
| | - Marco Orlandi
- Department of Earth and Environmental Sciences DISAT, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (D.M.); (S.M.); (D.S.); (L.Z.); (F.G.); (M.L.); (M.O.); (P.G.)
| | | | - Paolo Galli
- Department of Earth and Environmental Sciences DISAT, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (D.M.); (S.M.); (D.S.); (L.Z.); (F.G.); (M.L.); (M.O.); (P.G.)
- MaRHE Centre (Marine Research and High Education Center), Magoodhoo Island, Faafu Atoll 12030, Maldives
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23
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Gamero-Mora E, Collins AG, Boco SR, Geson SM, Morandini AC. Revealing hidden diversity among upside-down jellyfishes (Cnidaria: Scyphozoa: Rhizostomeae:. INVERTEBR SYST 2022. [DOI: 10.1071/is21002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Morphological variability within Cassiopea is well documented and has led to inaccuracies in the establishment of species boundaries in this taxon. Cassiopea medusae specimens from the Western Pacific (Japan and the Philippines) were analysed using multiple lines of complementary evidence, including types of cnidae, macro-morphology and molecular data. These observations lead to the recognition of two distinct species: Cassiopea mayeri, sp. nov. and a previously synonymised variety now raised to species level (Cassiopea culionensis, stat. nov.). These species can be distinguished from each other using morphological features. Herein, sexually dimorphic traits are included for the first time in the descriptions of Cassiopea species. Nematocyst types not previously observed in the genus are also reported. Molecular analyses, based on individual and combined markers (16S + cytochrome c oxidase I, COI), also support two distinct species; they are not sister taxa, and both are nested together within a clade of other Cassiopea members from the Australian and Indo-Pacific regions. Species richness is underestimated in the Western Pacific region, and integrative approaches are helpful to reveal and describe species. The systematics of Cassiopea is far from completely understood, but the present study represents an important further step. http://www.zoobank.org/References/B1A66787-009D-4465-954A-412C6878FCB4.
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24
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Terraneo TI, Mariappan KG, Forsman Z, Arrigoni R. Mitochondrial Genome of Nonmodel Marine Metazoans by Next-Generation Sequencing (NGS). Methods Mol Biol 2022; 2498:1-18. [PMID: 35727537 DOI: 10.1007/978-1-0716-2313-8_1] [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] [Indexed: 06/15/2023]
Abstract
Mitochondrial genomes (mtgenome) represent an important source of information for addressing fundamental evolutionary, phylogeographic, systematic, and ecological questions in marine organisms. In the last two decades the advent of high-throughput next-generation sequencing (NGS) has provided an unprecedented possibility to access large amount of genomic data and, as such, there has been a rapid growth in mtgenome resources and studies. In particular, NGS strategies represent a great advantage for investigating nonmodel marine organisms for which no or limited genomic resources are available. Here, we describe a routinely used standardized protocol to obtain mtgenome of nonmodel marine organisms by NGS. The protocol is composed of five main steps, including DNA extraction, DNA fragmentation, library preparation, high-throughput sequencing, and bioinformatic analyses. Each of the first three steps is followed by size/quality and concentration validations. The advantages of the described protocol rely on the assumption that no a priori information on mtgenome of the studied organism is needed and on its versatility as researchers may choose several kits for DNA extraction and library preparation and adopt different methods for DNA fragmentation depending on their needs, experience, and suppliers.
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Affiliation(s)
- Tullia I Terraneo
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Kiruthiga G Mariappan
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Zac Forsman
- Hawaii Institute of Marine Biology, Kaneohe, HI, USA
| | - Roberto Arrigoni
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Naples, Italy.
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25
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Wang X, Liao Q, Chen H, Gong G, Siu SWI, Chen Q, Kam H, Ung COL, Cheung KK, Rádis-Baptista G, Wong CTT, Lee SMY. Toxic Peptide From Palythoa caribaeorum Acting on the TRPV1 Channel Prevents Pentylenetetrazol-Induced Epilepsy in Zebrafish Larvae. Front Pharmacol 2021; 12:763089. [PMID: 34925021 PMCID: PMC8672801 DOI: 10.3389/fphar.2021.763089] [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: 08/23/2021] [Accepted: 11/08/2021] [Indexed: 11/25/2022] Open
Abstract
PcActx peptide, identified from the transcriptome of zoantharian Palythoa caribaeorum, was clustered into the phylogeny of analgesic polypeptides from sea anemone Heteractis crispa (known as APHC peptides). APHC peptides were considered as inhibitors of transient receptor potential cation channel subfamily V member 1 (TRPV1). TRPV1 is a calcium-permeable channel expressed in epileptic brain areas, serving as a potential target for preventing epileptic seizures. Through in silico and in vitro analysis, PcActx peptide was shown to be a potential TRPV1 channel blocker. In vivo studies showed that the linear and oxidized PcActx peptides caused concentration-dependent increases in mortality of zebrafish larvae. However, monotreatment with PcActx peptides below the maximum tolerated doses (MTD) did not affect locomotor behavior. Moreover, PcActx peptides (both linear and oxidized forms) could effectively reverse pentylenetetrazol (PTZ)-induced seizure-related behavior in zebrafish larvae and prevent overexpression of c-fos and npas4a at the mRNA level. The excessive production of ROS induced by PTZ was markedly attenuated by both linear and oxidized PcActx peptides. It was also verified that the oxidized PcActx peptide was more effective than the linear one. In particular, oxidized PcActx peptide notably modulated the mRNA expression of genes involved in calcium signaling and γ-aminobutyric acid (GABA)ergic-glutamatergic signaling, including calb1, calb2, gabra1, grm1, gria1b, grin2b, gat1, slc1a2b, gad1b, and glsa. Taken together, PcActx peptide, as a novel neuroactive peptide, exhibits prominent anti-epileptic activity, probably through modulating calcium signaling and GABAergic-glutamatergic signaling, and is a promising candidate for epilepsy management.
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Affiliation(s)
- Xiufen Wang
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Qiwen Liao
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China.,School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China
| | - Hanbin Chen
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Guiyi Gong
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Shirley Weng In Siu
- Department of Computer and Information Science, Faculty of Science and Technology, University of Macau, Macau, China
| | - Qian Chen
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Hiotong Kam
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Carolina Oi Lam Ung
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Kwok-Kuen Cheung
- Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong, China
| | - Gandhi Rádis-Baptista
- Laboratory of Biochemistry and Biotechnology, Institute for Marine Sciences, Federal University of Ceará, Fortaleza, Brazil
| | - Clarence Tsun Ting Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China
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26
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Fujita S, Kuranaga E, Nakajima YI. Regeneration Potential of Jellyfish: Cellular Mechanisms and Molecular Insights. Genes (Basel) 2021; 12:758. [PMID: 34067753 PMCID: PMC8156412 DOI: 10.3390/genes12050758] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/09/2021] [Accepted: 05/14/2021] [Indexed: 01/20/2023] Open
Abstract
Medusozoans, the Cnidarian subphylum, have multiple life stages including sessile polyps and free-swimming medusae or jellyfish, which are typically bell-shaped gelatinous zooplanktons that exhibit diverse morphologies. Despite having a relatively complex body structure with well-developed muscles and nervous systems, the adult medusa stage maintains a high regenerative ability that enables organ regeneration as well as whole body reconstitution from the part of the body. This remarkable regeneration potential of jellyfish has long been acknowledged in different species; however, recent studies have begun dissecting the exact processes underpinning regeneration events. In this article, we introduce the current understanding of regeneration mechanisms in medusae, particularly focusing on cellular behaviors during regeneration such as wound healing, blastema formation by stem/progenitor cells or cell fate plasticity, and the organism-level patterning that restores radial symmetry. We also discuss putative molecular mechanisms involved in regeneration processes and introduce a variety of novel model jellyfish species in the effort to understand common principles and diverse mechanisms underlying the regeneration of complex organs and the entire body.
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Affiliation(s)
- Sosuke Fujita
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Miyagi, Japan; (S.F.); (E.K.)
| | - Erina Kuranaga
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Miyagi, Japan; (S.F.); (E.K.)
| | - Yu-ichiro Nakajima
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Miyagi, Japan; (S.F.); (E.K.)
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai 980-8577, Miyagi, Japan
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27
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Tian P, Xiao J, Jia Z, Guo F, Wang X, Wang W, Wang J, Huang D, Niu W. Complete mitochondrial DNA sequence of the Psammocora profundacella (Scleractinia, Psammocoridae): mitogenome characterisation and phylogenetic implications. Biodivers Data J 2021; 9:e62395. [PMID: 33911915 PMCID: PMC8076163 DOI: 10.3897/bdj.9.e62395] [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: 12/23/2020] [Accepted: 04/13/2021] [Indexed: 11/12/2022] Open
Abstract
Complete mitochondrial DNA sequence data have played a significant role in phylogenetic and evolutionary studies of scleractinian corals. In this study, the complete mitogenome of Psammocora profundacella Gardiner, 1898, collected from Guangdong Province, China, was sequenced by next-generation sequencing for the first time. Psammocora profundacella is the first species for which a mitogenome has been sequenced in the family Psammocoridae. The length of its assembled mitogenome sequence was 16,274 bp, including 13 protein-coding genes, two tRNAs and two rRNAs. Its gene content and gene order were consistent with the other Scleractinia species. All genes were encoded on the H strand and the GC content of the mitochondrial genome was 30.49%. Gene content and order were consistent with the other Scleractinia species. Based on 13 protein-coding genes, Maximum Likelihood phylogenetic analysis showed that P. profundacella belongs to the "Robust" clade. Mitochondrial genome data provide important molecular information for understanding the phylogeny of stony corals. More variable markers and additional species should be sequenced to confirm the evolutionary relationships of Scleractinia in the future.
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Affiliation(s)
- Peng Tian
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China Third Institute of Oceanography, Ministry of Natural Resources Xiamen China
| | - Jiaguang Xiao
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China Third Institute of Oceanography, Ministry of Natural Resources Xiamen China
| | - Zhiyu Jia
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China Third Institute of Oceanography, Ministry of Natural Resources Xiamen China
| | - Feng Guo
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China Third Institute of Oceanography, Ministry of Natural Resources Xiamen China
| | - Xiaolei Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China Third Institute of Oceanography, Ministry of Natural Resources Xiamen China
| | - Wei Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China Third Institute of Oceanography, Ministry of Natural Resources Xiamen China
| | - Jianjia Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China Third Institute of Oceanography, Ministry of Natural Resources Xiamen China
| | - Dingyong Huang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China Third Institute of Oceanography, Ministry of Natural Resources Xiamen China
| | - Wentao Niu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China Third Institute of Oceanography, Ministry of Natural Resources Xiamen China
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28
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Hirose E, Sakai D, Iida A, Obayashi Y, Nishikawa J. Exumbrellar Surface of Jellyfish: A Comparative Fine Structure Study with Remarks on Surface Reflectance. Zoolog Sci 2021; 38:170-178. [PMID: 33812356 DOI: 10.2108/zs200111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/30/2020] [Indexed: 11/17/2022]
Abstract
The exumbrellar surfaces of six pelagic cnidarians from three classes were ultra-structurally compared to reveal their structural diversity in relation to their gelatinous, transparent bodies. We examined two hydrozoans (Diphyes chamissonis and Colobonema sericeum), a cubozoan (Chironex yamaguchii), and three scyphozoans (Atolla vanhöffeni, Aurelia coerulea, and Mastigias papua). The exumbrellar surfaces of the mesoglea in D. chamissonis, Ch. yamaguchii, Au. coerulea, and M. papua were covered with a simple epidermis; the shapes of the epidermal cells were remarkably different among the species. The epidermal cells of Ch. yamaguchii and M. papua possessed an array of microvilli on the apical side. The array possibly reduced light reflectance and provided some other surface properties, as seen for the cuticular nipple array in tunicates, considering the length, width, and pitch of the microvilli. The reduction of light reflectance on the array of microvilli was supported by the simulation with rigorous coupled wave analysis (RCWA). Microvilli were sparse and did not form an array in metephyrae of Au. coerulea. The mesoglea matrix beneath the basal side of the epidermis was loose in all of the species. The exumbrellar side of the mesoglea was exposed only in the mesopelagic species, At. vanhöffeni and Co. sericeum, and electron-dense layer(s) covered the surface of the mesoglea. It is uncertain whether the exumbrellar epidermis is absent in these species or the epidermal cells are completely exfoliated during the sampling and handling processes. In the latter case, the electron-dense layer(s) on the mesoglea surface might originally underlie the epidermis.
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Affiliation(s)
- Euichi Hirose
- Faculty of Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan,
| | - Daisuke Sakai
- School of Regional Innovation and Social Design Engineering, Kitami Institute of Technology, Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Akane Iida
- Graduate School of Bioscience, Tokai University, Orido, Shimizu, Shizuoka 424-8610, Japan
| | - Yumiko Obayashi
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Jun Nishikawa
- School of Marine Science and Technology, Tokai University, Orido, Shimizu, Shizuoka 424-8610, Japan
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29
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Hernandez AM, Ryan JF. Six-state Amino Acid Recoding is not an Effective Strategy to Offset Compositional Heterogeneity and Saturation in Phylogenetic Analyses. Syst Biol 2021; 70:1200-1212. [PMID: 33837789 PMCID: PMC8513762 DOI: 10.1093/sysbio/syab027] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 01/25/2023] Open
Abstract
Six-state amino acid recoding strategies are commonly applied to combat the effects of compositional heterogeneity and substitution saturation in phylogenetic analyses. While these methods have been endorsed from a theoretical perspective, their performance has never been extensively tested. Here, we test the effectiveness of six-state recoding approaches by comparing the performance of analyses on recoded and non-recoded data sets that have been simulated under gradients of compositional heterogeneity or saturation. In our simulation analyses, non-recoding approaches consistently outperform six-state recoding approaches. Our results suggest that six-state recoding strategies are not effective in the face of high saturation. Furthermore, while recoding strategies do buffer the effects of compositional heterogeneity, the loss of information that accompanies six-state recoding outweighs its benefits. In addition, we evaluate recoding schemes with 9, 12, 15, and 18 states and show that these consistently outperform six-state recoding. Our analyses of other recoding schemes suggest that under conditions of very high compositional heterogeneity, it may be advantageous to apply recoding using more than six states, but we caution that applying any recoding should include sufficient justification. Our results have important implications for the more than 90 published papers that have incorporated six-state recoding, many of which have significant bearing on relationships across the tree of life. [Compositional heterogeneity; Dayhoff 6-state recoding; S&R 6-state recoding; six-state amino acid recoding; substitution saturation.]
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Affiliation(s)
- Alexandra M Hernandez
- Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, 220 Bartram Hall, P.O. Box 118525, Gainesville, FL, 32611, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, 220 Bartram Hall, P.O. Box 118525, Gainesville, FL, 32611, USA
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30
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Shen CY, Wang PZ, Xue W, Liu ZH, Zhao JY, Tong XB, Liu C, Wu XF, Mao X, Tian S, Fu C. The complete mitochondrial genome of soft coral Sinularia penghuensis Ofwegen and Benayahu, 2012 (Octocorallia: Alcyonacea): the analysis of mitogenome organization and phylogeny. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1348-1350. [PMID: 33889745 PMCID: PMC8043561 DOI: 10.1080/23802359.2021.1906174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The complete mitochondrial genome of Sinularia penghuensis was sequenced and analyzed using next-generation sequencing. The present mitochondrial genome was 18730 bp in length, containing 14 protein-coding genes (PCGs) (cox1-cox3.nad1-nad6, nad4L, atp6, atp8, cytb, and MutS), two ribosomal RNA genes (rRNAs) (12S and 16S), and one transfer RNA gene (Met-tRNA). The phylogenetic analysis of family Alcyoniidae revealed that S. penghuensis and Sinularia maxima cluster together. Five species in Sinularia reveals high identity in mitogenome sequences that the lowest variable sites (SNPs) were found between S. penghuensis and S. maxima.
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Affiliation(s)
- Chun-Yang Shen
- Department of Biology, Chengde Medical University, Hebei Province, Chengde, PR China
| | - Pei-Zheng Wang
- College of Ecology and Environment, Hainan Tropical Ocean University, Sanya, PR China
| | - Wei Xue
- Department of Chemical Engineering, Chengde Petroleum College, Chengde, PR China
| | - Zhao-Hui Liu
- Department of Biology, Chengde Medical University, Hebei Province, Chengde, PR China
| | - Jing-Yi Zhao
- Department of Functional Center, Chengde Medical University, Hebei Province, Chengde, PR China
| | - Xiao-Bo Tong
- Hemorheology Center, Chengde Medical University, Hebei Province, Chengde, PR China
| | - Chunwei Liu
- College of Ecology and Environment, Hainan Tropical Ocean University, Sanya, PR China
| | - Xiao-Fang Wu
- College of Ecology and Environment, Hainan Tropical Ocean University, Sanya, PR China
| | - Xiaonan Mao
- Department of Biology, Chengde Medical University, Hebei Province, Chengde, PR China
| | - Sihan Tian
- Department of Biology, Chengde Medical University, Hebei Province, Chengde, PR China
| | - Chunzheng Fu
- Institute of Sericulture, Chengde Medical University, Hebei Province, Chengde, PR China
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31
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Jékely G, Godfrey-Smith P, Keijzer F. Reafference and the origin of the self in early nervous system evolution. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190764. [PMID: 33550954 PMCID: PMC7934971 DOI: 10.1098/rstb.2019.0764] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2020] [Indexed: 12/20/2022] Open
Abstract
Discussions of the function of early nervous systems usually focus on a causal flow from sensors to effectors, by which an animal coordinates its actions with exogenous changes in its environment. We propose, instead, that much early sensing was reafferent; it was responsive to the consequences of the animal's own actions. We distinguish two general categories of reafference-translocational and deformational-and use these to survey the distribution of several often-neglected forms of sensing, including gravity sensing, flow sensing and proprioception. We discuss sensing of these kinds in sponges, ctenophores, placozoans, cnidarians and bilaterians. Reafference is ubiquitous, as ongoing action, especially whole-body motility, will almost inevitably influence the senses. Corollary discharge-a pathway or circuit by which an animal tracks its own actions and their reafferent consequences-is not a necessary feature of reafferent sensing but a later-evolving mechanism. We also argue for the importance of reafferent sensing to the evolution of the body-self, a form of organization that enables an animal to sense and act as a single unit. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.
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Affiliation(s)
- Gáspár Jékely
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Peter Godfrey-Smith
- School of History and Philosophy of Science, University of Sydney, New South Wales 2006, Australia
| | - Fred Keijzer
- Department of Theoretical Philosophy, University of Groningen, Groningen, The Netherlands
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32
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Conci N, Vargas S, Wörheide G. The Biology and Evolution of Calcite and Aragonite Mineralization in Octocorallia. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.623774] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Octocorallia (class Anthozoa, phylum Cnidaria) is a group of calcifying corals displaying a wide diversity of mineral skeletons. This includes skeletal structures composed of different calcium carbonate polymorphs (aragonite and calcite). This represents a unique feature among anthozoans, as scleractinian corals (subclass Hexacorallia), main reef builders and focus of biomineralization research, are all characterized by an aragonite exoskeleton. From an evolutionary perspective, the presence of aragonitic skeletons in Octocorallia is puzzling as it is observed in very few species and has apparently originated during a Calcite sea (i.e., time interval characterized by calcite-inducing seawater conditions). Despite this, octocorals have been systematically overlooked in biomineralization studies. Here we review what is known about octocoral biomineralization, focusing on the evolutionary and biological processes that underlie calcite and aragonite formation. Although differences in research focus between octocorals and scleractinians are often mentioned, we highlight how strong variability also exists between different octocoral groups. Different main aspects of octocoral biomineralization have been in fact studied in a small set of species, including the (calcitic) gorgonian Leptogorgia virgulata and/or the precious coral Corallium rubrum. These include descriptions of calcifying cells (scleroblasts), calcium transport and chemistry of the calcification fluids. With the exception of few histological observations, no information on these features is available for aragonitic octocorals. Availability of sequencing data is also heterogeneous between groups, with no transcriptome or genome available, for instance, for the clade Calcaxonia. Although calcite represents by far the most common polymorph deposited by octocorals, we argue that studying aragonite-forming could provide insight on octocoral, and more generally anthozoan, biomineralization. First and foremost it would allow to compare calcification processes between octocoral groups, highlighting homologies and differences. Secondly, similarities (exoskeleton) between Heliopora and scleractinian skeletons, would provide further insight on which biomineralization features are driven by skeleton characteristics (shared by scleractinians and aragonitic octocorals) and those driven by taxonomy (shared by octocorals regardless of skeleton polymorph). Including the diversity of anthozoan mineralization strategies into biomineralization studies remains thus essential to comprehensively study how skeletons form and evolved within this ecologically important group of marine animals.
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33
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McFadden CS, Quattrini AM, Brugler MR, Cowman PF, Dueñas LF, Kitahara MV, Paz-García DA, Reimer JD, Rodríguez E. Phylogenomics, Origin, and Diversification of Anthozoans (Phylum Cnidaria). Syst Biol 2021; 70:635-647. [PMID: 33507310 DOI: 10.1093/sysbio/syaa103] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 01/19/2023] Open
Abstract
Anthozoan cnidarians (corals and sea anemones) include some of the world's most important foundation species, capable of building massive reef complexes that support entire ecosystems. Although previous molecular phylogenetic analyses have revealed widespread homoplasy of the morphological characters traditionally used to define orders and families of anthozoans, analyses using mitochondrial genes or rDNA have failed to resolve many key nodes in the phylogeny. With a fully resolved, time-calibrated phylogeny for 234 species constructed from hundreds of ultraconserved elements and exon loci, we explore the evolutionary origins of the major clades of Anthozoa and some of their salient morphological features. The phylogeny supports reciprocally monophyletic Hexacorallia and Octocorallia, with Ceriantharia as the earliest diverging hexacorals; two reciprocally monophyletic clades of Octocorallia; and monophyly of all hexacoral orders with the exception of the enigmatic sea anemone Relicanthus daphneae. Divergence dating analyses place Anthozoa in the Cryogenian to Tonian periods (648-894 Ma), older than has been suggested by previous studies. Ancestral state reconstructions indicate that the ancestral anthozoan was a solitary polyp that had bilateral symmetry and lacked a skeleton. Colonial growth forms and the ability to precipitate calcium carbonate evolved in the Ediacaran (578 Ma) and Cambrian (503 Ma) respectively; these hallmarks of reef-building species have subsequently arisen multiple times independently in different orders. Anthozoans formed associations with photosymbionts by the Devonian (383 Ma), and photosymbioses have been gained and lost repeatedly in all orders. Together, these results have profound implications for the interpretation of the Precambrian environment and the early evolution of metazoans.[Bilateral symmetry; coloniality; coral; early metazoans; exon capture; Hexacorallia; Octocorallia photosymbiosis; sea anemone; ultraconserved elements.].
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Affiliation(s)
- Catherine S McFadden
- Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave., Claremont, CA 91711 USA
| | - Andrea M Quattrini
- Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave., Claremont, CA 91711 USA.,Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Mercer R Brugler
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA.,Biological Sciences Department, NYC College of Technology, City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA.,Department of Natural Sciences, University of South Carolina Beaufort, 801 Carteret Street, Beaufort, SC 29902, USA
| | - Peter F Cowman
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia.,Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, Townsville, QLD 4810, Australia
| | - Luisa F Dueñas
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia-Sede Bogotá, Carrera 30 No.45-03 Edificio 421, Bogotá, D.C., Colombia
| | - Marcelo V Kitahara
- Department of Marine Science, Federal University of São Paulo, Santos, SP 11070-100 Brazil.,Centre for Marine Biology, University of São Paulo, São Sebastião, SP 11612-109 Brazil
| | - David A Paz-García
- CONACyT-Centro de Investigaciones Biológicas del Noroeste (CIBNOR). Laboratorio de Necton y Ecología de Arrecifes. Calle IPN 195, Col. Playa Palo de Santa Rita Sur, 23096 La Paz, B.C.S., México
| | - James D Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Marine Science, Chemistry, and Biology, Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan.,Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Estefanía Rodríguez
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
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34
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Leung TCN, Qu Z, Nong W, Hui JHL, Ngai SM. Proteomic Analysis of the Venom of Jellyfishes Rhopilema esculentum and Sanderia malayensis. Mar Drugs 2020; 18:md18120655. [PMID: 33371176 PMCID: PMC7766711 DOI: 10.3390/md18120655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 12/26/2022] Open
Abstract
Venomics, the study of biological venoms, could potentially provide a new source of therapeutic compounds, yet information on the venoms from marine organisms, including cnidarians (sea anemones, corals, and jellyfish), is limited. This study identified the putative toxins of two species of jellyfish—edible jellyfish Rhopilema esculentum Kishinouye, 1891, also known as flame jellyfish, and Amuska jellyfish Sanderia malayensis Goette, 1886. Utilizing nano-flow liquid chromatography tandem mass spectrometry (nLC–MS/MS), 3000 proteins were identified from the nematocysts in each of the above two jellyfish species. Forty and fifty-one putative toxins were identified in R. esculentum and S. malayensis, respectively, which were further classified into eight toxin families according to their predicted functions. Amongst the identified putative toxins, hemostasis-impairing toxins and proteases were found to be the most dominant members (>60%). The present study demonstrates the first proteomes of nematocysts from two jellyfish species with economic and environmental importance, and expands the foundation and understanding of cnidarian toxins.
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Affiliation(s)
- Thomas C. N. Leung
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China;
| | - Zhe Qu
- Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (Z.Q.); (W.N.)
| | - Wenyan Nong
- Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (Z.Q.); (W.N.)
| | - Jerome H. L. Hui
- Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (Z.Q.); (W.N.)
- Correspondence: (J.H.L.H.); (S.M.N.)
| | - Sai Ming Ngai
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China;
- Correspondence: (J.H.L.H.); (S.M.N.)
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35
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Seiblitz IGL, Capel KCC, Stolarski J, Quek ZBR, Huang D, Kitahara MV. The earliest diverging extant scleractinian corals recovered by mitochondrial genomes. Sci Rep 2020; 10:20714. [PMID: 33244171 PMCID: PMC7693180 DOI: 10.1038/s41598-020-77763-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/11/2020] [Indexed: 11/08/2022] Open
Abstract
Evolutionary reconstructions of scleractinian corals have a discrepant proportion of zooxanthellate reef-building species in relation to their azooxanthellate deep-sea counterparts. In particular, the earliest diverging "Basal" lineage remains poorly studied compared to "Robust" and "Complex" corals. The lack of data from corals other than reef-building species impairs a broader understanding of scleractinian evolution. Here, based on complete mitogenomes, the early onset of azooxanthellate corals is explored focusing on one of the most morphologically distinct families, Micrabaciidae. Sequenced on both Illumina and Sanger platforms, mitogenomes of four micrabaciids range from 19,048 to 19,542 bp and have gene content and order similar to the majority of scleractinians. Phylogenies containing all mitochondrial genes confirm the monophyly of Micrabaciidae as a sister group to the rest of Scleractinia. This topology not only corroborates the hypothesis of a solitary and azooxanthellate ancestor for the order, but also agrees with the unique skeletal microstructure previously found in the family. Moreover, the early-diverging position of micrabaciids followed by gardineriids reinforces the previously observed macromorphological similarities between micrabaciids and Corallimorpharia as well as its microstructural differences with Gardineriidae. The fact that both families share features with family Kilbuchophylliidae ultimately points towards a Middle Ordovician origin for Scleractinia.
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Affiliation(s)
- Isabela G L Seiblitz
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil.
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil.
| | - Kátia C C Capel
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
| | | | | | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Marcelo V Kitahara
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
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36
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Klompen AML, Macrander J, Reitzel AM, Stampar SN. Transcriptomic Analysis of Four Cerianthid (Cnidaria, Ceriantharia) Venoms. Mar Drugs 2020; 18:md18080413. [PMID: 32764303 PMCID: PMC7460484 DOI: 10.3390/md18080413] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/16/2020] [Accepted: 07/22/2020] [Indexed: 12/18/2022] Open
Abstract
Tube anemones, or cerianthids, are a phylogenetically informative group of cnidarians with complex life histories, including a pelagic larval stage and tube-dwelling adult stage, both known to utilize venom in stinging-cell rich tentacles. Cnidarians are an entirely venomous group that utilize their proteinaceous-dominated toxins to capture prey and defend against predators, in addition to several other ecological functions, including intraspecific interactions. At present there are no studies describing the venom for any species within cerianthids. Given their unique development, ecology, and distinct phylogenetic-placement within Cnidaria, our objective is to evaluate the venom-like gene diversity of four species of cerianthids from newly collected transcriptomic data. We identified 525 venom-like genes between all four species. The venom-gene profile for each species was dominated by enzymatic protein and peptide families, which is consistent with previous findings in other cnidarian venoms. However, we found few toxins that are typical of sea anemones and corals, and furthermore, three of the four species express toxin-like genes closely related to potent pore-forming toxins in box jellyfish. Our study is the first to provide a survey of the putative venom composition of cerianthids and contributes to our general understanding of the diversity of cnidarian toxins.
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Affiliation(s)
- Anna M. L. Klompen
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Ave., Lawrence, KS 66045, USA
- Correspondence:
| | - Jason Macrander
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28262, USA; (J.M.); (A.M.R.)
- Department of Biology, Florida Southern College, 111 Lake Hollingsworth, Drive Lakeland, FL 33801, USA
| | - Adam M. Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28262, USA; (J.M.); (A.M.R.)
| | - Sérgio N. Stampar
- Department of Biological Sciences, Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), FCL, Assis, SP 19806, Brazil;
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37
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Stampar SN, Reimer JD, Maronna MM, Lopes CSS, Ceriello H, Santos TB, Acuña FH, Morandini AC. Ceriantharia (Cnidaria) of the World: an annotated catalogue and key to species. Zookeys 2020; 952:1-63. [PMID: 32774111 PMCID: PMC7394777 DOI: 10.3897/zookeys.952.50617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/12/2020] [Indexed: 12/01/2022] Open
Abstract
The diversity of Ceriantharia is known from studies formally describing species from the late 18th Century onwards. However, no nomenclators including a list and discussion of all valid species have been produced since a list discussed by Carlgren in 1912. The present nomenclator presents a complete list of adult species of Ceriantharia of the World, including a discussion on each species. It includes the three families (Arachnactidae, Botrucnidiferidae, Cerianthidae) and the currently accepted 54 species based on their adult form. This study serves as a presentation of the “state-of-the-art” list of species of Ceriantharia, and includes a species identification key to support taxonomic identification. Additional in-depth species-by-species investigations for almost all cerianthid species is still needed, as the information available for most of these species is quite superficial.
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Affiliation(s)
- Sérgio N Stampar
- Universidade Estadual Paulista (UNESP), FCL/Assis, Laboratório de Evolução e Diversidade Aquática; LEDA, Departamento de Ciências Biológicas, Assis, Brazil.,Universidade Estadual Paulista (UNESP), Departamento de Zoologia, Instituto de Biociências, Botucatu, SP, Brazil
| | - James D Reimer
- University of The Ryukyus, Faculty of Science, Department of Biology, Chemistry, and Marine Science, MISE (Molecular Invertebrate Systematics and Ecology) Laboratory, Okinawa, Japan.,University of The Ryukyus, Tropical Biosphere Research Center, Okinawa, Japan
| | | | - Celine S S Lopes
- Universidade Estadual Paulista (UNESP), FCL/Assis, Laboratório de Evolução e Diversidade Aquática; LEDA, Departamento de Ciências Biológicas, Assis, Brazil.,Universidade Estadual Paulista (UNESP), Departamento de Zoologia, Instituto de Biociências, Botucatu, SP, Brazil
| | - Hellen Ceriello
- Universidade Estadual Paulista (UNESP), FCL/Assis, Laboratório de Evolução e Diversidade Aquática; LEDA, Departamento de Ciências Biológicas, Assis, Brazil.,Universidade Estadual Paulista (UNESP), Departamento de Zoologia, Instituto de Biociências, Botucatu, SP, Brazil
| | - Thais B Santos
- Universidade Estadual Paulista (UNESP), FCL/Assis, Laboratório de Evolução e Diversidade Aquática; LEDA, Departamento de Ciências Biológicas, Assis, Brazil.,University of The Ryukyus, Faculty of Science, Department of Biology, Chemistry, and Marine Science, MISE (Molecular Invertebrate Systematics and Ecology) Laboratory, Okinawa, Japan
| | - Fabián H Acuña
- Instituto de Investigaciones Marinas y Costeras (Iimyc) CONICET; Facultad De Ciencias Exactas y Naturales Universidad Nacional de Mar Del Plata Funes 3250. 7600 Mar Del Plata, Argentina.,Estación Científica Coiba (Coiba-Aip), Clayton, Panamá, República de Panamá
| | - André C Morandini
- Universidade de São Paulo (USP), Instituto de Biociências, São Paulo, SP, Brazil.,Universidade de São Paulo (USP), Centro de Biologia Marinha, São Sebastião, SP, Brazil
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38
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Technau U. Gastrulation and germ layer formation in the sea anemone Nematostella vectensis and other cnidarians. Mech Dev 2020; 163:103628. [PMID: 32603823 DOI: 10.1016/j.mod.2020.103628] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/23/2020] [Accepted: 06/19/2020] [Indexed: 01/03/2023]
Abstract
Among the basally branching metazoans, cnidarians display well-defined gastrulation processes leading to a diploblastic body plan, consisting of an endodermal and an ectodermal cell layer. As the outgroup to all Bilateria, cnidarians are an interesting group to investigate ancestral developmental mechanisms. Interestingly, all known gastrulation mechanisms known in Bilateria are already found in different species of Cnidaria. Here I review the morphogenetic processes found in different Cnidaria and focus on the investigation of the cellular and molecular mechanisms in the sea anemone Nematostella vectensis, which has been a major model organism among cnidarians for evolutionary developmental biology. Many of the genes involved in germ layer specification and morphogenetic processes in Bilateria are also found active during gastrulation of Nematostella and other cnidarians, suggesting an ancestral role of this process. The molecular analyses indicate a tight link between gastrulation and axis patterning processes by Wnt and FGF signaling. Interestingly, the endodermal layer displays many features of the mesodermal layer in Bilateria, while the pharyngeal ectoderm has an endodermal expression profile. Comparative analyses as well as experimental studies using embryonic aggregates suggest that minor differences in the gene regulatory networks allow the embryo to transition relatively easily from one mode of gastrulation to another.
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Affiliation(s)
- Ulrich Technau
- University of Vienna, Dept. of Neurosciences and Developmental Biology, Althanstrasse 14, 1090 Wien, Austria.
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39
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Niu W, Xiao J, Tian P, Guo F. The complete mitochondrial genome of Plesiastrea versipora (Scleractinia, Plesiastreidae) sheds light on its phylogeny and taxonomy of the family Plesiastreidae. Saudi J Biol Sci 2020; 27:1830-1834. [PMID: 32565703 PMCID: PMC7296481 DOI: 10.1016/j.sjbs.2020.04.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 11/15/2022] Open
Abstract
The genus Plesiastrea used to be a member of the traditional family Faviidae, falling into the challenging 'Bigmessidae' clade, and was re-established until recent molecular phylogenies published. The entire mitogenome of the symbiotic coral Plesiastrea versipora (Lamarck, 1816), the type species of the family Plesiastreidae, was sequenced. The length of the mitochondrial genome is 15,320 bp and it includes thirteen protein-coding genes (PCGs), two rRNAs and two tRNAs. The nucleotide composition of GC is 32%. We perform phylogenetic reconstruction based on maximum likelihood (ML) and Bayesian analysis(BI) using all PCGs. Our result indicates that P. versipora clusters closely with species which belong to Mussidae, Merulinidae and Lobophylliidae. Our phylogenetic analyses provide solid evidence for phylogenetic placement of P. versipora and the evolutionary relationships among different families within the traditional robust clade of Scleractinia. In addition, the mitogenome data provide useful information for further molecular systematic investigations on Plesiastreidae as well as conservation biology research of P. versipora.
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Affiliation(s)
| | | | - Peng Tian
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Feng Guo
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
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40
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Macias-Muñoz A, Murad R, Mortazavi A. Molecular evolution and expression of opsin genes in Hydra vulgaris. BMC Genomics 2019; 20:992. [PMID: 31847811 PMCID: PMC6918707 DOI: 10.1186/s12864-019-6349-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/28/2019] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The evolution of opsin genes is of great interest because it can provide insight into the evolution of light detection and vision. An interesting group in which to study opsins is Cnidaria because it is a basal phylum sister to Bilateria with much visual diversity within the phylum. Hydra vulgaris (H. vulgaris) is a cnidarian with a plethora of genomic resources to characterize the opsin gene family. This eyeless cnidarian has a behavioral reaction to light, but it remains unknown which of its many opsins functions in light detection. Here, we used phylogenetics and RNA-seq to investigate the molecular evolution of opsin genes and their expression in H. vulgaris. We explored where opsin genes are located relative to each other in an improved genome assembly and where they belong in a cnidarian opsin phylogenetic tree. In addition, we used RNA-seq data from different tissues of the H. vulgaris adult body and different time points during regeneration and budding stages to gain insight into their potential functions. RESULTS We identified 45 opsin genes in H. vulgaris, many of which were located near each other suggesting evolution by tandem duplications. Our phylogenetic tree of cnidarian opsin genes supported previous claims that they are evolving by lineage-specific duplications. We identified two H. vulgaris genes (HvOpA1 and HvOpB1) that fall outside of the two commonly determined Hydra groups; these genes possibly have a function in nematocytes and mucous gland cells respectively. We also found opsin genes that have similar expression patterns to phototransduction genes in H. vulgaris. We propose a H. vulgaris phototransduction cascade that has components of both ciliary and rhabdomeric cascades. CONCLUSIONS This extensive study provides an in-depth look at the molecular evolution and expression of H. vulgaris opsin genes. The expression data that we have quantified can be used as a springboard for additional studies looking into the specific function of opsin genes in this species. Our phylogeny and expression data are valuable to investigations of opsin gene evolution and cnidarian biology.
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Affiliation(s)
- Aide Macias-Muñoz
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA.
| | - Rabi Murad
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA.
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41
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Forero Mejia AC, Molodtsova T, Östman C, Bavestrello G, Rouse GW. Molecular phylogeny of Ceriantharia (Cnidaria: Anthozoa) reveals non-monophyly of traditionally accepted families. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
We present an integrative study with molecular phylogenetic reconstructions and morphological assessment across the three Ceriantharia families: Arachnactidae, Botrucnidiferidae and Cerianthidae. The Arachnactidae specimens (Isarachnanthus spp.) form a well-supported clade, whereas Cerianthidae and Botrucnidiferidae are not recovered as monophyletic. Consequently, the validity of the suborder Spirularia is questioned. Cerianthus was recovered as polyphyletic and Ceriantheomorphe may prove to be a junior synonym of Cerianthus. The taxonomic position of Cerianthus cf. mortenseni is also discussed. All specimens identified on morphology as belonging to Pachycerianthus are recovered as a clade. Further revision of taxa within Ceriantharia is necessary. Molecular phylogenetic analyses based on six mitochondrial or nuclear loci place Ceriantharia as sister to Hexacorallia s.s., but with no significant support relative to an alternative hypothesis that it is the sister taxon to Octocorallia. Further molecular sequence data and taxon sampling will be needed to resolve the position of Ceriantharia.
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Affiliation(s)
- Anny C Forero Mejia
- Università degli Studi di Genova, Dipartimento di Scienze della Terra, dell’Ambiente e della Vita (DISTAV), Genova, Italy
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Division of Biological and Environmental Sciences & Engineering, Thuwal, Saudi Arabia
| | - Tina Molodtsova
- P.P. Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow, Russia
| | - Carina Östman
- Uppsala University, Department of Organismal Biology, Uppsala, Sweden
| | - Giorgio Bavestrello
- Università degli Studi di Genova, Dipartimento di Scienze della Terra, dell’Ambiente e della Vita (DISTAV), Genova, Italy
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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42
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Xiao M, Brugler MR, Broe MB, Gusmão LC, Daly M, Rodríguez E. Mitogenomics suggests a sister relationship of Relicanthus daphneae (Cnidaria: Anthozoa: Hexacorallia: incerti ordinis) with Actiniaria. Sci Rep 2019; 9:18182. [PMID: 31796816 PMCID: PMC6890759 DOI: 10.1038/s41598-019-54637-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/07/2019] [Indexed: 11/09/2022] Open
Abstract
Relicanthus daphneae (formerly Boloceroides daphneae) was first described in 2006 as a giant sea anemone based on morphology. In 2014, its classification was challenged based on molecular data: using five genes, Relicanthus was resolved sister to zoanthideans, but with mixed support. To better understand the evolutionary relationship of Relicanthus with other early-branching metazoans, we present 15 newly-sequenced sea anemone mitochondrial genomes and a mitogenome-based phylogeny including all major cnidarian groups, sponges, and placozoans. Our phylogenetic reconstruction reveals a moderately supported sister relationship between Relicanthus and the Actiniaria. Morphologically, the cnidae of Relicanthus has apical flaps, the only existing synapomorphy for sea anemones. Based on both molecular and morphological results, we propose a third suborder (Helenmonae) within the Actiniaria to accommodate Relicanthus. Although Relicanthus shares the same gene order and content with other available actiniarian mitogenomes, it is clearly distinct at the nucleotide level from anemones within the existing suborders. The phylogenetic position of Relicanthus could reflect its association with the periphery of isolated hydrothermal vents, which, although patchy and ephemeral, harbor unique chemosynthetic communities that provide a relatively stable food source to higher trophic levels over long evolutionary timescales. The ability to colonize the deep sea and the periphery of new vent systems may be facilitated by Relicanthus’ large and extremely yolky eggs.
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Affiliation(s)
- Madelyne Xiao
- Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
| | - Mercer R Brugler
- Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.,Biological Sciences Department, NYC College of Technology (CUNY), 285 Jay Street, Brooklyn, NY, 11201, USA
| | - Michael B Broe
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 300 Aronoff Laboratory, Columbus, OH, 43210, USA
| | - Luciana C Gusmão
- Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
| | - Marymegan Daly
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 300 Aronoff Laboratory, Columbus, OH, 43210, USA.
| | - Estefanía Rodríguez
- Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
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43
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Silvestri S, Figueroa DF, Hicks D, Figueroa NJ. Mitogenomic phylogenetic analyses of Leptogorgia virgulata and Leptogorgia hebes (Anthozoa: Octocorallia) from the Gulf of Mexico provides insight on Gorgoniidae divergence between Pacific and Atlantic lineages. Ecol Evol 2019; 9:14114-14129. [PMID: 31938507 PMCID: PMC6953674 DOI: 10.1002/ece3.5847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 11/28/2022] Open
Abstract
The use of genetics in recent years has brought to light the need to reevaluate the classification of many gorgonian octocorals. This study focuses on two Leptogorgia species-Leptogorgia virgulata and Leptogorgia hebes-from the northwestern Gulf of Mexico (GOM). We target complete mitochondrial genomes and mtMutS sequences, and integrate this data with previous genetic research of gorgonian corals to resolve phylogenetic relationships and estimate divergence times. This study contributes the first complete mitochondrial genomes for L. ptogorgia virgulata and L. hebes. Our resulting phylogenies stress the need to redefine the taxonomy of the genus Leptogorgia in its entirety. The fossil-calibrated divergence times for Eastern Pacific and Western Atlantic Leptogorgia species based on complete mitochondrial genomes shows that the use of multiple genes results in estimates of more recent speciation events than previous research based on single genes. These more recent divergence times are in agreement with geologic data pertaining to the formation of the Isthmus of Panama.
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Affiliation(s)
- Samantha Silvestri
- School of Earth, Environmental, and Marine SciencesUniversity of Texas Rio Grande ValleyBrownsvilleTXUSA
| | - Diego F. Figueroa
- School of Earth, Environmental, and Marine SciencesUniversity of Texas Rio Grande ValleyBrownsvilleTXUSA
| | - David Hicks
- School of Earth, Environmental, and Marine SciencesUniversity of Texas Rio Grande ValleyBrownsvilleTXUSA
| | - Nicole J. Figueroa
- School of Earth, Environmental, and Marine SciencesUniversity of Texas Rio Grande ValleyBrownsvilleTXUSA
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Figueroa DF, Hicks D, Figueroa NJ. The complete mitochondrial genome of Tanacetipathes thamnea Warner, 1981 (Antipatharia: Myriopathidae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:4109-4110. [PMID: 33366341 PMCID: PMC7707681 DOI: 10.1080/23802359.2019.1692701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Specimens of the black coral Tanacetipathes thamnea were collected from the Northwestern Gulf of Mexico. The complete mitochondrial genome of one of these specimens was obtained from genomic DNA by next-generation sequencing technology on the Illumina HiSeq 2500. Only three species of black corals have a completely sequenced mitochondrial genome. These were used to reconstruct the phylogeny for the order Antipatharia. The mitochondrial genome of T. thamnea is 17,712 base pairs and contains 13 protein-coding genes, 2 ribosomal RNAs, and 2 transfer RNAs in the following order: 16s RNA, COX3, COX1 (with intron), ND4L, COX2, ND4, ND6, ATP8, ATP6, and ND5 (with intron and copies of ND1 and ND3), tRNA-Trp, ND2, 12s RNA, CYTB, tRNA-Met. The gene arrangement is the same as that for Myriopathes japonica with a nearly identical sequence (99.35% identical). These results show that the mitochondrial genome within the family Myriopathidae is highly conserved.
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Affiliation(s)
- Diego Francisco Figueroa
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, One West University Boulevard, Brownsville, TX, USA
| | - David Hicks
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, One West University Boulevard, Brownsville, TX, USA
| | - Nicole Jewel Figueroa
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, One West University Boulevard, Brownsville, TX, USA
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Shen CY, Dan YT, Asem A, Wang PZ, Xue W, Tong XB, Li W. The complete mitochondrial genome of soft coral Sarcophyton trocheliophorum (Cnidaria: Anthozoa) using next-generation sequencing. Mitochondrial DNA B Resour 2019; 4:3734-3735. [PMID: 33366165 PMCID: PMC7707615 DOI: 10.1080/23802359.2019.1679677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/25/2019] [Indexed: 11/30/2022] Open
Abstract
The complete mitochondrial genome of Sarcophyton trocheliophorum was completed using next-generation sequencing (NGS) method. The mitochondrial genome is a circular molecule of 18,508 bp in length, containing 14 protein-coding genes, two ribosomal RNA genes and one transfer RNA gene (Met-tRNA). The base composition is 30.45% A, 16.03% C, 19.13% G, and 34.40% T, with an A + T content of 64.85%. A phylogenetic analysis of Alcyoniidae showed that genus Sarcophyton had the closest relationship with Sinularia.
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Affiliation(s)
- Chun-Yang Shen
- Department of Biology, Chengde Medical University, Chengde, Hebei Province, China
| | - Ya-Ting Dan
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China
| | - Alireza Asem
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China
| | - Pei-Zheng Wang
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China
| | - Wei Xue
- Department of Chemical Engineering, Chengde Petroleum College, Chengde, China
| | - Xiao-Bo Tong
- Department of Physiology, Chengde Medical University, Chengde, Hebei Province, China
| | - Weidong Li
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China
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46
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Richards ZT, Carvajal JI, Wallace CC, Wilson NG. Phylotranscriptomics confirms Alveopora is sister to Montipora within the family Acroporidae. Mar Genomics 2019; 50:100703. [PMID: 31466869 DOI: 10.1016/j.margen.2019.100703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/14/2019] [Accepted: 08/16/2019] [Indexed: 01/17/2023]
Abstract
The genus Alveopora is a scleractinian coral taxon whose phylogenetic classification has recently changed from the family Poritidae to Acroporidae. This change, which was made based on single-locus genetic data, has led to uncertainty about the placement of Alveopora and the ability for deep evolutionary relationships in these groups to be accurately recovered and represented by limited genetic datasets. We sought to characterize the higher-level position of Alveopora using newly available transcriptome data to confirm its placement within Acroporidae and resolve its closest ancestor. Here we present an analysis of a new 2031 gene dataset that confirms the placement of Alveopora within Acroporidae corroborating other single-locus (COI, 16S and ITS) analyses and a mitogenome dataset. We also resolve the position of Alveopora as sister to the genus Montipora. This has allowed the re-interpretation of morphology, and a rediagnosis of the family Acroporidae and the genus Alveopora.
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Affiliation(s)
- Zoe T Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6012, Australia; Department of Aquatic Zoology, Western Australian Museum, Kew Street, Welshpool, WA, 6106, Australia.
| | - Jose I Carvajal
- Molecular Systematics Unit, Western Australian Museum, Kew Street, Welshpool, WA 6106, Australia
| | - Carden C Wallace
- Biodiversity and Geosciences Program, Queensland Museum, Brisbane, Queensland 4101, Australia
| | - Nerida G Wilson
- Molecular Systematics Unit, Western Australian Museum, Kew Street, Welshpool, WA 6106, Australia; School of Biological Sciences, University of Western Australia, Crawley, Perth, Western Australia 6009, Australia
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Hogan RI, Hopkins K, Wheeler AJ, Allcock AL, Yesson C. Novel diversity in mitochondrial genomes of deep-sea Pennatulacea (Cnidaria: Anthozoa: Octocorallia). Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:764-777. [PMID: 31317811 DOI: 10.1080/24701394.2019.1634699] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We present the first documented complete mitogenomes of deep-sea Pennatulacea, representing nine genera and eight families. These include one species each of the deep-sea genera Funiculina, Halipteris, Protoptilum and Distichoptilum, four species each of Umbellula and Pennatula, three species of Kophobelemnon and two species of Anthoptilum, as well as one species of the epi- and mesobenthic genus Virgularia. Seventeen circular genomes ranged from 18,513 bp (Halipteris cf. finmarchica) to 19,171 bp (Distichoptilum gracile) and contained all genes standard to octocoral mitochondrial genomes (14 protein-coding genes, two ribosomal RNA genes and one transfer RNA). We found at least three different gene orders in Pennatulacea: the ancestral gene order, the gene order found in bamboo corals (Family Isididae), and a novel gene order. The mitogenome of one species of Umbellula has a bipartite genome (∼13 kbp and ∼5 kbp), with good evidence that both parts are circular.
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Affiliation(s)
- Raissa I Hogan
- Department of Zoology, Ryan Institute, National University of Ireland , Galway , Ireland
| | - Kevin Hopkins
- Institute of Zoology, Zoological Society of London, Regent's Park , London , UK
| | - Andrew J Wheeler
- School of Biological, Earth and Environmental Sciences/iCRAG/ERI, University College Cork , Cork , Ireland
| | - A Louise Allcock
- Department of Zoology, Ryan Institute, National University of Ireland , Galway , Ireland
| | - Chris Yesson
- Institute of Zoology, Zoological Society of London, Regent's Park , London , UK
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48
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Ohdera A, Ames CL, Dikow RB, Kayal E, Chiodin M, Busby B, La S, Pirro S, Collins AG, Medina M, Ryan JF. Box, stalked, and upside-down? Draft genomes from diverse jellyfish (Cnidaria, Acraspeda) lineages: Alatina alata (Cubozoa), Calvadosia cruxmelitensis (Staurozoa), and Cassiopea xamachana (Scyphozoa). Gigascience 2019; 8:giz069. [PMID: 31257419 PMCID: PMC6599738 DOI: 10.1093/gigascience/giz069] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 03/27/2019] [Accepted: 05/21/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Anthozoa, Endocnidozoa, and Medusozoa are the 3 major clades of Cnidaria. Medusozoa is further divided into 4 clades, Hydrozoa, Staurozoa, Cubozoa, and Scyphozoa-the latter 3 lineages make up the clade Acraspeda. Acraspeda encompasses extraordinary diversity in terms of life history, numerous nuisance species, taxa with complex eyes rivaling other animals, and some of the most venomous organisms on the planet. Genomes have recently become available within Scyphozoa and Cubozoa, but there are currently no published genomes within Staurozoa and Cubozoa. FINDINGS Here we present 3 new draft genomes of Calvadosia cruxmelitensis (Staurozoa), Alatina alata (Cubozoa), and Cassiopea xamachana (Scyphozoa) for which we provide a preliminary orthology analysis that includes an inventory of their respective venom-related genes. Additionally, we identify synteny between POU and Hox genes that had previously been reported in a hydrozoan, suggesting this linkage is highly conserved, possibly dating back to at least the last common ancestor of Medusozoa, yet likely independent of vertebrate POU-Hox linkages. CONCLUSIONS These draft genomes provide a valuable resource for studying the evolutionary history and biology of these extraordinary animals, and for identifying genomic features underlying venom, vision, and life history traits in Acraspeda.
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Affiliation(s)
- Aki Ohdera
- Department of Biology, Pennsylvania State University, 326 Mueller, University Park, PA, 16801, USA
| | - Cheryl L Ames
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th Street & Constitution Avenue NW, Washington DC, 20560, USA
- National Center for Biotechnology Information, 8600 Rockville Pike MSC 3830, Bethesda, MD, 20894, USA
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, 10th Street & Constitution Avenue NW, Washington DC, 20560, USA
| | - Ehsan Kayal
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th Street & Constitution Avenue NW, Washington DC, 20560, USA
- UPMC, CNRS, FR2424, ABiMS, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | - Marta Chiodin
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Boulevard, St. Augustine, FL, 32080, USA
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Ben Busby
- National Center for Biotechnology Information, 8600 Rockville Pike MSC 3830, Bethesda, MD, 20894, USA
| | - Sean La
- National Center for Biotechnology Information, 8600 Rockville Pike MSC 3830, Bethesda, MD, 20894, USA
- Department of Mathematics, Simon Fraser University, 8888 University Drive, Barnaby, British Columbia, BC, V5A 1S6, Canada
| | - Stacy Pirro
- Iridian Genomes, Inc., 6213 Swords Way, Bethesda, MD, 20817, USA
| | - Allen G Collins
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th Street & Constitution Avenue NW, Washington DC, 20560, USA
- National Systematics Laboratory of NOAA's Fisheries Service, 1315 East-West Highway, Silver Spring, MD, 20910, USA
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, 326 Mueller, University Park, PA, 16801, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Boulevard, St. Augustine, FL, 32080, USA
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
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49
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Inhibitory Effects of Crude and Filtered Extracts from Oral Disk of Sea Anemone (Stichodactyla haddoni) on MCF-7 Cell Line. Jundishapur J Nat Pharm Prod 2019. [DOI: 10.5812/jjnpp.65799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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50
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Effects of missing data and data type on phylotranscriptomic analysis of stony corals (Cnidaria: Anthozoa: Scleractinia). Mol Phylogenet Evol 2019; 134:12-23. [DOI: 10.1016/j.ympev.2019.01.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 01/28/2023]
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