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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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Abstract
The POU genes represent a diverse class of animal-specific transcription factors that play important roles in neurogenesis, pluripotency, and cell-type specification. Although previous attempts have been made to reconstruct the evolution of the POU class, these studies have been limited by a small number of representative taxa, and a lack of sequences from basally branching organisms. In this study, we performed comparative analyses on available genomes and sequences recovered through "gene fishing" to better resolve the topology of the POU gene tree. We then used ancestral state reconstruction to map the most likely changes in amino acid evolution for the conserved domains. Our work suggests that four of the six POU families evolved before the last common ancestor of living animals-doubling previous estimates-and were followed by extensive clade-specific gene loss. Amino acid changes are distributed unequally across the gene tree, consistent with a neofunctionalization model of protein evolution. We consider our results in the context of early animal evolution, and the role of POU5 genes in maintaining stem cell pluripotency.
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Affiliation(s)
- David A Gold
- Department of Ecology and Evolution, University of California, Los Angeles
| | - Ruth D Gates
- Department of Ecology and Evolution, University of California, Los Angeles
| | - David K Jacobs
- Department of Ecology and Evolution, University of California, Los Angeles
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Chen CK, Chen WY, Chien CT. The POU-domain protein Pdm3 regulates axonal targeting of R neurons in the Drosophila ellipsoid body. Dev Neurobiol 2012; 72:1422-32. [PMID: 22190420 DOI: 10.1002/dneu.22003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 11/29/2011] [Accepted: 12/01/2011] [Indexed: 11/06/2022]
Abstract
The ability of axons to project correctly to the target is essential for the formation of complex neural networks. The intrinsic regulation of this process is still unclear. Here, we show that POU domain motif 3 (Pdm3) is required in ring (R) neurons to control precise axon targeting to the Drosophila ellipsoid body (EB). Pdm3 is expressed in neurons of the central nervous system in larvae and adults and required for the normal development of the EB of the central complex in the adult brain. The normal EB structure is abolished in pdm3 mutants, and this phenotype is rescued by pdm3 expression in R neurons, suggesting that the defect in axonal targeting of R neurons is the major cause in EB malformation in pdm3 mutants. We show that cell fate determination, dendritic arborization, and initial axon projection of R neurons are normal while the axonal targeting to the EB is defective in pdm3 mutants.
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Affiliation(s)
- Chien-Kuo Chen
- Institute of Neuroscience, National Yang-Ming University, Taipei, Taiwan
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Degnan BM, Vervoort M, Larroux C, Richards GS. Early evolution of metazoan transcription factors. Curr Opin Genet Dev 2009; 19:591-9. [PMID: 19880309 DOI: 10.1016/j.gde.2009.09.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2009] [Revised: 09/16/2009] [Accepted: 09/27/2009] [Indexed: 11/29/2022]
Abstract
Analyses of recently sequenced sponge, cnidarian, placozoan, and choanoflagellate genomes have revealed that most transcription factor (TF) classes and families expressed during bilaterian development originated at the dawn of the animal kingdom, before the divergence of contemporary animal lineages. The ancestral metazoan genome included members of the bHLH, Mef2, Fox, Sox, T-box, ETS, nuclear receptor, Rel/NF-kappaB, bZIP, and Smad families, and a diversity of homeobox-containing classes, including ANTP, Prd-like, Pax, POU, LIM-HD, Six, and TALE. As many of these TF classes and families appear to be metazoan specific and not present in choanoflagellates, fungi and more distant eukaryotes, their genesis and expansion may have contributed to the evolution of animal multicellularity.
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Affiliation(s)
- Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia.
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6
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Schierwater B, Kamm K, Srivastava M, Rokhsar D, Rosengarten RD, Dellaporta SL. The early ANTP gene repertoire: insights from the placozoan genome. PLoS One 2008; 3:e2457. [PMID: 18716659 PMCID: PMC2515636 DOI: 10.1371/journal.pone.0002457] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Accepted: 04/29/2008] [Indexed: 11/18/2022] Open
Abstract
The evolution of ANTP genes in the Metazoa has been the subject of conflicting hypotheses derived from full or partial gene sequences and genomic organization in higher animals. Whole genome sequences have recently filled in some crucial gaps for the basal metazoan phyla Cnidaria and Porifera. Here we analyze the complete genome of Trichoplax adhaerens, representing the basal metazoan phylum Placozoa, for its set of ANTP class genes. The Trichoplax genome encodes representatives of Hox/ParaHox-like, NKL, and extended Hox genes. This repertoire possibly mirrors the condition of a hypothetical cnidarian-bilaterian ancestor. The evolution of the cnidarian and bilaterian ANTP gene repertoires can be deduced by a limited number of cis-duplications of NKL and “extended Hox” genes and the presence of a single ancestral “ProtoHox” gene.
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Affiliation(s)
- Bernd Schierwater
- Division of Ecology and Evolution, Stiftung Tieraerztliche Hochschule Hannover, Hannover, Germany
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Kai Kamm
- Division of Ecology and Evolution, Stiftung Tieraerztliche Hochschule Hannover, Hannover, Germany
- * E-mail:
| | - Mansi Srivastava
- Center for Integrative Genomics and Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Daniel Rokhsar
- Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
- Center for Integrative Genomics and Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Rafael D. Rosengarten
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Stephen L. Dellaporta
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
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