1
|
Sabin KZ, Chen S, Hill EM, Weaver KJ, Yonke J, Kirkman M, Redwine WB, Klompen AML, Zhao X, Guo F, McKinney MC, Dewey JL, Gibson MC. Graded FGF activity patterns distinct cell types within the apical sensory organ of the sea anemone Nematostella vectensis. Dev Biol 2024; 510:50-65. [PMID: 38521499 DOI: 10.1016/j.ydbio.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/25/2024]
Abstract
Bilaterian animals have evolved complex sensory organs comprised of distinct cell types that function coordinately to sense the environment. Each sensory unit has a defined architecture built from component cell types, including sensory cells, non-sensory support cells, and dedicated sensory neurons. Whether this characteristic cellular composition is present in the sensory organs of non-bilaterian animals is unknown. Here, we interrogate the cell type composition and gene regulatory networks controlling development of the larval apical sensory organ in the sea anemone Nematostella vectensis. Using single cell RNA sequencing and imaging approaches, we reveal two unique cell types in the Nematostella apical sensory organ, GABAergic sensory cells and a putative non-sensory support cell population. Further, we identify the paired-like (PRD) homeodomain gene prd146 as a specific sensory cell marker and show that Prd146+ sensory cells become post-mitotic after gastrulation. Genetic loss of function approaches show that Prd146 is essential for apical sensory organ development. Using a candidate gene knockdown approach, we place prd146 downstream of FGF signaling in the apical sensory organ gene regulatory network. Further, we demonstrate that an aboral FGF activity gradient coordinately regulates the specification of both sensory and support cells. Collectively, these experiments define the genetic basis for apical sensory organ development in a non-bilaterian animal and reveal an unanticipated degree of complexity in a prototypic sensory structure.
Collapse
Affiliation(s)
- Keith Z Sabin
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Shiyuan Chen
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Eric M Hill
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Kyle J Weaver
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Jacob Yonke
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | | | | | - Xia Zhao
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Fengli Guo
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | | | - Matthew C Gibson
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA.
| |
Collapse
|
2
|
Knabl P, Schauer A, Pomreinke AP, Zimmermann B, Rogers KW, Čapek D, Müller P, Genikhovich G. Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. eLife 2024; 13:e80803. [PMID: 38323609 PMCID: PMC10849676 DOI: 10.7554/elife.80803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 01/28/2024] [Indexed: 02/08/2024] Open
Abstract
BMP signaling has a conserved function in patterning the dorsal-ventral body axis in Bilateria and the directive axis in anthozoan cnidarians. So far, cnidarian studies have focused on the role of different BMP signaling network components in regulating pSMAD1/5 gradient formation. Much less is known about the target genes downstream of BMP signaling. To address this, we generated a genome-wide list of direct pSMAD1/5 target genes in the anthozoan Nematostella vectensis, several of which were conserved in Drosophila and Xenopus. Our ChIP-seq analysis revealed that many of the regulatory molecules with documented bilaterally symmetric expression in Nematostella are directly controlled by BMP signaling. We identified several so far uncharacterized BMP-dependent transcription factors and signaling molecules, whose bilaterally symmetric expression may be indicative of their involvement in secondary axis patterning. One of these molecules is zswim4-6, which encodes a novel nuclear protein that can modulate the pSMAD1/5 gradient and potentially promote BMP-dependent gene repression.
Collapse
Affiliation(s)
- Paul Knabl
- Department of Neurosciences and Developmental Biology, University of ViennaViennaAustria
- Vienna Doctoral School of Ecology and Evolution (VDSEE), University of ViennaViennaAustria
| | - Alexandra Schauer
- Department of Neurosciences and Developmental Biology, University of ViennaViennaAustria
| | | | - Bob Zimmermann
- Department of Neurosciences and Developmental Biology, University of ViennaViennaAustria
| | | | | | - Patrick Müller
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
- University of KonstanzKonstanzGermany
| | - Grigory Genikhovich
- Department of Neurosciences and Developmental Biology, University of ViennaViennaAustria
| |
Collapse
|
3
|
Zimmermann B, Montenegro JD, Robb SMC, Fropf WJ, Weilguny L, He S, Chen S, Lovegrove-Walsh J, Hill EM, Chen CY, Ragkousi K, Praher D, Fredman D, Schultz D, Moran Y, Simakov O, Genikhovich G, Gibson MC, Technau U. Topological structures and syntenic conservation in sea anemone genomes. Nat Commun 2023; 14:8270. [PMID: 38092765 PMCID: PMC10719294 DOI: 10.1038/s41467-023-44080-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
There is currently little information about the evolution of gene clusters, genome architectures and karyotypes in early branching animals. Slowly evolving anthozoan cnidarians can be particularly informative about the evolution of these genome features. Here we report chromosome-level genome assemblies of two related anthozoans, the sea anemones Nematostella vectensis and Scolanthus callimorphus. We find a robust set of 15 chromosomes with a clear one-to-one correspondence between the two species. Both genomes show chromosomal conservation, allowing us to reconstruct ancestral cnidarian and metazoan chromosomal blocks, consisting of at least 19 and 16 ancestral linkage groups, respectively. We show that, in contrast to Bilateria, the Hox and NK clusters of investigated cnidarians are largely disintegrated, despite the presence of staggered hox/gbx expression in Nematostella. This loss of microsynteny conservation may be facilitated by shorter distances between cis-regulatory sequences and their cognate transcriptional start sites. We find no clear evidence for topologically associated domains, suggesting fundamental differences in long-range gene regulation compared to vertebrates. These data suggest that large sets of ancestral metazoan genes have been retained in ancestral linkage groups of some extant lineages; yet, higher order gene regulation with associated 3D architecture may have evolved only after the cnidarian-bilaterian split.
Collapse
Affiliation(s)
- Bob Zimmermann
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Research platform SinCeReSt, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Juan D Montenegro
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Research platform SinCeReSt, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Sofia M C Robb
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Whitney J Fropf
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Lukas Weilguny
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Shuonan He
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Shiyuan Chen
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Jessica Lovegrove-Walsh
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Eric M Hill
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Cheng-Yi Chen
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Katerina Ragkousi
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
- Department of Biology, Amherst College, Amherst, MA, 01002, USA
| | - Daniela Praher
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - David Fredman
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Darrin Schultz
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Yehu Moran
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Oleg Simakov
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Research platform SinCeReSt, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Grigory Genikhovich
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Matthew C Gibson
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.
| | - Ulrich Technau
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Research platform SinCeReSt, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Max Perutz laboratories, University of Vienna, Dr. Bohrgasse 5, 1030, Vienna, Austria.
| |
Collapse
|
4
|
Schnitzler CE, Chang ES, Waletich J, Quiroga-Artigas G, Wong WY, Nguyen AD, Barreira SN, Doonan L, Gonzalez P, Koren S, Gahan JM, Sanders SM, Bradshaw B, DuBuc TQ, Febrimarsa, de Jong D, Nawrocki EP, Larson A, Klasfeld S, Gornik SG, Moreland RT, Wolfsberg TG, Phillippy AM, Mullikin JC, Simakov O, Cartwright P, Nicotra M, Frank U, Baxevanis AD. The genome of the colonial hydroid Hydractinia reveals their stem cells utilize a toolkit of evolutionarily shared genes with all animals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554815. [PMID: 37786714 PMCID: PMC10541594 DOI: 10.1101/2023.08.25.554815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Hydractinia is a colonial marine hydroid that exhibits remarkable biological properties, including the capacity to regenerate its entire body throughout its lifetime, a process made possible by its adult migratory stem cells, known as i-cells. Here, we provide an in-depth characterization of the genomic structure and gene content of two Hydractinia species, H. symbiolongicarpus and H. echinata, placing them in a comparative evolutionary framework with other cnidarian genomes. We also generated and annotated a single-cell transcriptomic atlas for adult male H. symbiolongicarpus and identified cell type markers for all major cell types, including key i-cell markers. Orthology analyses based on the markers revealed that Hydractinia's i-cells are highly enriched in genes that are widely shared amongst animals, a striking finding given that Hydractinia has a higher proportion of phylum-specific genes than any of the other 41 animals in our orthology analysis. These results indicate that Hydractinia's stem cells and early progenitor cells may use a toolkit shared with all animals, making it a promising model organism for future exploration of stem cell biology and regenerative medicine. The genomic and transcriptomic resources for Hydractinia presented here will enable further studies of their regenerative capacity, colonial morphology, and ability to distinguish self from non-self.
Collapse
Affiliation(s)
- Christine E Schnitzler
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - E Sally Chang
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Justin Waletich
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Gonzalo Quiroga-Artigas
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier CEDEX 05, France
| | - Wai Yee Wong
- Department of Molecular Evolution and Development, Faculty of Life Science, University of Vienna, A-1090 Vienna, Austria
| | - Anh-Dao Nguyen
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sofia N Barreira
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Liam Doonan
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Paul Gonzalez
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sergey Koren
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James M Gahan
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Steven M Sanders
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Brian Bradshaw
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Timothy Q DuBuc
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
- Swarthmore College, Swarthmore, PA 19081, USA
| | - Febrimarsa
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Danielle de Jong
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Eric P Nawrocki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra Larson
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Samantha Klasfeld
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sebastian G Gornik
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
- Centre for Organismal Studies, University of Heidelberg, Germany
| | - R Travis Moreland
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tyra G Wolfsberg
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam M Phillippy
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James C Mullikin
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- NIH Intramural Sequencing Center, Rockville, MD 20852, USA
| | - Oleg Simakov
- Department of Molecular Evolution and Development, Faculty of Life Science, University of Vienna, A-1090 Vienna, Austria
| | - Paulyn Cartwright
- Department of Evolution and Ecology, University of Kansas, Lawrence, KS 66045, USA
| | - Matthew Nicotra
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Uri Frank
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Andreas D Baxevanis
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
5
|
He S, Shao W, Chen SC, Wang T, Gibson MC. Spatial transcriptomics reveals a cnidarian segment polarity program in Nematostella vectensis. Curr Biol 2023:S0960-9822(23)00676-0. [PMID: 37315559 DOI: 10.1016/j.cub.2023.05.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/16/2023] [Accepted: 05/18/2023] [Indexed: 06/16/2023]
Abstract
During early animal evolution, the emergence of axially polarized segments was central to the diversification of complex bilaterian body plans. Nevertheless, precisely how and when segment polarity pathways arose remains obscure. Here, we demonstrate the molecular basis for segment polarization in developing larvae of the sea anemone Nematostella vectensis. Utilizing spatial transcriptomics, we first constructed a 3D gene expression atlas of developing larval segments. Capitalizing on accurate in silico predictions, we identified Lbx and Uncx, conserved homeodomain-containing genes that occupy opposing subsegmental domains under the control of both bone morphogenetic protein (BMP) signaling and the Hox-Gbx cascade. Functionally, Lbx mutagenesis eliminated all molecular evidence of segment polarization at the larval stage and caused an aberrant mirror-symmetric pattern of retractor muscles (RMs) in primary polyps. These results demonstrate the molecular basis for segment polarity in a non-bilaterian animal, suggesting that polarized metameric structures were present in the Cnidaria-Bilateria common ancestor over 600 million years ago.
Collapse
Affiliation(s)
- Shuonan He
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Wanqing Shao
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Matthew C Gibson
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Anatomy and Cell Biology, The University of Kansas School of Medicine, Kansas City, KS 66160, USA.
| |
Collapse
|
6
|
He S, Shao W, Chen S(C, Wang T, Gibson MC. Spatial transcriptomics reveals a conserved segment polarity program that governs muscle patterning in Nematostella vectensis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523347. [PMID: 36711919 PMCID: PMC9882047 DOI: 10.1101/2023.01.09.523347] [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: 01/12/2023]
Abstract
During early animal evolution, the emergence of axially-polarized segments was central to the diversification of complex bilaterian body plans. Nevertheless, precisely how and when segment polarity pathways arose remains obscure. Here we demonstrate the molecular basis for segment polarization in developing larvae of the pre-bilaterian sea anemone Nematostella vectensis . Utilizing spatial transcriptomics, we first constructed a 3-D gene expression atlas of developing larval segments. Capitalizing on accurate in silico predictions, we identified Lbx and Uncx, conserved homeodomain-containing genes that occupy opposing subsegmental domains under the control of both BMP signaling and the Hox-Gbx cascade. Functionally, Lbx mutagenesis eliminated all molecular evidence of segment polarization at larval stage and caused an aberrant mirror-symmetric pattern of retractor muscles in primary polyps. These results demonstrate the molecular basis for segment polarity in a pre-bilaterian animal, suggesting that polarized metameric structures were present in the Cnidaria-Bilateria common ancestor over 600 million years ago. Highlights Nematostella endomesodermal tissue forms metameric segments and displays a transcriptomic profile similar to that observed in bilaterian mesoderm Construction of a comprehensive 3-D gene expression atlas enables systematic dissection of segmental identity in endomesoderm Lbx and Uncx , two conserved homeobox-containing genes, establish segment polarity in Nematostella The Cnidarian-Bilaterian common ancestor likely possessed the genetic toolkit to generate polarized metameric structures.
Collapse
Affiliation(s)
- Shuonan He
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA,Current Address: Howard Hughes Medical Institute, Department of Organismic & Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA
| | - Wanqing Shao
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA,Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA,Current Address: Research Computing, Boston Children’s Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
| | | | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA,Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Matthew C. Gibson
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA,Department of Anatomy and Cell Biology, The University of Kansas School of Medicine, Kansas City, Kansas 66160, USA,Correspodence:
| |
Collapse
|
7
|
Abstract
Hox genes encode evolutionarily conserved transcription factors that are essential for the proper development of bilaterian organisms. Hox genes are unique because they are spatially and temporally regulated during development in a manner that is dictated by their tightly linked genomic organization. Although their genetic function during embryonic development has been interrogated, less is known about how these transcription factors regulate downstream genes to direct morphogenetic events. Moreover, the continued expression and function of Hox genes at postnatal and adult stages highlights crucial roles for these genes throughout the life of an organism. Here, we provide an overview of Hox genes, highlighting their evolutionary history, their unique genomic organization and how this impacts the regulation of their expression, what is known about their protein structure, and their deployment in development and beyond.
Collapse
Affiliation(s)
- Katharine A. Hubert
- Program in Genetics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Deneen M. Wellik
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| |
Collapse
|
8
|
Steinworth BM, Martindale MQ, Ryan JF. Gene Loss may have Shaped the Cnidarian and Bilaterian Hox and ParaHox Complement. Genome Biol Evol 2022; 15:6889381. [PMID: 36508343 PMCID: PMC9825252 DOI: 10.1093/gbe/evac172] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 11/21/2022] [Accepted: 11/25/2022] [Indexed: 12/14/2022] Open
Abstract
Hox and ParaHox transcription factors are important for specifying cell fates along the primary body axes during the development of most animals. Within Cnidaria, much of the research on Hox/ParaHox genes has focused on Anthozoa (anemones and corals) and Hydrozoa (hydroids) and has concentrated on the evolution and function of cnidarian Hox genes in relation to their bilaterian counterparts. Here we analyze together the full complement of Hox and ParaHox genes from species representing all four medusozoan classes (Staurozoa, Cubozoa, Hydrozoa, and Scyphozoa) and both anthozoan classes (Octocorallia and Hexacorallia). Our results show that Hox genes involved in patterning the directive axes of anthozoan polyps are absent in the stem leading to Medusozoa. For the first time, we show spatial and temporal expression patterns of Hox and ParaHox genes in the upside-down jellyfish Cassiopea xamachana (Scyphozoa), which are consistent with diversification of medusozoan Hox genes both from anthozoans and within medusozoa. Despite unprecedented taxon sampling, our phylogenetic analyses, like previous studies, are characterized by a lack of clear homology between most cnidarian and bilaterian Hox and Hox-related genes. Unlike previous studies, we propose the hypothesis that the cnidarian-bilaterian ancestor possessed a remarkably large Hox complement and that extensive loss of Hox genes was experienced by both cnidarian and bilaterian lineages.
Collapse
Affiliation(s)
- Bailey M Steinworth
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, Florida 32080,Department of Biology, University of Florida, Gainesville, Florida 32611
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, Florida 32080,Department of Biology, University of Florida, Gainesville, Florida 32611
| | | |
Collapse
|
9
|
Shum CW, Nong W, So WL, Li Y, Qu Z, Yip HY, Swale T, Ang PO, Chan KM, Chan TF, Chu KH, Chui AP, Lau KF, Ngai SM, Xu F, Hui JH. Genome of the sea anemone Exaiptasia pallida and transcriptome profiles during tentacle regeneration. Front Cell Dev Biol 2022; 10:900321. [PMID: 36072338 PMCID: PMC9444052 DOI: 10.3389/fcell.2022.900321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/08/2022] [Indexed: 12/19/2022] Open
Abstract
Cnidarians including sea anemones, corals, hydra, and jellyfishes are a group of animals well known for their regeneration capacity. However, how non-coding RNAs such as microRNAs (also known as miRNAs) contribute to cnidarian tissue regeneration is poorly understood. Here, we sequenced and assembled the genome of the sea anemone Exaiptasia pallida collected in Hong Kong waters. The assembled genome size of E. pallida is 229.21 Mb with a scaffold N50 of 10.58 Mb and BUSCO completeness of 91.1%, representing a significantly improved genome assembly of this species. The organization of ANTP-class homeobox genes in this anthozoan further supported the previous findings in jellyfishes, where most of these genes are mainly located on three scaffolds. Tentacles of E. pallida were excised, and both mRNA and miRNA were sequenced at 9 time points (0 h, 6 h, 12 h, 18 h, 1 day, 2, 3, 6, and 8 days) from regenerating tentacles. In addition to the Wnt signaling pathway and homeobox genes that are shown to be likely involved in tissue regeneration as in other cnidarians, we have shown that GLWamide neuropeptides, and for the first time sesquiterpenoid pathway genes could potentially be involved in the late phase of cnidarian tissue regeneration. The established sea anemone model will be useful for further investigation of biology and evolution in, and the effect of climate change on this important group of animals.
Collapse
Affiliation(s)
- Cheryl W.Y. Shum
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai Lok So
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yiqian Li
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhe Qu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ho Yin Yip
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Thomas Swale
- Dovetail Genomics, Scotts Valley, CA, United States
| | - Put O. Ang
- Institute of Space and Earth Information Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - King Ming Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ting Fung Chan
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka Hou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Apple P.Y. Chui
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kwok Fai Lau
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Sai Ming Ngai
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Fei Xu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jerome H.L. Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- *Correspondence: Jerome H.L. Hui,
| |
Collapse
|
10
|
Holstein TW. The role of cnidarian developmental biology in unraveling axis formation and Wnt signaling. Dev Biol 2022; 487:74-98. [DOI: 10.1016/j.ydbio.2022.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 12/12/2022]
|
11
|
Nong W, Yu Y, Aase-Remedios ME, Xie Y, So WL, Li Y, Wong CF, Baril T, Law STS, Lai SY, Haimovitz J, Swale T, Chen SS, Kai ZP, Sun X, Wu Z, Hayward A, Ferrier DEK, Hui JHL. Genome of the ramshorn snail Biomphalaria straminea-an obligate intermediate host of schistosomiasis. Gigascience 2022; 11:6528774. [PMID: 35166339 PMCID: PMC8848322 DOI: 10.1093/gigascience/giac012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/02/2022] [Accepted: 01/25/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Schistosomiasis, or bilharzia, is a parasitic disease caused by trematode flatworms of the genus Schistosoma. Infection by Schistosoma mansoni in humans results when cercariae emerge into water from freshwater snails in the genus Biomphalaria and seek out and penetrate human skin. The snail Biomphalaria straminea is native to South America and is now also present in Central America and China, and represents a potential vector host for spreading schistosomiasis. To date, genomic information for the genus is restricted to the neotropical species Biomphalaria glabrata. This limits understanding of the biology and management of other schistosomiasis vectors, such as B. straminea. FINDINGS Using a combination of Illumina short-read, 10X Genomics linked-read, and Hi-C sequencing data, our 1.005 Gb B. straminea genome assembly is of high contiguity, with a scaffold N50 of 25.3 Mb. Transcriptomes from adults were also obtained. Developmental homeobox genes, hormonal genes, and stress-response genes were identified, and repeat content was annotated (40.68% of genomic content). Comparisons with other mollusc genomes (including Gastropoda, Bivalvia, and Cephalopoda) revealed syntenic conservation, patterns of homeobox gene linkage indicative of evolutionary changes to gene clusters, expansion of heat shock protein genes, and the presence of sesquiterpenoid and cholesterol metabolic pathway genes in Gastropoda. In addition, hormone treatment together with RT-qPCR assay reveal a sesquiterpenoid hormone responsive system in B. straminea, illustrating that this renowned insect hormonal system is also present in the lophotrochozoan lineage. CONCLUSION This study provides the first genome assembly for the snail B. straminea and offers an unprecedented opportunity to address a variety of phenomena related to snail vectors of schistosomiasis, as well as evolutionary and genomics questions related to molluscs more widely.
Collapse
Affiliation(s)
- Wenyan Nong
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yifei Yu
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Madeleine E Aase-Remedios
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St. Andrews, St. Andrews, UK
| | - Yichun Xie
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai Lok So
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yiqian Li
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Cheuk Fung Wong
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Sean T S Law
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Sheung Yee Lai
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | | | | | - Shan-Shan Chen
- Institute of Agro-food Standard and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Zhen-Peng Kai
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Xi Sun
- Sun Yat-sen University, Guangdong, China
| | | | | | - David E K Ferrier
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St. Andrews, St. Andrews, UK
| | - Jerome H L Hui
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| |
Collapse
|
12
|
Nematostella vectensis, an Emerging Model for Deciphering the Molecular and Cellular Mechanisms Underlying Whole-Body Regeneration. Cells 2021; 10:cells10102692. [PMID: 34685672 PMCID: PMC8534814 DOI: 10.3390/cells10102692] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/18/2022] Open
Abstract
The capacity to regenerate lost or injured body parts is a widespread feature within metazoans and has intrigued scientists for centuries. One of the most extreme types of regeneration is the so-called whole body regenerative capacity, which enables regeneration of fully functional organisms from isolated body parts. While not exclusive to this habitat, whole body regeneration is widespread in aquatic/marine invertebrates. Over the past decade, new whole-body research models have emerged that complement the historical models Hydra and planarians. Among these, the sea anemone Nematostella vectensis has attracted increasing interest in regard to deciphering the cellular and molecular mechanisms underlying the whole-body regeneration process. This manuscript will present an overview of the biological features of this anthozoan cnidarian as well as the available tools and resources that have been developed by the scientific community studying Nematostella. I will further review our current understanding of the cellular and molecular mechanisms underlying whole-body regeneration in this marine organism, with emphasis on how comparing embryonic development and regeneration in the same organism provides insight into regeneration specific elements.
Collapse
|
13
|
Hajirnis N, Mishra RK. Homeotic Genes: Clustering, Modularity, and Diversity. Front Cell Dev Biol 2021; 9:718308. [PMID: 34458272 PMCID: PMC8386295 DOI: 10.3389/fcell.2021.718308] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
Hox genes code for transcription factors and are evolutionarily conserved. They regulate a plethora of downstream targets to define the anterior-posterior (AP) body axis of a developing bilaterian embryo. Early work suggested a possible role of clustering and ordering of Hox to regulate their expression in a spatially restricted manner along the AP axis. However, the recent availability of many genome assemblies for different organisms uncovered several examples that defy this constraint. With recent advancements in genomics, the current review discusses the arrangement of Hox in various organisms. Further, we revisit their discovery and regulation in Drosophila melanogaster. We also review their regulation in different arthropods and vertebrates, with a significant focus on Hox expression in the crustacean Parahyale hawaiensis. It is noteworthy that subtle changes in the levels of Hox gene expression can contribute to the development of novel features in an organism. We, therefore, delve into the distinct regulation of these genes during primary axis formation, segment identity, and extra-embryonic roles such as in the formation of hair follicles or misregulation leading to cancer. Toward the end of each section, we emphasize the possibilities of several experiments involving various organisms, owing to the advancements in the field of genomics and CRISPR-based genome engineering. Overall, we present a holistic view of the functioning of Hox in the animal world.
Collapse
Affiliation(s)
- Nikhil Hajirnis
- CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Rakesh K. Mishra
- CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
- AcSIR – Academy of Scientific and Innovative Research, Ghaziabad, India
- Tata Institute for Genetics and Society (TIGS), Bangalore, India
| |
Collapse
|
14
|
Abstract
The Ediacara Biota preserves the oldest fossil evidence of abundant, complex metazoans. Despite their significance, assigning individual taxa to specific phylogenetic groups has proved problematic. To better understand these forms, we identify developmentally controlled characters in representative taxa from the Ediacaran White Sea assemblage and compare them with the regulatory tools underlying similar traits in modern organisms. This analysis demonstrates that the genetic pathways for multicellularity, axial polarity, musculature, and a nervous system were likely present in some of these early animals. Equally meaningful is the absence of evidence for major differentiation of macroscopic body units, including distinct organs, localized sensory machinery or appendages. Together these traits help to better constrain the phylogenetic position of several key Ediacara taxa and inform our views of early metazoan evolution. An apparent lack of heads with concentrated sensory machinery or ventral nerve cords in such taxa supports the hypothesis that these evolved independently in disparate bilaterian clades.
Collapse
Affiliation(s)
- Scott D Evans
- Department of Paleobiology MRC-121, National Museum of Natural History, Washington, DC 20013-7012, USA
| | - Mary L Droser
- Department of Earth and Planetary Sciences, University of California, Riverside, CA 92521, USA
| | - Douglas H Erwin
- Department of Paleobiology MRC-121, National Museum of Natural History, Washington, DC 20013-7012, USA
| |
Collapse
|
15
|
Johnson AB, Lambert JD. The Caudal ParaHox gene is required for hindgut development in the mollusc Tritia (a.k.a. Ilyanassa). Dev Biol 2020; 470:1-9. [PMID: 33191200 DOI: 10.1016/j.ydbio.2020.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 11/26/2022]
Abstract
Caudal homeobox genes are found across animals, typically linked to two other homeobox genes in what has been called the ParaHox cluster. These genes have been proposed to pattern the anterior-posterior axis of the endoderm ancestrally, but the expression of Caudal in extant groups is varied and often occurs in other germ layers. Here we examine the role of Caudal in the embryo of the mollusc Tritia (Ilyanassa) obsoleta. ToCaudal expression is initially broad, then becomes progressively restricted and is finally only in the developing hindgut (a.k.a. intestine). Knockdown of ToCaudal using morpholino oligonucleotides specifically blocks hindgut development, indicating that despite its initially broad expression, the functional role of ToCaudal is in hindgut patterning. This is the first functional characterization of Caudal in an animal with spiralian development, which is an ancient mode of embryogenesis that arose early in bilaterian animal evolution. These results are consistent with the hypothesis that the ancestral role of the ParaHox genes was anterior-posterior patterning of the endoderm.
Collapse
Affiliation(s)
- Adam B Johnson
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - J David Lambert
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA.
| |
Collapse
|
16
|
Hamada M, Satoh N, Khalturin K. A Reference Genome from the Symbiotic Hydrozoan, Hydra viridissima. G3 (BETHESDA, MD.) 2020; 10:3883-3895. [PMID: 32900905 PMCID: PMC7642931 DOI: 10.1534/g3.120.401411] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/03/2020] [Indexed: 11/18/2022]
Abstract
Various Hydra species have been employed as model organisms since the 18th century. Introduction of transgenic and knock-down technologies made them ideal experimental systems for studying cellular and molecular mechanisms involved in regeneration, body-axis formation, senescence, symbiosis, and holobiosis. In order to provide an important reference for genetic studies, the Hydra magnipapillata genome (species name has been changed to H. vulgaris) was sequenced a decade ago (Chapman et al., 2010) and the updated genome assembly, Hydra 2.0, was made available by the National Human Genome Research Institute in 2017. While H. vulgaris belongs to the non-symbiotic brown hydra lineage, the green hydra, Hydra viridissima, harbors algal symbionts and belongs to an early diverging clade that separated from the common ancestor of brown and green hydra lineages at least 100 million years ago (Schwentner and Bosch 2015; Khalturin et al., 2019). While interspecific interactions between H. viridissima and endosymbiotic unicellular green algae of the genus Chlorella have been a subject of interest for decades, genomic information about green hydras was nonexistent. Here we report a draft 280-Mbp genome assembly for Hydra viridissima strain A99, with a scaffold N50 of 1.1 Mbp. The H. viridissima genome contains an estimated 21,476 protein-coding genes. Comparative analysis of Pfam domains and orthologous proteins highlights characteristic features of H. viridissima, such as diversification of innate immunity genes that are important for host-symbiont interactions. Thus, the H. viridissima assembly provides an important hydrozoan genome reference that will facilitate symbiosis research and better comparisons of metazoan genome architectures.
Collapse
Affiliation(s)
- Mayuko Hamada
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
- Ushimado Marine Institute, Okayama University, Setouchi, Okayama 701-4303, Japan
- Zoological Institute, Kiel University, Kiel 24118, Germany
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Konstantin Khalturin
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| |
Collapse
|
17
|
Heger P, Zheng W, Rottmann A, Panfilio KA, Wiehe T. The genetic factors of bilaterian evolution. eLife 2020; 9:e45530. [PMID: 32672535 PMCID: PMC7535936 DOI: 10.7554/elife.45530] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
The Cambrian explosion was a unique animal radiation ~540 million years ago that produced the full range of body plans across bilaterians. The genetic mechanisms underlying these events are unknown, leaving a fundamental question in evolutionary biology unanswered. Using large-scale comparative genomics and advanced orthology evaluation techniques, we identified 157 bilaterian-specific genes. They include the entire Nodal pathway, a key regulator of mesoderm development and left-right axis specification; components for nervous system development, including a suite of G-protein-coupled receptors that control physiology and behaviour, the Robo-Slit midline repulsion system, and the neurotrophin signalling system; a high number of zinc finger transcription factors; and novel factors that previously escaped attention. Contradicting the current view, our study reveals that genes with bilaterian origin are robustly associated with key features in extant bilaterians, suggesting a causal relationship.
Collapse
Affiliation(s)
- Peter Heger
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Wen Zheng
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Anna Rottmann
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Kristen A Panfilio
- Institute for Zoology: Developmental Biology, Cologne Biocenter, University of CologneCologneGermany
- School of Life Sciences, University of Warwick, Gibbet Hill CampusCoventryUnited Kingdom
| | - Thomas Wiehe
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| |
Collapse
|
18
|
Arenas Gómez CM, Sabin KZ, Echeverri K. Wound healing across the animal kingdom: Crosstalk between the immune system and the extracellular matrix. Dev Dyn 2020; 249:834-846. [PMID: 32314465 PMCID: PMC7383677 DOI: 10.1002/dvdy.178] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/10/2020] [Accepted: 04/11/2020] [Indexed: 12/11/2022] Open
Abstract
Tissue regeneration is widespread in the animal kingdom. To date, key roles for different molecular and cellular programs in regeneration have been described, but the ultimate blueprint for this talent remains elusive. In animals capable of tissue regeneration, one of the most crucial stages is wound healing, whose main goal is to close the wound and prevent infection. In this stage, it is necessary to avoid scar formation to facilitate the activation of the immune system and remodeling of the extracellular matrix, key factors in promoting tissue regeneration. In this review, we will discuss the current state of knowledge regarding the role of the immune system and the interplay with the extracellular matrix to trigger a regenerative response.
Collapse
Affiliation(s)
- Claudia M. Arenas Gómez
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological LaboratoryWoods HoleMassachusettsUSA
| | - Keith Z. Sabin
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological LaboratoryWoods HoleMassachusettsUSA
| | - Karen Echeverri
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological LaboratoryWoods HoleMassachusettsUSA
| |
Collapse
|
19
|
Cdx2 Animal Models Reveal Developmental Origins of Cancers. Genes (Basel) 2019; 10:genes10110928. [PMID: 31739541 PMCID: PMC6895827 DOI: 10.3390/genes10110928] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/06/2019] [Accepted: 11/13/2019] [Indexed: 12/12/2022] Open
Abstract
The Cdx2 homeobox gene is important in assigning positional identity during the finely orchestrated process of embryogenesis. In adults, regenerative responses to tissues damage can require a replay of these same developmental pathways. Errors in reassigning positional identity during regeneration can cause metaplasias-normal tissue arising in an abnormal location-and this in turn, is a well-recognized cancer risk factor. In animal models, a gain of Cdx2 function can elicit a posterior shift in tissue identity, modeling intestinal-type metaplasias of the esophagus (Barrett's esophagus) and stomach. Conversely, loss of Cdx2 function can elicit an anterior shift in tissue identity, inducing serrated-type lesions expressing gastric markers in the colon. These metaplasias are major risk factors for the later development of esophageal, stomach and colon cancer. Leukemia, another cancer in which Cdx2 is ectopically expressed, may have mechanistic parallels with epithelial cancers in terms of stress-induced reprogramming. This review will address how animal models have refined our understanding of the role of Cdx2 in these common human cancers.
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Medusozoan genomes inform the evolution of the jellyfish body plan. Nat Ecol Evol 2019; 3:811-822. [PMID: 30988488 DOI: 10.1038/s41559-019-0853-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 02/26/2019] [Indexed: 01/01/2023]
Abstract
Cnidarians are astonishingly diverse in body form and lifestyle, including the presence of a jellyfish stage in medusozoans and its absence in anthozoans. Here, we sequence the genomes of Aurelia aurita (a scyphozoan) and Morbakka virulenta (a cubozoan) to understand the molecular mechanisms responsible for the origin of the jellyfish body plan. We show that the magnitude of genetic differences between the two jellyfish types is equivalent, on average, to the level of genetic differences between humans and sea urchins in the bilaterian lineage. About one-third of Aurelia genes with jellyfish-specific expression have no matches in the genomes of the coral and sea anemone, indicating that the polyp-to-jellyfish transition requires a combination of conserved and novel, medusozoa-specific genes. While no genomic region is specifically associated with the ability to produce a jellyfish stage, the arrangement of genes involved in the development of a nematocyte-a phylum-specific cell type-is highly structured and conserved in cnidarian genomes; thus, it represents a phylotypic gene cluster.
Collapse
|
22
|
Kim HM, Weber JA, Lee N, Park SG, Cho YS, Bhak Y, Lee N, Jeon Y, Jeon S, Luria V, Karger A, Kirschner MW, Jo YJ, Woo S, Shin K, Chung O, Ryu JC, Yim HS, Lee JH, Edwards JS, Manica A, Bhak J, Yum S. The genome of the giant Nomura's jellyfish sheds light on the early evolution of active predation. BMC Biol 2019; 17:28. [PMID: 30925871 PMCID: PMC6441219 DOI: 10.1186/s12915-019-0643-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 02/28/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Unique among cnidarians, jellyfish have remarkable morphological and biochemical innovations that allow them to actively hunt in the water column and were some of the first animals to become free-swimming. The class Scyphozoa, or true jellyfish, are characterized by a predominant medusa life-stage consisting of a bell and venomous tentacles used for hunting and defense, as well as using pulsed jet propulsion for mobility. Here, we present the genome of the giant Nomura's jellyfish (Nemopilema nomurai) to understand the genetic basis of these key innovations. RESULTS We sequenced the genome and transcriptomes of the bell and tentacles of the giant Nomura's jellyfish as well as transcriptomes across tissues and developmental stages of the Sanderia malayensis jellyfish. Analyses of the Nemopilema and other cnidarian genomes revealed adaptations associated with swimming, marked by codon bias in muscle contraction and expansion of neurotransmitter genes, along with expanded Myosin type II family and venom domains, possibly contributing to jellyfish mobility and active predation. We also identified gene family expansions of Wnt and posterior Hox genes and discovered the important role of retinoic acid signaling in this ancient lineage of metazoans, which together may be related to the unique jellyfish body plan (medusa formation). CONCLUSIONS Taken together, the Nemopilema jellyfish genome and transcriptomes genetically confirm their unique morphological and physiological traits, which may have contributed to the success of jellyfish as early multi-cellular predators.
Collapse
Affiliation(s)
- Hak-Min Kim
- Korean Genomics Industrialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Jessica A Weber
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Nayoung Lee
- Ecological Risk Research Division, Korea Institute of Ocean Science and Technology (KIOST), Geoje, 53201, Republic of Korea
| | - Seung Gu Park
- Korean Genomics Industrialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Yun Sung Cho
- Korean Genomics Industrialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- Clinomics Inc., Ulsan, 44919, Republic of Korea
| | - Youngjune Bhak
- Korean Genomics Industrialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Nayun Lee
- Ecological Risk Research Division, Korea Institute of Ocean Science and Technology (KIOST), Geoje, 53201, Republic of Korea
| | - Yeonsu Jeon
- Korean Genomics Industrialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Sungwon Jeon
- Korean Genomics Industrialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Victor Luria
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Amir Karger
- IT - Research Computing, Harvard Medical School, Boston, MA, 02115, USA
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ye Jin Jo
- Ecological Risk Research Division, Korea Institute of Ocean Science and Technology (KIOST), Geoje, 53201, Republic of Korea
| | - Seonock Woo
- Faculty of Marine Environmental Science, University of Science and Technology (UST), Geoje, 53201, Republic of Korea
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology (KIOST), Busan, 49111, Republic of Korea
| | - Kyoungsoon Shin
- Ballast Water Center, Korea Institute of Ocean Science and Technology (KIOST), Geoje, 53201, Republic of Korea
| | - Oksung Chung
- Clinomics Inc., Ulsan, 44919, Republic of Korea
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea
| | - Jae-Chun Ryu
- Cellular and Molecular Toxicology Laboratory, Center for Environment, Health and Welfare Research, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Hyung-Soon Yim
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology (KIOST), Busan, 49111, Republic of Korea
| | - Jung-Hyun Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology (KIOST), Busan, 49111, Republic of Korea
| | - Jeremy S Edwards
- Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Jong Bhak
- Korean Genomics Industrialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Clinomics Inc., Ulsan, 44919, Republic of Korea.
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea.
| | - Seungshic Yum
- Ecological Risk Research Division, Korea Institute of Ocean Science and Technology (KIOST), Geoje, 53201, Republic of Korea.
- Faculty of Marine Environmental Science, University of Science and Technology (UST), Geoje, 53201, Republic of Korea.
| |
Collapse
|
23
|
Leclère L, Horin C, Chevalier S, Lapébie P, Dru P, Peron S, Jager M, Condamine T, Pottin K, Romano S, Steger J, Sinigaglia C, Barreau C, Quiroga Artigas G, Ruggiero A, Fourrage C, Kraus JEM, Poulain J, Aury JM, Wincker P, Quéinnec E, Technau U, Manuel M, Momose T, Houliston E, Copley RR. The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle. Nat Ecol Evol 2019; 3:801-810. [PMID: 30858591 DOI: 10.1038/s41559-019-0833-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 01/30/2019] [Indexed: 12/14/2022]
Abstract
Jellyfish (medusae) are a distinctive life-cycle stage of medusozoan cnidarians. They are major marine predators, with integrated neurosensory, muscular and organ systems. The genetic foundations of this complex form are largely unknown. We report the draft genome of the hydrozoan jellyfish Clytia hemisphaerica and use multiple transcriptomes to determine gene use across life-cycle stages. Medusa, planula larva and polyp are each characterized by distinct transcriptome signatures reflecting abrupt life-cycle transitions and all deploy a mixture of phylogenetically old and new genes. Medusa-specific transcription factors, including many with bilaterian orthologues, associate with diverse neurosensory structures. Compared to Clytia, the polyp-only hydrozoan Hydra has lost many of the medusa-expressed transcription factors, despite similar overall rates of gene content evolution and sequence evolution. Absence of expression and gene loss among Clytia orthologues of genes patterning the anthozoan aboral pole, secondary axis and endomesoderm support simplification of planulae and polyps in Hydrozoa, including loss of bilateral symmetry. Consequently, although the polyp and planula are generally considered the ancestral cnidarian forms, in Clytia the medusa maximally deploys the ancestral cnidarian-bilaterian transcription factor gene complement.
Collapse
Affiliation(s)
- Lucas Leclère
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Coralie Horin
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Sandra Chevalier
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Pascal Lapébie
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.,Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Marseille, France
| | - Philippe Dru
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Sophie Peron
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Muriel Jager
- Evolution Paris-Seine, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, Paris, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB UMR 7205), Sorbonne Université, MNHN, CNRS, EPHE, Paris, France
| | - Thomas Condamine
- Evolution Paris-Seine, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, Paris, France
| | - Karen Pottin
- Evolution Paris-Seine, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, Paris, France.,Laboratoire de Biologie du Développement (IBPS-LBD, UMR7622), Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Paris, France
| | - Séverine Romano
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Julia Steger
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.,Laboratoire de Biologie du Développement (IBPS-LBD, UMR7622), Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Paris, France
| | - Chiara Sinigaglia
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.,Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, CNRS UMR 5242-INRA USC 1370, Lyon cedex 07, France
| | - Carine Barreau
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Gonzalo Quiroga Artigas
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.,The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
| | - Antonella Ruggiero
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.,Centre de Recherche de Biologie cellulaire de Montpellier, CNRS UMR 5237, Université de Montpellier, Montpellier Cedex 5, France
| | - Cécile Fourrage
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.,Service de Génétique UMR 781, Hôpital Necker-APHP, Paris, France
| | - Johanna E M Kraus
- Department for Molecular Evolution and Development, Centre of Organismal Systems Biology, University of Vienna, Vienna, Austria.,Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique, Université Paris-Saclay, Evry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Eric Quéinnec
- Evolution Paris-Seine, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, Paris, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB UMR 7205), Sorbonne Université, MNHN, CNRS, EPHE, Paris, France
| | - Ulrich Technau
- Department for Molecular Evolution and Development, Centre of Organismal Systems Biology, University of Vienna, Vienna, Austria
| | - Michaël Manuel
- Evolution Paris-Seine, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, Paris, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB UMR 7205), Sorbonne Université, MNHN, CNRS, EPHE, Paris, France
| | - Tsuyoshi Momose
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Evelyn Houliston
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Richard R Copley
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.
| |
Collapse
|
24
|
Abstract
Regeneration of lost body parts is essential to regain the fitness of the organism for successful living. In the animal kingdom, organisms from different clades exhibit varied regeneration abilities. Hydra is one of the few organisms that possess tremendous regeneration potential, capable of regenerating complete organism from small tissue fragments or even from dissociated cells. This peculiar property has made this genus one of the most invaluable model organisms for understanding the process of regeneration. Multiple studies in Hydra led to the current understanding of gross morphological changes, basic cellular dynamics, and the role of molecular signalling such as the Wnt signalling pathway. However, cell-to-cell communication by cell adhesion, role of extracellular components such as extracellular matrix (ECM), and nature of cell types that contribute to the regeneration process need to be explored in depth. Additionally, roles of developmental signalling pathways need to be elucidated to enable more comprehensive understanding of regeneration in Hydra. Further research on cross communication among extracellular, cellular, and molecular signalling in Hydra will advance the field of regeneration biology. Here, we present a review of the existing literature on Hydra regeneration biology and outline the future perspectives.
Collapse
Affiliation(s)
- Puli Chandramouli Reddy
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India.
| | - Akhila Gungi
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - Manu Unni
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| |
Collapse
|
25
|
Gold DA, Katsuki T, Li Y, Yan X, Regulski M, Ibberson D, Holstein T, Steele RE, Jacobs DK, Greenspan RJ. The genome of the jellyfish Aurelia and the evolution of animal complexity. Nat Ecol Evol 2018; 3:96-104. [PMID: 30510179 DOI: 10.1038/s41559-018-0719-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 10/12/2018] [Indexed: 11/09/2022]
Abstract
We present the genome of the moon jellyfish Aurelia, a genome from a cnidarian with a medusa life stage. Our analyses suggest that gene gain and loss in Aurelia is comparable to what has been found in its morphologically simpler relatives-the anthozoan corals and sea anemones. RNA sequencing analysis does not support the hypothesis that taxonomically restricted (orphan) genes play an oversized role in the development of the medusa stage. Instead, genes broadly conserved across animals and eukaryotes play comparable roles throughout the life cycle. All life stages of Aurelia are significantly enriched in the expression of genes that are hypothesized to interact in protein networks found in bilaterian animals. Collectively, our results suggest that increased life cycle complexity in Aurelia does not correlate with an increased number of genes. This leads to two possible evolutionary scenarios: either medusozoans evolved their complex medusa life stage (with concomitant shifts into new ecological niches) primarily by re-working genetic pathways already present in the last common ancestor of cnidarians, or the earliest cnidarians had a medusa life stage, which was subsequently lost in the anthozoans. While we favour the earlier hypothesis, the latter is consistent with growing evidence that many of the earliest animals were more physically complex than previously hypothesized.
Collapse
Affiliation(s)
- David A Gold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA. .,Department of Earth and Planetary Sciences, University of California Davis, Davis, CA, USA.
| | - Takeo Katsuki
- Kavli Institute for Brain and Mind, University of California San Diego, La Jolla, CA, USA.
| | - Yang Li
- Department of Computer Science, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Xifeng Yan
- Department of Computer Science, University of California Santa Barbara, Santa Barbara, CA, USA
| | | | - David Ibberson
- Deep Sequencing Core Facility, Cell Networks, Heidelberg University, Heidelberg, Germany
| | - Thomas Holstein
- Department of Molecular Evolution and Genomics, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Robert E Steele
- Department of Biological Chemistry and Developmental Biology Center, University of California Irvine, Irvine, CA, USA
| | - David K Jacobs
- Department of Ecology and Evolution, University of California Los Angeles, Los Angeles, CA, USA
| | - Ralph J Greenspan
- Kavli Institute for Brain and Mind, University of California San Diego, La Jolla, CA, USA. .,Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA. .,Department of Cognitive Science, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
26
|
He S, Del Viso F, Chen CY, Ikmi A, Kroesen AE, Gibson MC. An axial Hox code controls tissue segmentation and body patterning in Nematostella vectensis. Science 2018; 361:1377-1380. [PMID: 30262503 DOI: 10.1126/science.aar8384] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 08/09/2018] [Indexed: 11/02/2022]
Abstract
Hox genes encode conserved developmental transcription factors that govern anterior-posterior (A-P) pattering in diverse bilaterian animals, which display bilateral symmetry. Although Hox genes are also present within Cnidaria, these simple animals lack a definitive A-P axis, leaving it unclear how and when a functionally integrated Hox code arose during evolution. We used short hairpin RNA (shRNA)-mediated knockdown and CRISPR-Cas9 mutagenesis to demonstrate that a Hox-Gbx network controls radial segmentation of the larval endoderm during development of the sea anemone Nematostella vectensis. Loss of Hox-Gbx activity also elicits marked defects in tentacle patterning along the directive (orthogonal) axis of primary polyps. On the basis of our results, we propose that an axial Hox code may have controlled body patterning and tissue segmentation before the evolution of the bilaterian A-P axis.
Collapse
Affiliation(s)
- Shuonan He
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Cheng-Yi Chen
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Aissam Ikmi
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Amanda E Kroesen
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Matthew C Gibson
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA. .,Department of Anatomy and Cell Biology, The University of Kansas School of Medicine, Kansas City, KS 66160, USA
| |
Collapse
|
27
|
Ying H, Cooke I, Sprungala S, Wang W, Hayward DC, Tang Y, Huttley G, Ball EE, Forêt S, Miller DJ. Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages. Genome Biol 2018; 19:175. [PMID: 30384840 PMCID: PMC6214176 DOI: 10.1186/s13059-018-1552-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 09/28/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Despite the biological and economic significance of scleractinian reef-building corals, the lack of large molecular datasets for a representative range of species limits understanding of many aspects of their biology. Within the Scleractinia, based on molecular evidence, it is generally recognised that there are two major clades, Complexa and Robusta, but the genomic bases of significant differences between them remain unclear. RESULTS Draft genome assemblies and annotations were generated for three coral species: Galaxea fascicularis (Complexa), Fungia sp., and Goniastrea aspera (Robusta). Whilst phylogenetic analyses strongly support a deep split between Complexa and Robusta, synteny analyses reveal a high level of gene order conservation between all corals, but not between corals and sea anemones or between sea anemones. HOX-related gene clusters are, however, well preserved across all of these combinations. Differences between species are apparent in the distribution and numbers of protein domains and an apparent correlation between number of HSP20 proteins and stress tolerance. Uniquely amongst animals, a complete histidine biosynthesis pathway is present in robust corals but not in complex corals or sea anemones. This pathway appears to be ancestral, and its retention in the robust coral lineage has important implications for coral nutrition and symbiosis. CONCLUSIONS The availability of three new coral genomes enabled recognition of a de novo histidine biosynthesis pathway in robust corals which is only the second identified biosynthetic difference between corals. These datasets provide a platform for understanding many aspects of coral biology, particularly the interactions of corals with their endosymbionts.
Collapse
Affiliation(s)
- Hua Ying
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Ira Cooke
- Comparative Genomics Centre, Department of Molecular and Cell Biology, James Cook University, Townsville, QLD 4811 Australia
| | - Susanne Sprungala
- Comparative Genomics Centre, Department of Molecular and Cell Biology, James Cook University, Townsville, QLD 4811 Australia
| | - Weiwen Wang
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - David C. Hayward
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Yurong Tang
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
- Computational Biology and Bioinformatics Unit, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Gavin Huttley
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
- Computational Biology and Bioinformatics Unit, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Eldon E. Ball
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | - Sylvain Forêt
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | - David J. Miller
- Comparative Genomics Centre, Department of Molecular and Cell Biology, James Cook University, Townsville, QLD 4811 Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| |
Collapse
|
28
|
|
29
|
Brauchle M, Bilican A, Eyer C, Bailly X, Martínez P, Ladurner P, Bruggmann R, Sprecher SG. Xenacoelomorpha Survey Reveals That All 11 Animal Homeobox Gene Classes Were Present in the First Bilaterians. Genome Biol Evol 2018; 10:2205-2217. [PMID: 30102357 PMCID: PMC6125248 DOI: 10.1093/gbe/evy170] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2018] [Indexed: 11/13/2022] Open
Abstract
Homeodomain transcription factors are involved in many developmental processes across animals and have been linked to body plan evolution. Detailed classifications of these proteins identified 11 distinct classes of homeodomain proteins in animal genomes, each harboring specific sequence composition and protein domains. Although humans contain the full set of classes, Drosophila melanogaster and Caenorhabditis elegans each lack one specific class. Furthermore, representative previous analyses in sponges, ctenophores, and cnidarians could not identify several classes in those nonbilaterian metazoan taxa. Consequently, it is currently unknown when certain homeodomain protein classes first evolved during animal evolution. Here, we investigate representatives of the sister group to all remaining bilaterians, the Xenacoelomorpha. We analyzed three acoel, one nemertodermatid, and one Xenoturbella transcriptomes and identified their expressed homeodomain protein content. We report the identification of representatives of all 11 classes of animal homeodomain transcription factors in Xenacoelomorpha and we describe and classify their homeobox genes relative to the established animal homeodomain protein families. Our findings suggest that the genome of the last common ancestor of bilateria contained the full set of these gene classes, supporting the subsequent diversification of bilaterians.
Collapse
Affiliation(s)
- Michael Brauchle
- Department of Biology, Institute of Zoology, University of Fribourg, Switzerland.,Department of Biology, Institute of Cell Biology, University of Bern, Switzerland.,These authors contributed equally to this work
| | - Adem Bilican
- Department of Biology, Interfaculty Bioinformatics Unit, University of Bern, Switzerland.,These authors contributed equally to this work
| | - Claudia Eyer
- Department of Biology, Interfaculty Bioinformatics Unit, University of Bern, Switzerland
| | - Xavier Bailly
- UPMC-CNRS FR2424, Station Biologique de Roscoff, Roscoff, France
| | - Pedro Martínez
- Departament de Genètica, Universitat de Barcelona, Catalonia, Spain.,Institut Català de Recerca i Estudis Avancats (ICREA), Barcelona, Spain
| | - Peter Ladurner
- Institute of Zoology and Center of Molecular Bioscience Innsbruck, University of Innsbruck, Austria
| | - Rémy Bruggmann
- Department of Biology, Interfaculty Bioinformatics Unit, University of Bern, Switzerland
| | - Simon G Sprecher
- Department of Biology, Institute of Zoology, University of Fribourg, Switzerland
| |
Collapse
|
30
|
Abstract
Distantly related animals have spectacularly different shapes and body plans, which can render it difficult to understand which of their body parts may have a shared evolutionary origin. Studying the molecular regulation of the development of these body parts during embryogenesis can help identifying commonalities that are not visible by eye.
Collapse
|
31
|
Hox and Wnt pattern the primary body axis of an anthozoan cnidarian before gastrulation. Nat Commun 2018; 9:2007. [PMID: 29789526 PMCID: PMC5964151 DOI: 10.1038/s41467-018-04184-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 04/06/2018] [Indexed: 11/17/2022] Open
Abstract
Hox gene transcription factors are important regulators of positional identity along the anterior–posterior axis in bilaterian animals. Cnidarians (e.g., sea anemones, corals, and hydroids) are the sister group to the Bilateria and possess genes related to both anterior and central/posterior class Hox genes. Here we report a previously unrecognized domain of Hox expression in the starlet sea anemone, Nematostella vectensis, beginning at early blastula stages. We explore the relationship of two opposing Hox genes (NvAx6/NvAx1) expressed on each side of the blastula during early development. Functional perturbation reveals that NvAx6 and NvAx1 not only regulate their respective expression domains, but also interact with Wnt genes to pattern the entire oral–aboral axis. These findings suggest an ancient link between Hox/Wnt patterning during axis formation and indicate that oral–aboral domains are likely established during blastula formation in anthozoan cnidarians. Hox genes regulate anterior–posterior axis formation but their role in cnidarians is unclear. Here, the authors disrupt Hox genes NvAx1 and NvAx6 in the starlet sea anemone, Nematostella vectensis, showing antagonist function in patterning the oral–aboral axis and a link to Wnt signaling.
Collapse
|
32
|
Abstract
Bilaterality – the possession of two orthogonal body axes – is the name-giving trait of all bilaterian animals. These body axes are established during early embryogenesis and serve as a three-dimensional coordinate system that provides crucial spatial cues for developing cells, tissues, organs and appendages. The emergence of bilaterality was a major evolutionary transition, as it allowed animals to evolve more complex body plans. Therefore, how bilaterality evolved and whether it evolved once or several times independently is a fundamental issue in evolutionary developmental biology. Recent findings from non-bilaterian animals, in particular from Cnidaria, the sister group to Bilateria, have shed new light into the evolutionary origin of bilaterality. Here, we compare the molecular control of body axes in radially and bilaterally symmetric cnidarians and bilaterians, identify the minimal set of traits common for Bilateria, and evaluate whether bilaterality arose once or more than once during evolution.
Collapse
Affiliation(s)
- Grigory Genikhovich
- Department for Molecular Evolution and Development, Centre of Organismal Systems Biology, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria
| | - Ulrich Technau
- Department for Molecular Evolution and Development, Centre of Organismal Systems Biology, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria
| |
Collapse
|
33
|
A bipolar role of the transcription factor ERG for cnidarian germ layer formation and apical domain patterning. Dev Biol 2017; 430:346-361. [PMID: 28818668 DOI: 10.1016/j.ydbio.2017.08.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/29/2017] [Accepted: 08/09/2017] [Indexed: 02/06/2023]
Abstract
Germ layer formation and axial patterning are biological processes that are tightly linked during embryonic development of most metazoans. In addition to canonical WNT, it has been proposed that ERK-MAPK signaling is involved in specifying oral as well as aboral territories in cnidarians. However, the effector and the molecular mechanism underlying latter phenomenon is unknown. By screening for potential effectors of ERK-MAPK signaling in both domains, we identified a member of the ETS family of transcription factors, Nverg that is bi-polarily expressed prior to gastrulation. We further describe the crucial role of NvERG for gastrulation, endomesoderm as well as apical domain formation. The molecular characterization of the obtained NvERG knock-down phenotype using previously described as well as novel potential downstream targets, provides evidence that a single transcription factor, NvERG, simultaneously controls expression of two different sets of downstream targets, leading to two different embryonic gene regulatory networks (GRNs) in opposite poles of the developing embryo. We also highlight the molecular interaction of cWNT and MEK/ERK/ERG signaling that provides novel insight into the embryonic axial organization of Nematostella, and show a cWNT repressive role of MEK/ERK/ERG signaling in segregating the endomesoderm in two sub-domains, while a common input of both pathways is required for proper apical domain formation. Taking together, we build the first blueprint for a global cnidarian embryonic GRN that is the foundation for additional gene specific studies addressing the evolution of embryonic and larval development.
Collapse
|
34
|
Antagonistic BMP-cWNT signaling in the cnidarian Nematostella vectensis reveals insight into the evolution of mesoderm. Proc Natl Acad Sci U S A 2017; 114:E5608-E5615. [PMID: 28652368 DOI: 10.1073/pnas.1701607114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Gastrulation was arguably the key evolutionary innovation that enabled metazoan diversification, leading to the formation of distinct germ layers and specialized tissues. Differential gene expression specifying cell fate is governed by the inputs of intracellular and/or extracellular signals. Beta-catenin/Tcf and the TGF-beta bone morphogenetic protein (BMP) provide critical molecular signaling inputs during germ layer specification in bilaterian metazoans, but there has been no direct experimental evidence for a specific role for BMP signaling during endomesoderm specification in the early branching metazoan Nematostella vectensis (an anthozoan cnidarian). Using forward transcriptomics, we show that beta-catenin/Tcf signaling and BMP2/4 signaling provide differential inputs into the cnidarian endomesodermal gene regulatory network (GRN) at the onset of gastrulation (24 h postfertilization) in N. vectensis Surprisingly, beta-catenin/Tcf signaling and BMP2/4 signaling regulate a subset of common downstream target genes in the GRN in opposite ways, leading to the spatial and temporal differentiation of fields of cells in the developing embryo. Thus, we show that regulatory interactions between beta-catenin/Tcf signaling and BMP2/4 signaling are required for the specification and determination of different embryonic regions and the patterning of the oral-aboral axis in Nematostella We also show functionally that the conserved "kernel" of the bilaterian heart mesoderm GRN is operational in N. vectensis, which reinforces the hypothesis that the endoderm and mesoderm in triploblastic bilaterians evolved from the bifunctional endomesoderm (gastrodermis) of a diploblastic ancestor, and that slow rhythmic contractions might have been one of the earliest functions of mesodermal tissue.
Collapse
|
35
|
A transcriptional time-course analysis of oral vs. aboral whole-body regeneration in the Sea anemone Nematostella vectensis. BMC Genomics 2016; 17:718. [PMID: 27605362 PMCID: PMC5015328 DOI: 10.1186/s12864-016-3027-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/20/2016] [Indexed: 02/07/2023] Open
Abstract
Background The ability of regeneration is essential for the homeostasis of all animals as it allows the repair and renewal of tissues and body parts upon normal turnover or injury. The extent of this ability varies greatly in different animals with the sea anemone Nematostella vectensis, a basal cnidarian model animal, displaying remarkable whole-body regeneration competence. Results In order to study this process in Nematostella we performed an RNA-Seq screen wherein we analyzed and compared the transcriptional response to bisection in the wound-proximal body parts undergoing oral (head) or aboral (tail) regeneration at several time points up to the initial restoration of the basic body shape. The transcriptional profiles of regeneration responsive genes were analyzed so as to define the temporal pattern of differential gene expression associated with the tissue-specific oral and aboral regeneration. The identified genes were characterized according to their GO (gene ontology) assignations revealing groups that were enriched in the regeneration process with particular attention to their affiliation to the major developmental signaling pathways. While some of the genes and gene groups thus analyzed were previously known to be active in regeneration, we have also revealed novel and surprising candidate genes such as cilia-associated genes that likely participate in this important developmental program. Conclusions This work highlighted the main groups of genes which showed polarization upon regeneration, notably the proteinases, multiple transcription factors and the Wnt pathway genes that were highly represented, all displaying an intricate temporal balance between the two sides. In addition, the evolutionary comparison performed between regeneration in different animal model systems may reveal the basic mechanisms playing a role in this fascinating process. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3027-1) contains supplementary material, which is available to authorized users.
Collapse
|
36
|
Layden MJ, Johnston H, Amiel AR, Havrilak J, Steinworth B, Chock T, Röttinger E, Martindale MQ. MAPK signaling is necessary for neurogenesis in Nematostella vectensis. BMC Biol 2016; 14:61. [PMID: 27480076 PMCID: PMC4968017 DOI: 10.1186/s12915-016-0282-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 07/04/2016] [Indexed: 11/16/2022] Open
Abstract
Background The nerve net of Nematostella is generated using a conserved cascade of neurogenic transcription factors. For example, NvashA, a homolog of the achaete-scute family of basic helix-loop-helix transcription factors, is necessary and sufficient to specify a subset of embryonic neurons. However, positive regulators required for the expression of neurogenic transcription factors remain poorly understood. Results We show that treatment with the MEK/MAPK inhibitor U0126 severely reduces the expression of known neurogenic genes, Nvath-like, NvsoxB(2), and NvashA, and known markers of differentiated neurons, suggesting that MAPK signaling is necessary for neural development. Interestingly, ectopic NvashA fails to rescue the expression of neural markers in U0126-treated animals. Double fluorescence in situ hybridization and transgenic analysis confirmed that NvashA targets represent both unique and overlapping populations of neurons. Finally, we used a genome-wide microarray to identify additional patterning genes downstream of MAPK that might contribute to neurogenesis. We identified 18 likely neural transcription factors, and surprisingly identified ~40 signaling genes and transcription factors that are expressed in either the aboral domain or animal pole that gives rise to the endomesoderm at late blastula stages. Conclusions Together, our data suggest that MAPK is a key early regulator of neurogenesis, and that it is likely required at multiple steps. Initially, MAPK promotes neurogenesis by positively regulating expression of NvsoxB(2), Nvath-like, and NvashA. However, we also found that MAPK is necessary for the activity of the neurogenic transcription factor NvashA. Our forward molecular approach provided insight about the mechanisms of embryonic neurogenesis. For instance, NvashA suppression of Nvath-like suggests that inhibition of progenitor identity is an active process in newly born neurons, and we show that downstream targets of NvashA reflect multiple neural subtypes rather than a uniform neural fate. Lastly, analysis of the MAPK targets in the early embryo suggests that MAPK signaling is critical not only to neurogenesis, but also endomesoderm formation and aboral patterning. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0282-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Michael J Layden
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA.
| | - Hereroa Johnston
- Université Nice Sophia Antipolis UMR 7284, CNRS UMR 7284, INSERM U1081, Institute for Research on Cancer and Aging, Nice, France
| | - Aldine R Amiel
- Université Nice Sophia Antipolis UMR 7284, CNRS UMR 7284, INSERM U1081, Institute for Research on Cancer and Aging, Nice, France
| | - Jamie Havrilak
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Bailey Steinworth
- The Whitney Marine Laboratory for Marine Science, University of Florida, St. Augustine, Florida, USA
| | - Taylor Chock
- The Whitney Marine Laboratory for Marine Science, University of Florida, St. Augustine, Florida, USA
| | - Eric Röttinger
- Université Nice Sophia Antipolis UMR 7284, CNRS UMR 7284, INSERM U1081, Institute for Research on Cancer and Aging, Nice, France
| | - Mark Q Martindale
- The Whitney Marine Laboratory for Marine Science, University of Florida, St. Augustine, Florida, USA.
| |
Collapse
|
37
|
Urdy S, Goudemand N, Pantalacci S. Looking Beyond the Genes: The Interplay Between Signaling Pathways and Mechanics in the Shaping and Diversification of Epithelial Tissues. Curr Top Dev Biol 2016; 119:227-90. [PMID: 27282028 DOI: 10.1016/bs.ctdb.2016.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The core of Evo-Devo lies in the intuition that the way tissues grow during embryonic development, the way they sustain their structure and function throughout lifetime, and the way they evolve are closely linked. Epithelial tissues are ubiquitous in metazoans, covering the gut and internal branched organs, as well as the skin and its derivatives (ie, teeth). Here, we discuss in vitro, in vivo, and in silico studies on epithelial tissues to illustrate the conserved, dynamical, and complex aspects of their development. We then explore the implications of the dynamical and nonlinear nature of development on the evolution of their size and shape at the phenotypic and genetic levels. In rare cases, when the interplay between signaling and mechanics is well understood at the cell level, it is becoming clear that the structure of development leads to covariation of characters, an integration which in turn provides some predictable structure to evolutionary changes. We suggest that such nonlinear systems are prone to genetic drift, cryptic genetic variation, and context-dependent mutational effects. We argue that experimental and theoretical studies at the cell level are critical to our understanding of the phenotypic and genetic evolution of epithelial tissues, including carcinomas.
Collapse
Affiliation(s)
- S Urdy
- University of Zürich, Institute of Physics, Zürich, Switzerland.
| | - N Goudemand
- Univ Lyon, ENS Lyon, CNRS, Université Claude Bernard Lyon 1, Institut de Génomique Fonctionnelle de Lyon, UMR 5242, Lyon Cedex 07, France
| | - S Pantalacci
- Univ Lyon, ENS Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratory of Biology and Modelling of the Cell, UMR 5239, INSERM U1210, Lyon Cedex 07, France
| |
Collapse
|
38
|
Arendt D, Tosches MA, Marlow H. From nerve net to nerve ring, nerve cord and brain--evolution of the nervous system. Nat Rev Neurosci 2016; 17:61-72. [PMID: 26675821 DOI: 10.1038/nrn.2015.15] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The puzzle of how complex nervous systems emerged remains unsolved. Comparative studies of neurodevelopment in cnidarians and bilaterians suggest that this process began with distinct integration centres that evolved on opposite ends of an initial nerve net. The 'apical nervous system' controlled general body physiology, and the 'blastoporal nervous system' coordinated feeding movements and locomotion. We propose that expansion, integration and fusion of these centres gave rise to the bilaterian nerve cord and brain.
Collapse
Affiliation(s)
- Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 699117 Heidelberg, Germany
| | - Maria Antonietta Tosches
- Max Planck Institute for Brain Research, Max-von-Laue-Strasse 4, 60438 Frankfurt am Main, Germany
| | - Heather Marlow
- Pasteur Institute, 25-28 Rue du Dr Roux, 75015 Paris, France
| |
Collapse
|
39
|
Hueber SD, Frickey T. Solving Classification Problems for Large Sets of Protein Sequences with the Example of Hox and ParaHox Proteins. J Dev Biol 2016; 4:jdb4010008. [PMID: 29615576 PMCID: PMC5831817 DOI: 10.3390/jdb4010008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 01/25/2016] [Accepted: 01/27/2016] [Indexed: 11/16/2022] Open
Abstract
Phylogenetic methods are key to providing models for how a given protein family evolved. However, these methods run into difficulties when sequence divergence is either too low or too high. Here, we provide a case study of Hox and ParaHox proteins so that additional insights can be gained using a new computational approach to help solve old classification problems. For two (Gsx and Cdx) out of three ParaHox proteins the assignments differ between the currently most established view and four alternative scenarios. We use a non-phylogenetic, pairwise-sequence-similarity-based method to assess which of the previous predictions, if any, are best supported by the sequence-similarity relationships between Hox and ParaHox proteins. The overall sequence-similarities show Gsx to be most similar to Hox2–3, and Cdx to be most similar to Hox4–8. The results indicate that a purely pairwise-sequence-similarity-based approach can provide additional information not only when phylogenetic inference methods have insufficient information to provide reliable classifications (as was shown previously for central Hox proteins), but also when the sequence variation is so high that the resulting phylogenetic reconstructions are likely plagued by long-branch-attraction artifacts.
Collapse
Affiliation(s)
- Stefanie D Hueber
- Department of Biology, University of Konstanz, Konstanz 78464, Germany.
| | - Tancred Frickey
- Department of Biology, University of Konstanz, Konstanz 78464, Germany.
| |
Collapse
|
40
|
Abstract
My aim in this article is to soften certain rigid concepts concerning the radial and bilateral symmetry of the animal body plan, and to offer a more flexible framework of thinking for them, based on recent understandings of how morphogenesis is regulated by the mosaically acting gene regulatory networks. Based on general principles of the genetic regulation of morphogenesis, it can be seen that the difference between the symmetry of the whole body and that of minor anatomical structures is only a question of a diverse timing during development. I propose that the animal genome, as such, is capable of expressing both radial and bilateral symmetries, and deploys them according to the functional requirements which must be satisfied by both the anatomical structure and body as a whole. Although it may seem paradoxical, this flexible view of symmetry, together with the idea that symmetry is strongly determined by function, bolsters the concept that the presence of the two main symmetries in the animal world is not due to chance: they are necessary biological patterns emerging in evolution.
Collapse
Affiliation(s)
- Gábor Holló
- Institute of Psychology , University of Debrecen , PO Box 28, 4010 Debrecen , Hungary
| |
Collapse
|
41
|
Reddy PC, Unni MK, Gungi A, Agarwal P, Galande S. Evolution of Hox-like genes in Cnidaria: Study of Hydra Hox repertoire reveals tailor-made Hox-code for Cnidarians. Mech Dev 2015; 138 Pt 2:87-96. [DOI: 10.1016/j.mod.2015.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 08/05/2015] [Accepted: 08/07/2015] [Indexed: 11/26/2022]
|
42
|
Bürglin TR, Affolter M. Homeodomain proteins: an update. Chromosoma 2015; 125:497-521. [PMID: 26464018 PMCID: PMC4901127 DOI: 10.1007/s00412-015-0543-8] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 09/20/2015] [Accepted: 09/21/2015] [Indexed: 12/17/2022]
Abstract
Here, we provide an update of our review on homeobox genes that we wrote together with Walter Gehring in 1994. Since then, comprehensive surveys of homeobox genes have become possible due to genome sequencing projects. Using the 103 Drosophila homeobox genes as example, we present an updated classification. In animals, there are 16 major classes, ANTP, PRD, PRD-LIKE, POU, HNF, CUT (with four subclasses: ONECUT, CUX, SATB, and CMP), LIM, ZF, CERS, PROS, SIX/SO, plus the TALE superclass with the classes IRO, MKX, TGIF, PBC, and MEIS. In plants, there are 11 major classes, i.e., HD-ZIP (with four subclasses: I to IV), WOX, NDX, PHD, PLINC, LD, DDT, SAWADEE, PINTOX, and the two TALE classes KNOX and BEL. Most of these classes encode additional domains apart from the homeodomain. Numerous insights have been obtained in the last two decades into how homeodomain proteins bind to DNA and increase their specificity by interacting with other proteins to regulate cell- and tissue-specific gene expression. Not only protein-DNA base pair contacts are important for proper target selection; recent experiments also reveal that the shape of the DNA plays a role in specificity. Using selected examples, we highlight different mechanisms of homeodomain protein-DNA interaction. The PRD class of homeobox genes was of special interest to Walter Gehring in the last two decades. The PRD class comprises six families in Bilateria, and tinkers with four different motifs, i.e., the PAIRED domain, the Groucho-interacting motif EH1 (aka Octapeptide or TN), the homeodomain, and the OAR motif. Homologs of the co-repressor protein Groucho are also present in plants (TOPLESS), where they have been shown to interact with small amphipathic motives (EAR), and in yeast (TUP1), where we find an EH1-like motif in MATα2.
Collapse
Affiliation(s)
- Thomas R. Bürglin
- />Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
- />Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Markus Affolter
- />Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| |
Collapse
|
43
|
Technau U, Schwaiger M. Recent advances in genomics and transcriptomics of cnidarians. Mar Genomics 2015; 24 Pt 2:131-8. [PMID: 26421490 DOI: 10.1016/j.margen.2015.09.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/20/2015] [Accepted: 09/21/2015] [Indexed: 01/05/2023]
Abstract
The advent of the genomic era has provided important and surprising insights into the deducted genetic composition of the common ancestor of cnidarians and bilaterians. This has changed our view of how genomes of metazoans evolve and when crucial gene families arose and diverged in animal evolution. Sequencing of several cnidarian genomes showed that cnidarians share a great part of their gene repertoire as well as genome synteny with vertebrates, with less gene losses in the anthozoan cnidarian lineage than for example in ecdysozoans like Drosophila melanogaster or Caenorhabditis elegans. The Hydra genome on the other hand has evolved more rapidly indicated by more divergent sequences, more cases of gene losses and many taxonomically restricted genes. Cnidarian genomes also contain a rich repertoire of transcription factors, including those that in bilaterian model organisms regulate the development of key bilaterian traits such as mesoderm, nervous system development and bilaterality. The sea anemone Nematostella vectensis, and possibly cnidarians in general, does not only share its complex gene repertoire with bilaterians, but also the regulation of crucial developmental regulatory genes via distal enhancer elements. In addition, epigenetic modifications on DNA and chromatin are shared among eumetazoans. This suggests that most conserved genes present in our genomes today, as well as the mechanisms guiding their expression, evolved before the divergence of cnidarians and bilaterians about 600 Myr ago.
Collapse
Affiliation(s)
- Ulrich Technau
- Department of Molecular Evolution and Development, Centre of Organismal Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
| | - Michaela Schwaiger
- Department of Molecular Evolution and Development, Centre of Organismal Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| |
Collapse
|
44
|
Abstract
The most diverse marine ecosystems, coral reefs, depend upon a functional symbiosis between a cnidarian animal host (the coral) and intracellular photosynthetic dinoflagellate algae. The molecular and cellular mechanisms underlying this endosymbiosis are not well understood, in part because of the difficulties of experimental work with corals. The small sea anemone Aiptasia provides a tractable laboratory model for investigating these mechanisms. Here we report on the assembly and analysis of the Aiptasia genome, which will provide a foundation for future studies and has revealed several features that may be key to understanding the evolution and function of the endosymbiosis. These features include genomic rearrangements and taxonomically restricted genes that may be functionally related to the symbiosis, aspects of host dependence on alga-derived nutrients, a novel and expanded cnidarian-specific family of putative pattern-recognition receptors that might be involved in the animal-algal interactions, and extensive lineage-specific horizontal gene transfer. Extensive integration of genes of prokaryotic origin, including genes for antimicrobial peptides, presumably reflects an intimate association of the animal-algal pair also with its prokaryotic microbiome.
Collapse
|
45
|
Merabet S, Galliot B. The TALE face of Hox proteins in animal evolution. Front Genet 2015; 6:267. [PMID: 26347770 PMCID: PMC4539518 DOI: 10.3389/fgene.2015.00267] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 07/31/2015] [Indexed: 01/22/2023] Open
Abstract
Hox genes are major regulators of embryonic development. One of their most conserved functions is to coordinate the formation of specific body structures along the anterior-posterior (AP) axis in Bilateria. This architectural role was at the basis of several morphological innovations across bilaterian evolution. In this review, we traced the origin of the Hox patterning system by considering the partnership with PBC and Meis proteins. PBC and Meis belong to the TALE-class of homeodomain-containing transcription factors and act as generic cofactors of Hox proteins for AP axis patterning in Bilateria. Recent data indicate that Hox proteins acquired the ability to interact with their TALE partners in the last common ancestor of Bilateria and Cnidaria. These interactions relied initially on a short peptide motif called hexapeptide (HX), which is present in Hox and non-Hox protein families. Remarkably, Hox proteins can also recruit the TALE cofactors by using specific PBC Interaction Motifs (SPIMs). We describe how a functional Hox/TALE patterning system emerged in eumetazoans through the acquisition of SPIMs. We anticipate that interaction flexibility could be found in other patterning systems, being at the heart of the astonishing morphological diversity observed in the animal kingdom.
Collapse
Affiliation(s)
- Samir Merabet
- Centre National de Recherche Scientifique, Institut de Génomique Fonctionnelle de Lyon Lyon, France ; Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon Lyon, France
| | - Brigitte Galliot
- Department of Genetics and Evolution, Faculty of Science, Institute of Genetics and Genomics in Geneva, University of Geneva Geneva, Switzerland
| |
Collapse
|
46
|
Fortunato SAV, Adamski M, Adamska M. Comparative analyses of developmental transcription factor repertoires in sponges reveal unexpected complexity of the earliest animals. Mar Genomics 2015; 24 Pt 2:121-9. [PMID: 26253310 DOI: 10.1016/j.margen.2015.07.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 07/27/2015] [Accepted: 07/27/2015] [Indexed: 12/18/2022]
Abstract
Developmental transcription factors (DTFs) control development of animals by affecting expression of target genes, some of which are transcription factors themselves. In bilaterians and cnidarians, conserved DTFs are involved in homologous processes such as gastrulation or specification of neurons. The genome of Amphimedon queenslandica, the first sponge to be sequenced, revealed that only a fraction of these conserved DTF families are present in demosponges. This finding was in line with the view that morphological complexity in the animal lineage correlates with developmental toolkit complexity. However, as the phylum Porifera is very diverse, Amphimedon's genome may not be representative of all sponges. The recently sequenced genomes of calcareous sponges Sycon ciliatum and Leucosolenia complicata allowed investigations of DTFs in a sponge lineage evolutionarily distant from demosponges. Surprisingly, the phylogenetic analyses of identified DTFs revealed striking differences between the calcareous sponges and Amphimedon. As these differences appear to be a result of independent gene loss events in the two sponge lineages, the last common ancestor of sponges had to possess a much more diverse repertoire of DTFs than extant sponges. Developmental expression of sponge homologs of genes involved in specification of the Bilaterian endomesoderm and the neurosensory cells suggests that roles of many DTFs date back to the last common ancestor of all animals. Strikingly, even DTFs displaying apparent pan-metazoan conservation of sequence and function are not immune to being lost from individual species genomes. The quest for a comprehensive picture of the developmental toolkit in the last common metazoan ancestor is thus greatly benefitting from the increasing accessibility of sequencing, allowing comparisons of multiple genomes within each phylum.
Collapse
Affiliation(s)
- Sofia A V Fortunato
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway; Department of Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway
| | - Marcin Adamski
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway
| | - Maja Adamska
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway.
| |
Collapse
|
47
|
Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes. Nature 2014; 514:620-3. [PMID: 25355364 DOI: 10.1038/nature13881] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 09/22/2014] [Indexed: 11/08/2022]
Abstract
Sponges are simple animals with few cell types, but their genomes paradoxically contain a wide variety of developmental transcription factors, including homeobox genes belonging to the Antennapedia (ANTP) class, which in bilaterians encompass Hox, ParaHox and NK genes. In the genome of the demosponge Amphimedon queenslandica, no Hox or ParaHox genes are present, but NK genes are linked in a tight cluster similar to the NK clusters of bilaterians. It has been proposed that Hox and ParaHox genes originated from NK cluster genes after divergence of sponges from the lineage leading to cnidarians and bilaterians. On the other hand, synteny analysis lends support to the notion that the absence of Hox and ParaHox genes in Amphimedon is a result of secondary loss (the ghost locus hypothesis). Here we analysed complete suites of ANTP-class homeoboxes in two calcareous sponges, Sycon ciliatum and Leucosolenia complicata. Our phylogenetic analyses demonstrate that these calcisponges possess orthologues of bilaterian NK genes (Hex, Hmx and Msx), a varying number of additional NK genes and one ParaHox gene, Cdx. Despite the generation of scaffolds spanning multiple genes, we find no evidence of clustering of Sycon NK genes. All Sycon ANTP-class genes are developmentally expressed, with patterns suggesting their involvement in cell type specification in embryos and adults, metamorphosis and body plan patterning. These results demonstrate that ParaHox genes predate the origin of sponges, thus confirming the ghost locus hypothesis, and highlight the need to analyse the genomes of multiple sponge lineages to obtain a complete picture of the ancestral composition of the first animal genome.
Collapse
|
48
|
Biscotti MA, Canapa A, Forconi M, Barucca M. HoxandParaHoxgenes: A review on molluscs. Genesis 2014; 52:935-45. [DOI: 10.1002/dvg.22839] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 11/10/2014] [Accepted: 11/11/2014] [Indexed: 01/28/2023]
Affiliation(s)
- Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; Ancona Italy
| | - Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; Ancona Italy
| | - Mariko Forconi
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; Ancona Italy
| | - Marco Barucca
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; Ancona Italy
| |
Collapse
|
49
|
Bosch TC. Rethinking the role of immunity: lessons from Hydra. Trends Immunol 2014; 35:495-502. [DOI: 10.1016/j.it.2014.07.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 07/28/2014] [Accepted: 07/29/2014] [Indexed: 12/24/2022]
|
50
|
Shinzato C, Mungpakdee S, Satoh N, Shoguchi E. A genomic approach to coral-dinoflagellate symbiosis: studies of Acropora digitifera and Symbiodinium minutum. Front Microbiol 2014; 5:336. [PMID: 25071748 PMCID: PMC4083563 DOI: 10.3389/fmicb.2014.00336] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 06/17/2014] [Indexed: 12/16/2022] Open
Abstract
Far more intimate knowledge of scleractinian coral biology is essential in order to understand how diverse coral-symbiont endosymbioses have been established. In particular, molecular and cellular mechanisms enabling the establishment and maintenance of obligate endosymbiosis with photosynthetic dinoflagellates require further clarification. By extension, such understanding may also shed light upon environmental conditions that promote the collapse of this mutualism. Genomic data undergird studies of all symbiotic processes. Here we review recent genomic data derived from the scleractinian coral, Acropora digitifera, and the endosymbiotic dinoflagellate, Symbiodinium minutum. We discuss Acropora genes involved in calcification, embryonic development, innate immunity, apoptosis, autophagy, UV resistance, fluorescence, photoreceptors, circadian clocks, etc. We also detail gene loss in amino acid metabolism that may explain at least part of the Acropora stress-response. Characteristic features of the Symbiodinium genome are also reviewed, focusing on the expansion of certain gene families, the molecular basis for permanently condensed chromatin, unique spliceosomal splicing, and unusual gene arrangement. Salient features of the Symbiodinium plastid and mitochondrial genomes are also illuminated. Although many questions regarding these interdependent genomes remain, we summarize information necessary for future studies of coral-dinoflagellate endosymbiosis.
Collapse
Affiliation(s)
- Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University Okinawa, Japan
| | - Sutada Mungpakdee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University Okinawa, Japan
| | - Nori Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University Okinawa, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University Okinawa, Japan
| |
Collapse
|