1
|
Vargas A, DeBiasse M, Dykes L, Edgar A, Hayes T, Groso D, Babonis L, Martindale M, Ryan J. Morphological and dietary changes encoded in the genome of Beroe ovata, a ctenophore-eating ctenophore. NAR Genom Bioinform 2024; 6:lqae072. [PMID: 38895105 PMCID: PMC11184263 DOI: 10.1093/nargab/lqae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/03/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
As the sister group to all other animals, ctenophores (comb jellies) are important for understanding the emergence and diversification of numerous animal traits. Efforts to explore the evolutionary processes that promoted diversification within Ctenophora are hindered by undersampling genomic diversity within this clade. To address this gap, we present the sequence, assembly and initial annotation of the genome of Beroe ovata. Beroe possess unique morphology, behavior, ecology and development. Unlike their generalist carnivorous kin, beroid ctenophores feed exclusively on other ctenophores. Accordingly, our analyses revealed a loss of chitinase, an enzyme critical for the digestion of most non-ctenophore prey, but superfluous for ctenophorivores. Broadly, our genomic analysis revealed that extensive gene loss and changes in gene regulation have shaped the unique biology of B. ovata. Despite the gene losses in B. ovata, our phylogenetic analyses on photosensitive opsins and several early developmental regulatory genes show that these genes are conserved in B. ovata. This additional sampling contributes to a more complete reconstruction of the ctenophore ancestor and points to the need for extensive comparisons within this ancient and diverse clade of animals. To promote further exploration of these data, we present BovaDB (http://ryanlab.whitney.ufl.edu/bovadb/), a portal for the B. ovata genome.
Collapse
Affiliation(s)
- Alexandra M Vargas
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, Radford University, Radford, VA 24142, USA
| | - Lana L Dykes
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Allison Edgar
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Federated Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - T Danielle Hayes
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Daniel J Groso
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Leslie S Babonis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| |
Collapse
|
2
|
Kulakova MA, Maslakov GP, Poliushkevich LO. Irreducible Complexity of Hox Gene: Path to the Canonical Function of the Hox Cluster. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:987-1001. [PMID: 38981695 DOI: 10.1134/s0006297924060014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 07/11/2024]
Abstract
The evolution of major taxa is often associated with the emergence of new gene families. In all multicellular animals except sponges and comb jellies, the genomes contain Hox genes, which are crucial regulators of development. The canonical function of Hox genes involves colinear patterning of body parts in bilateral animals. This general function is implemented through complex, precisely coordinated mechanisms, not all of which are evolutionarily conserved and fully understood. We suggest that the emergence of this regulatory complexity was preceded by a stage of cooperation between more ancient morphogenetic programs or their individual elements. Footprints of these programs may be present in modern animals to execute non-canonical Hox functions. Non-canonical functions of Hox genes are involved in maintaining terminal nerve cell specificity, autophagy, oogenesis, pre-gastrulation embryogenesis, vertical signaling, and a number of general biological processes. These functions are realized by the basic properties of homeodomain protein and could have triggered the evolution of ParaHoxozoa and Nephrozoa subsequently. Some of these non-canonical Hox functions are discussed in our review.
Collapse
Affiliation(s)
- Milana A Kulakova
- Department of Embryology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia.
| | - Georgy P Maslakov
- Department of Embryology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Liudmila O Poliushkevich
- Department of Embryology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| |
Collapse
|
3
|
Mitchell DG, Edgar A, Mateu JR, Ryan JF, Martindale MQ. The ctenophore Mnemiopsis leidyi deploys a rapid injury response dating back to the last common animal ancestor. Commun Biol 2024; 7:203. [PMID: 38374160 PMCID: PMC10876535 DOI: 10.1038/s42003-024-05901-7] [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: 06/29/2023] [Accepted: 02/08/2024] [Indexed: 02/21/2024] Open
Abstract
Regenerative potential is widespread but unevenly distributed across animals. However, our understanding of the molecular mechanisms underlying regenerative processes is limited to a handful of model organisms, restricting robust comparative analyses. Here, we conduct a time course of RNA-seq during whole body regeneration in Mnemiopsis leidyi (Ctenophora) to uncover gene expression changes that correspond with key events during the regenerative timeline of this species. We identified several genes highly enriched in this dataset beginning as early as 10 minutes after surgical bisection including transcription factors in the early timepoints, peptidases in the middle timepoints, and cytoskeletal genes in the later timepoints. We validated the expression of early response transcription factors by whole mount in situ hybridization, showing that these genes exhibited high expression in tissues surrounding the wound site. These genes exhibit a pattern of transient upregulation as seen in a variety of other organisms, suggesting that they may be initiators of an ancient gene regulatory network linking wound healing to the initiation of a regenerative response.
Collapse
Affiliation(s)
- Dorothy G Mitchell
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Allison Edgar
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
| | - Júlia Ramon Mateu
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA.
- Department of Biology, University of Florida, Gainesville, FL, USA.
| |
Collapse
|
4
|
Travert M, Boohar R, Sanders SM, Boosten M, Leclère L, Steele RE, Cartwright P. Coevolution of the Tlx homeobox gene with medusa development (Cnidaria: Medusozoa). Commun Biol 2023; 6:709. [PMID: 37433830 DOI: 10.1038/s42003-023-05077-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/27/2023] [Indexed: 07/13/2023] Open
Abstract
Cnidarians display a wide diversity of life cycles. Among the main cnidarian clades, only Medusozoa possesses a swimming life cycle stage called the medusa, alternating with a benthic polyp stage. The medusa stage was repeatedly lost during medusozoan evolution, notably in the most diverse medusozoan class, Hydrozoa. Here, we show that the presence of the homeobox gene Tlx in Cnidaria is correlated with the presence of the medusa stage, the gene having been lost in clades that ancestrally lack a medusa (anthozoans, endocnidozoans) and in medusozoans that secondarily lost the medusa stage. Our characterization of Tlx expression indicate an upregulation of Tlx during medusa development in three distantly related medusozoans, and spatially restricted expression patterns in developing medusae in two distantly related species, the hydrozoan Podocoryna carnea and the scyphozoan Pelagia noctiluca. These results suggest that Tlx plays a key role in medusa development and that the loss of this gene is likely linked to the repeated loss of the medusa life cycle stage in the evolution of Hydrozoa.
Collapse
Affiliation(s)
- Matthew Travert
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.
| | - Reed Boohar
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | - Steven M Sanders
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Manon Boosten
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Villefranche-sur-Mer, France
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | - Lucas Leclère
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Villefranche-sur-Mer, France
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Banyuls-sur-Mer, France
| | - Robert E Steele
- Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Paulyn Cartwright
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| |
Collapse
|
5
|
Cocci P, Mosconi G, Palermo FA. Effect of polycyclic aromatic hydrocarbons on homeobox gene expression during embryonic development of cuttlefish, Sepia officinalis. CHEMOSPHERE 2023; 325:138315. [PMID: 36889469 DOI: 10.1016/j.chemosphere.2023.138315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/24/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are persistent organic pollutants (POPs) commonly found in marine environments. Their bioaccumulation can cause harm to aquatic organisms, including invertebrates, particularly during the early stages of embryonic development. In this study, we evaluated, for the first time, the patterns of PAH accumulation in both capsule and embryo of common cuttlefish (Sepia officinalis). In addition, we explored the effects of PAHs by analysing the expression profiles of seven homeobox genes [i.e., gastrulation brain homeobox (GBX), paralogy group labial/Hox1 (HOX1), paralogy group Hox3 (HOX3), dorsal root ganglia homeobox (DRGX), visual system homeobox (VSX), aristaless-like homeobox (ARX) and LIM-homeodomain transcription factor (LHX3/4)]. We found that PAH levels in egg capsules were higher than those observed in chorion membranes (35.1 ± 13.3 ng/g vs 16.4 ± 5.9 ng/g). Furthermore, PAHs were also found in perivitellin fluid (11.5 ± 5.0 ng/ml). Naphthalene and acenaphthene were the congeners present at highest concentrations in each analysed egg component suggesting higher bioaccumulation rates. Embryos with high concentrations of PAHs also showed a significant increase in mRNA expression for each of the analysed homeobox genes. In particular, we observed a 15-fold increase in the ARX expression levels. Additionally, the statistically significant variation in homeobox gene expression patterns was accompanied by a concomitant increase in mRNA levels of both aryl hydrocarbon receptor (AhR) and estrogen receptor (ER). These findings suggest that bioaccumulation of PAHs may modulate developmental processes of cuttlefish embryos by targeting homeobox gene-mediated transcriptional outcomes. Mechanisms underlying the upregulation of homeobox genes could be related to the ability of PAHs to directly activate AhR- or ER-related signaling pathways.
Collapse
Affiliation(s)
- Paolo Cocci
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III Da Varano, I-62032, Camerino, MC, Italy
| | - Gilberto Mosconi
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III Da Varano, I-62032, Camerino, MC, Italy
| | - Francesco Alessandro Palermo
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III Da Varano, I-62032, Camerino, MC, Italy.
| |
Collapse
|
6
|
Puzakov MV, Puzakova LV, Ulupova YN. Differential Activity of Genes with IS630/TC1/MARINER Transposon Fragments in the Genome of the Ctenophore Mnemiopsis leidyi. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2022. [DOI: 10.3103/s089141682204005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2023]
|
7
|
Hayakawa E, Guzman C, Horiguchi O, Kawano C, Shiraishi A, Mohri K, Lin MF, Nakamura R, Nakamura R, Kawai E, Komoto S, Jokura K, Shiba K, Shigenobu S, Satake H, Inaba K, Watanabe H. Mass spectrometry of short peptides reveals common features of metazoan peptidergic neurons. Nat Ecol Evol 2022; 6:1438-1448. [PMID: 35941202 PMCID: PMC9525235 DOI: 10.1038/s41559-022-01835-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 06/21/2022] [Indexed: 12/21/2022]
Abstract
The evolutionary origins of neurons remain unknown. Although recent genome data of extant early-branching animals have shown that neural genes existed in the common ancestor of animals, the physiological and genetic properties of neurons in the early evolutionary phase are still unclear. Here, we performed a mass spectrometry-based comprehensive survey of short peptides from early-branching lineages Cnidaria, Porifera and Ctenophora. We identified a number of mature ctenophore neuropeptides that are expressed in neurons associated with sensory, muscular and digestive systems. The ctenophore peptides are stored in vesicles in cell bodies and neurites, suggesting volume transmission similar to that of cnidarian and bilaterian peptidergic systems. A comparison of genetic characteristics revealed that the peptide-expressing cells of Cnidaria and Ctenophora express the vast majority of genes that have pivotal roles in maturation, secretion and degradation of neuropeptides in Bilateria. Functional analysis of neuropeptides and prediction of receptors with machine learning demonstrated peptide regulation of a wide range of target effector cells, including cells of muscular systems. The striking parallels between the peptidergic neuronal properties of Cnidaria and Bilateria and those of Ctenophora, the most basal neuron-bearing animals, suggest a common evolutionary origin of metazoan peptidergic nervous systems.
Collapse
Affiliation(s)
- Eisuke Hayakawa
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
| | - Christine Guzman
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Osamu Horiguchi
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Chihiro Kawano
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Akira Shiraishi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Kurato Mohri
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Mei-Fang Lin
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- College of Marine Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Ryotaro Nakamura
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Ryo Nakamura
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Erina Kawai
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Shinya Komoto
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Imaging Section, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Kei Jokura
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Kogiku Shiba
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
| | - Shuji Shigenobu
- Center for the Development of New Model Organisms, National Institute for Basic Biology, Okazaki, Japan
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Kazuo Inaba
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
| | - Hiroshi Watanabe
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
| |
Collapse
|
8
|
Nazar AP, Delgado MJ, Lavore A. Empty-spiracles is maternally expressed and essential for neurodevelopment and early embryo determination in Rhodnius prolixus. Dev Biol 2022; 490:144-154. [PMID: 35988717 DOI: 10.1016/j.ydbio.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/10/2022] [Accepted: 08/04/2022] [Indexed: 11/03/2022]
Abstract
Since empty-spiracles (ems) was identified and characterized in Drosophila melanogaster as a head-gap gene, several studies have been carried out in other insect orders to confirm its evolutionary conserved function. Using the blood-sucking bug Rhodnius prolixus as biological model, we found an ems transcript with three highly conserved regions: Box-A, Box-B, and the homeodomain. R. prolixus embryos silenced by parental RNAi for two of these ems conserved regions showed both maternal and zygotic defects. Rp-emsB fragment results in early lethal embryogenesis, with eggs without any embryonic structure inside. Rp-emsB expression pattern is only maternally expressed and localized in the ovary tropharium, follicular cells, and in the unfertilized female pronucleus. Rp-emsA fragment is zygotically expressed during early blastoderm formation until late developmental stages in two main patterns: anterior in the antennal segment, and in a segmentary in the neuroblast and tracheal pits. R. prolixus knockdown embryos for Rp-emsA showed an incomplete larval hatching, reduced heads, and severe neuromotor defects. Furthermore, in situ hybridization revealed a spatial and temporal expression pattern that highly correlates with Rp-ems observed function. Here,Rp-ems function in R. prolixus development was validated, showing that empty-spiracles does not act as a true head-gap gene, but it is necessary for proper head development and crucial for early embryo determination and neurodevelopment.
Collapse
Affiliation(s)
- Ada Paula Nazar
- Hospital Interzonal de Agudos "San José" de Pergamino, Argentina.
| | - María José Delgado
- Centro de Bioinvestigaciones (CeBio) and Centro de Investigación y Transferencia del Noroeste de Buenos Aires (CITNOBA-CONICET), Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Pergamino, Argentina.
| | - Andrés Lavore
- Centro de Bioinvestigaciones (CeBio) and Centro de Investigación y Transferencia del Noroeste de Buenos Aires (CITNOBA-CONICET), Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Pergamino, Argentina.
| |
Collapse
|
9
|
Multigenerational laboratory culture of pelagic ctenophores and CRISPR-Cas9 genome editing in the lobate Mnemiopsis leidyi. Nat Protoc 2022; 17:1868-1900. [PMID: 35697825 DOI: 10.1038/s41596-022-00702-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 03/23/2022] [Indexed: 11/08/2022]
Abstract
Despite long-standing experimental interest in ctenophores due to their unique biology, ecological influence and evolutionary status, previous work has largely been constrained by the periodic seasonal availability of wild-caught animals and difficulty in reliably closing the life cycle. To address this problem, we have developed straightforward protocols that can be easily implemented to establish long-term multigenerational cultures for biological experimentation in the laboratory. In this protocol, we describe the continuous culture of the Atlantic lobate ctenophore Mnemiopsis leidyi. A rapid 3-week egg-to-egg generation time makes Mnemiopsis suitable for a wide range of experimental genetic, cellular, embryological, physiological, developmental, ecological and evolutionary studies. We provide recommendations for general husbandry to close the life cycle of Mnemiopsis in the laboratory, including feeding requirements, light-induced spawning, collection of embryos and rearing of juveniles to adults. These protocols have been successfully applied to maintain long-term multigenerational cultures of several species of pelagic ctenophores, and can be utilized by laboratories lacking easy access to the ocean. We also provide protocols for targeted genome editing via microinjection with CRISPR-Cas9 that can be completed within ~2 weeks, including single-guide RNA synthesis, early embryo microinjection, phenotype assessment and sequence validation of genome edits. These protocols provide a foundation for using Mnemiopsis as a model organism for functional genomic analyses in ctenophores.
Collapse
|
10
|
Martindale MQ. Emerging models: The "development" of the ctenophore Mnemiopsis leidyi and the cnidarian Nematostella vectensis as useful experimental models. Curr Top Dev Biol 2022; 147:93-120. [PMID: 35337468 DOI: 10.1016/bs.ctdb.2022.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The goal of this chapter is to explain the reasoning for developing two understudied invertebrate animal species for asking specific biological questions. The first is the ctenophore (comb jelly) Mnemiopsis leidyi and the second is the anthozoan cnidarian (starlet sea anemone) Nematostella vectensis. Although these two taxa belong to some of the earliest branching extant metazoan clades, their developmental features could hardly be more different from one another. This should serve as a general warning to be careful when extrapolating comparisons of one species to another. Two-taxon comparisons are especially flawed; and to interpret features in a phylogenetic context one must sample carefully within a given taxon to determine how representative certain features are before comparing with other clades. The other benefit of this comparison is to identify key practical factors when attempting to develop new species for experimental investigation.
Collapse
Affiliation(s)
- Mark Q Martindale
- Whitney Lab for Marine Bioscience, University of Florida, St. Augustine, FL, United States.
| |
Collapse
|
11
|
Puzakov MV, Puzakova LV, Cheresiz SV, Sang Y. The IS630/Tc1/mariner transposons in three ctenophore genomes. Mol Phylogenet Evol 2021; 163:107231. [PMID: 34133948 DOI: 10.1016/j.ympev.2021.107231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/31/2021] [Accepted: 06/11/2021] [Indexed: 10/21/2022]
Abstract
Transposable elements (TEs) exert a significant effect on the structure and functioning of the genomes and also serve as a source of the new genes. The study of the TE diversity and evolution in different taxa is indispensable for the fundamental understanding of their roles in the genomes. IS630/Tc1/mariner (ITm) transposable elements represent the most prevalent and diverse group of DNA transposons. In this work, we studied the diversity, evolutionary dynamics and the phylogenetic relationships of the ITm transposons found in three ctenophore species: Mnemiopsis leidyi, Pleurobrachia bachei, Beroe ovata. We identified 29 ITm transposons, seven of which possess the terminal inverted repeats (TIRs) and an intact transposase, and, thus, are, presumably, active. Four other ITm transposons have the features of domesticated TEs. According to the results of the phylogenetic analysis, the ITm transposons of the ctenophores represent five groups - MLE/DD34D, TLE/DD34-38E, mosquito/DD37E, Visiror/DD41D and pogo/DDxD. Pogo/DDxD superfamily turnes out to be the most diverse and prevalent, since it accounts for more than 40% of the TEs identified. The data obtained in this research will fill the gap of knowledge of the diversity and evolution of the ITm transposons in the multicellular genomes and will lay the ground for the study of the TE effects on the evolution of the ctenophores.
Collapse
Affiliation(s)
- Mikhail V Puzakov
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Nakhimov av., 2, Sevastopol 299011, Russia.
| | - Ludmila V Puzakova
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Nakhimov av., 2, Sevastopol 299011, Russia
| | - Sergey V Cheresiz
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogova st., 1, Novosibirsk 630090, Russia; State Scientific Research Institute of Physiology and Basic Medicine, P.O. Box 237, Novosibirsk 630117, Russia
| | - Yatong Sang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| |
Collapse
|
12
|
Moreland RT, Nguyen AD, Ryan JF, Baxevanis AD. The Mnemiopsis Genome Project Portal: integrating new gene expression resources and improving data visualization. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5834871. [PMID: 32386298 DOI: 10.1093/database/baaa029] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 03/22/2020] [Indexed: 11/13/2022]
Abstract
Following the completion of the genome sequencing and gene prediction of Mnemiopsis leidyi, a lobate ctenophore that is native to the coastal waters of the western Atlantic Ocean, we developed and implemented the Mnemiopsis Genome Project Portal (MGP Portal), a comprehensive Web-based data portal for navigating the genome sequence and gene annotations. In the years following the first release of the MGP Portal, it has become evident that the inclusion of data from significant published studies on Mnemiopsis has been critical to its adoption as the centralized resource for this emerging model organism. With this most recent update, the Portal has significantly expanded to include in situ images, temporal developmental expression profiles and single-cell expression data. Recent enhancements also include implementations of an updated BLAST interface, new graphical visualization tools and updates to gene pages that integrate all new data types. Database URL: https://research.nhgri.nih.gov/mnemiopsis/.
Collapse
Affiliation(s)
- R Travis Moreland
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anh-Dao Nguyen
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA.,Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Andreas D Baxevanis
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| |
Collapse
|
13
|
Brunet T, Larson BT, Linden TA, Vermeij MJA, McDonald K, King N. Light-regulated collective contractility in a multicellular choanoflagellate. Science 2020; 366:326-334. [PMID: 31624206 DOI: 10.1126/science.aay2346] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 09/16/2019] [Indexed: 12/11/2022]
Abstract
Collective cell contractions that generate global tissue deformations are a signature feature of animal movement and morphogenesis. However, the origin of collective contractility in animals remains unclear. While surveying the Caribbean island of Curaçao for choanoflagellates, the closest living relatives of animals, we isolated a previously undescribed species (here named Choanoeca flexa sp. nov.) that forms multicellular cup-shaped colonies. The colonies rapidly invert their curvature in response to changing light levels, which they detect through a rhodopsin-cyclic guanosine monophosphate pathway. Inversion requires actomyosin-mediated apical contractility and allows alternation between feeding and swimming behavior. C. flexa thus rapidly converts sensory inputs directly into multicellular contractions. These findings may inform reconstructions of hypothesized animal ancestors that existed before the evolution of specialized sensory and contractile cells.
Collapse
Affiliation(s)
- Thibaut Brunet
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Ben T Larson
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,Biophysics Graduate Group, University of California, Berkeley, CA, USA
| | - Tess A Linden
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Mark J A Vermeij
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, CARMABI, Piscaderabaai z/n Willemstad, Curaçao
| | - Kent McDonald
- Electron Microscopy Laboratory, University of California, Berkeley, CA, USA
| | - Nicole King
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
| |
Collapse
|
14
|
Reddy PC, Gungi A, Ubhe S, Pradhan SJ, Kolte A, Galande S. Molecular signature of an ancient organizer regulated by Wnt/β-catenin signalling during primary body axis patterning in Hydra. Commun Biol 2019; 2:434. [PMID: 31799436 PMCID: PMC6879750 DOI: 10.1038/s42003-019-0680-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 11/06/2019] [Indexed: 11/20/2022] Open
Abstract
Wnt/β-catenin signalling has been shown to play a critical role during head organizer formation in Hydra. Here, we characterized the Wnt signalling regulatory network involved in formation of the head organizer. We found that Wnt signalling regulates genes that are important in tissue morphogenesis. We identified that majority of transcription factors (TFs) regulated by Wnt/β-catenin signalling belong to the homeodomain and forkhead families. Silencing of Margin, one of the Wnt regulated homeodomain TFs, results in loss of the ectopic tentacle phenotype typically seen upon activation of Wnt signalling. Furthermore, we show that the Margin promoter is directly bound and regulated by β-catenin. Ectopic expression of Margin in zebrafish embryos results in body axis abnormalities suggesting that Margin plays a role in axis patterning. Our findings suggest that homeobox TFs came under the regulatory umbrella of Wnt/β-catenin signalling presumably resulting in the evolution of primary body axis in animal phyla.
Collapse
Affiliation(s)
- Puli Chandramouli Reddy
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, 411008 India
| | - Akhila Gungi
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, 411008 India
| | - Suyog Ubhe
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, 411008 India
| | - Saurabh J. Pradhan
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, 411008 India
| | - Amol Kolte
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, 411008 India
| | - Sanjeev Galande
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, 411008 India
| |
Collapse
|
15
|
Martín-Durán JM, Hejnol A. A developmental perspective on the evolution of the nervous system. Dev Biol 2019; 475:181-192. [PMID: 31610146 DOI: 10.1016/j.ydbio.2019.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 06/02/2018] [Accepted: 10/04/2019] [Indexed: 12/20/2022]
Abstract
The evolution of nervous systems in animals has always fascinated biologists, and thus multiple evolutionary scenarios have been proposed to explain the appearance of neurons and complex neuronal centers. However, the absence of a robust phylogenetic framework for animal interrelationships, the lack of a mechanistic understanding of development, and a recapitulative view of animal ontogeny have traditionally limited these scenarios. Only recently, the integration of advanced molecular and morphological studies in a broad range of animals has allowed to trace the evolution of developmental and neuronal characters on a better-resolved animal phylogeny. This has falsified most traditional scenarios for nervous system evolution, paving the way for the emergence of new testable hypotheses. Here we summarize recent progress in studies of nervous system development in major animal lineages and formulate some of the arising questions. In particular, we focus on how lineage analyses of nervous system development and a comparative study of the expression of neural-related genes has influenced our understanding of the evolution of an elaborated central nervous system in Bilateria. We argue that a phylogeny-guided study of neural development combining thorough descriptive and functional analyses is key to establish more robust scenarios for the origin and evolution of animal nervous systems.
Collapse
Affiliation(s)
- José M Martín-Durán
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thørmohlensgate 55, 5006, Bergen, Norway; School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thørmohlensgate 55, 5006, Bergen, Norway.
| |
Collapse
|
16
|
Treffkorn S, Mayer G. Expression of NK genes that are not part of the NK cluster in the onychophoran Euperipatoides rowelli (Peripatopsidae). BMC DEVELOPMENTAL BIOLOGY 2019; 19:7. [PMID: 30987579 PMCID: PMC6466738 DOI: 10.1186/s12861-019-0185-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 03/12/2019] [Indexed: 12/25/2022]
Abstract
Background NK genes are a group of homeobox transcription factors that are involved in various molecular pathways across bilaterians. They are typically divided into two subgroups, the NK cluster (NKC) and NK-linked genes (NKL). While the NKC genes have been studied in various bilaterians, corresponding data of many NKL genes are missing to date. To further investigate the ancestral roles of NK family genes, we analyzed the expression patterns of NKL genes in the onychophoran Euperipatoides rowelli. Results The NKL gene complement of E. rowelli comprises eight genes, including BarH, Bari, Emx, Hhex, Nedx, NK2.1, vax and NK2.2, of which only NK2.2 was studied previously. Our data for the remaining seven NKL genes revealed expression in different structures associated with the developing nervous system in embryos of E. rowelli. While NK2.1 and vax are expressed in distinct medial regions of the developing protocerebrum early in development, BarH, Bari, Emx, Hhex and Nedx are expressed in late developmental stages, after all major structures of the nervous system have been established. Furthermore, BarH and Nedx are expressed in distinct mesodermal domains in the developing limbs. Conclusions Comparison of our expression data to those of other bilaterians revealed similar patterns of NK2.1, vax, BarH and Emx in various aspects of neural development, such as the formation of anterior neurosecretory cells mediated by a conserved molecular mechanism including NK2.1 and vax, and the development of the central and peripheral nervous system involving BarH and Emx. A conserved role in neural development has also been reported from NK2.2, suggesting that the NKL genes might have been primarily involved in neural development in the last common ancestor of bilaterians or at least nephrozoans (all bilaterians excluding xenacoelomorphs). The lack of comparative data for many of the remaining NKL genes, including Bari, Hhex and Nedx currently hampers further evolutionary conclusions. Hence, future studies should focus on the expression of these genes in other bilaterians, which would provide a basis for comparative studies and might help to better understand the role of NK genes in the diversification of bilaterians. Electronic supplementary material The online version of this article (10.1186/s12861-019-0185-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sandra Treffkorn
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany.
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
| |
Collapse
|
17
|
Babonis LS, DeBiasse MB, Francis WR, Christianson LM, Moss AG, Haddock SHD, Martindale MQ, Ryan JF. Integrating Embryonic Development and Evolutionary History to Characterize Tentacle-Specific Cell Types in a Ctenophore. Mol Biol Evol 2018; 35:2940-2956. [PMID: 30169705 PMCID: PMC6278862 DOI: 10.1093/molbev/msy171] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The origin of novel traits can promote expansion into new niches and drive speciation. Ctenophores (comb jellies) are unified by their possession of a novel cell type: the colloblast, an adhesive cell found only in the tentacles. Although colloblast-laden tentacles are fundamental for prey capture among ctenophores, some species have tentacles lacking colloblasts and others have lost their tentacles completely. We used transcriptomes from 36 ctenophore species to identify gene losses that occurred specifically in lineages lacking colloblasts and tentacles. We cross-referenced these colloblast- and tentacle-specific candidate genes with temporal RNA-Seq during embryogenesis in Mnemiopsis leidyi and found that both sets of candidates are preferentially expressed during tentacle morphogenesis. We also demonstrate significant upregulation of candidates from both data sets in the tentacle bulb of adults. Both sets of candidates were enriched for an N-terminal signal peptide and protein domains associated with secretion; among tentacle candidates we also identified orthologs of cnidarian toxin proteins, presenting tantalizing evidence that ctenophore tentacles may secrete toxins along with their adhesive. Finally, using cell lineage tracing, we demonstrate that colloblasts and neurons share a common progenitor, suggesting the evolution of colloblasts involved co-option of a neurosecretory gene regulatory network. Together these data offer an initial glimpse into the genetic architecture underlying ctenophore cell-type diversity.
Collapse
Affiliation(s)
- Leslie S Babonis
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL
| | - Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL
| | - Warren R Francis
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA
| | | | - Anthony G Moss
- Department of Biological Sciences, Auburn University, Auburn, AL
| | | | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL
| |
Collapse
|
18
|
Abstract
A complex genetic repertoire underlies the apparently simple body plan of sponges. Among the genes present in poriferans are those fundamental to the sensory and nervous systems of other animals. Sponges are dynamic and sensitive animals and it is intuitive to link these genes to behaviour. The proposal that ctenophores are the earliest diverging metazoan has led to the question of whether sponges possess a 'pre-nervous' system or have undergone nervous system loss. Both lines of thought generally assume that the last common ancestor of sponges and eumetazoans possessed the genetic modules that underlie sensory abilities. By corollary extant sponges may possess a sensory cell homologous to one present in the last common ancestor, a hypothesis that has been studied by gene expression. We have performed a meta-analysis of all gene expression studies published to date to explore whether gene expression is indicative of a feature's sensory function. In sponges we find that eumetazoan sensory-neural markers are not particularly expressed in structures with known sensory functions. Instead it is common for these genes to be expressed in cells with no known or uncharacterized sensory function. Indeed, many sensory-neural markers so far studied are expressed during development, perhaps because many are transcription factors. This suggests that the genetic signal of a sponge sensory cell is dissimilar enough to be unrecognizable when compared to a bilaterian sensory or neural cell. It is possible that sensory-neural markers have as yet unknown functions in sponge cells, such as assembling an immunological synapse in the larval globular cell. Furthermore, the expression of sensory-neural markers in non-sensory cells, such as adult and larval epithelial cells, suggest that these cells may have uncharacterized sensory functions. While this does not rule out the co-option of ancestral sensory modules in later evolving groups, a distinct genetic foundation may underlie the sponge sensory system.
Collapse
Affiliation(s)
- Jasmine L Mah
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Sally P Leys
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
| |
Collapse
|
19
|
Gendrel M, Atlas EG, Hobert O. A cellular and regulatory map of the GABAergic nervous system of C. elegans. eLife 2016; 5. [PMID: 27740909 PMCID: PMC5065314 DOI: 10.7554/elife.17686] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/22/2016] [Indexed: 12/16/2022] Open
Abstract
Neurotransmitter maps are important complements to anatomical maps and represent an invaluable resource to understand nervous system function and development. We report here a comprehensive map of neurons in the C. elegans nervous system that contain the neurotransmitter GABA, revealing twice as many GABA-positive neuron classes as previously reported. We define previously unknown glia-like cells that take up GABA, as well as 'GABA uptake neurons' which do not synthesize GABA but take it up from the extracellular environment, and we map the expression of previously uncharacterized ionotropic GABA receptors. We use the map of GABA-positive neurons for a comprehensive analysis of transcriptional regulators that define the GABA phenotype. We synthesize our findings of specification of GABAergic neurons with previous reports on the specification of glutamatergic and cholinergic neurons into a nervous system-wide regulatory map which defines neurotransmitter specification mechanisms for more than half of all neuron classes in C. elegans. DOI:http://dx.doi.org/10.7554/eLife.17686.001
Collapse
Affiliation(s)
- Marie Gendrel
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, United States
| | - Emily G Atlas
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, United States
| | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, United States
| |
Collapse
|
20
|
Ctenophores: an evolutionary-developmental perspective. Curr Opin Genet Dev 2016; 39:85-92. [PMID: 27351593 DOI: 10.1016/j.gde.2016.05.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 05/04/2016] [Accepted: 05/30/2016] [Indexed: 11/22/2022]
Abstract
Ctenophores are non-bilaterian metazoans of uncertain phylogenetic position, some recent studies placing them as sister-group to all other animals whereas others suggest this placement is artefactual and ctenophores are more closely allied with cnidarians and bilaterians, with which they share nerve cells, muscles and gut. Available information about developmental genes and their expression and function in ctenophores is reviewed. These data not only unveil some conserved aspects of molecular developmental mechanisms with other basal metazoan lineages, but also can be expected to enlighten the genomic and molecular bases of the evolution of ctenophore-specific traits, including their unique embryonic development, complex anatomy and high cell type diversity.
Collapse
|
21
|
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
|
22
|
The hidden biology of sponges and ctenophores. Trends Ecol Evol 2015; 30:282-91. [DOI: 10.1016/j.tree.2015.03.003] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 02/27/2015] [Accepted: 03/02/2015] [Indexed: 12/21/2022]
|
23
|
Exploring the potential of small RNA subunit and ITS sequences for resolving phylogenetic relationships within the phylum Ctenophora. ZOOLOGY 2015; 118:102-14. [DOI: 10.1016/j.zool.2014.06.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 06/13/2014] [Accepted: 06/17/2014] [Indexed: 11/17/2022]
|
24
|
Focareta L, Sesso S, Cole AG. Characterization of homeobox genes reveals sophisticated regionalization of the central nervous system in the European cuttlefish Sepia officinalis. PLoS One 2014; 9:e109627. [PMID: 25286399 PMCID: PMC4186843 DOI: 10.1371/journal.pone.0109627] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 09/11/2014] [Indexed: 01/21/2023] Open
Abstract
Cephalopod mollusks possess a number of anatomical traits that often parallel vertebrates in morphological complexity, including a centralized nervous system with sophisticated cognitive functionality. Very little is known about the genetic mechanisms underlying patterning of the cephalopod embryo to arrive at this anatomical structure. Homeodomain (HD) genes are transcription factors that regulate transcription of downstream genes through DNA binding, and as such are integral parts of gene regulatory networks controlling the specification and patterning of body parts across lineages. We have used a degenerate primer strategy to isolate homeobox genes active during late-organogenesis from the European cuttlefish Sepia officinalis. With this approach we have isolated fourteen HD gene fragments and examine the expression profiles of five of these genes during late stage (E24-28) embryonic development (Sof-Gbx, Sof-Hox3, Sof-Arx, Sof-Lhx3/4, Sof-Vsx). All five genes are expressed within the developing central nervous system in spatially restricted and largely non-overlapping domains. Our data provide a first glimpse into the diversity of HD genes in one of the largest, yet least studied, metazoan clades and illustrate how HD gene expression patterns reflect the functional partitioning of the cephalopod brain.
Collapse
|
25
|
Expression pattern of empty-spiracles, a conserved head-patterning gene, in honeybee (Apis mellifera) embryos. Gene Expr Patterns 2014; 15:142-8. [PMID: 24999162 DOI: 10.1016/j.gep.2014.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 06/19/2014] [Accepted: 06/20/2014] [Indexed: 11/21/2022]
|
26
|
Jager M, Dayraud C, Mialot A, Quéinnec E, le Guyader H, Manuel M. Evidence for involvement of Wnt signalling in body polarities, cell proliferation, and the neuro-sensory system in an adult ctenophore. PLoS One 2013; 8:e84363. [PMID: 24391946 PMCID: PMC3877318 DOI: 10.1371/journal.pone.0084363] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 11/22/2013] [Indexed: 11/19/2022] Open
Abstract
Signalling through the Wnt family of secreted proteins originated in a common metazoan ancestor and greatly influenced the evolution of animal body plans. In bilaterians, Wnt signalling plays multiple fundamental roles during embryonic development and in adult tissues, notably in axial patterning, neural development and stem cell regulation. Studies in various cnidarian species have particularly highlighted the evolutionarily conserved role of the Wnt/β-catenin pathway in specification and patterning of the primary embryonic axis. However in another key non-bilaterian phylum, Ctenophora, Wnts are not involved in early establishment of the body axis during embryogenesis. We analysed the expression in the adult of the ctenophore Pleurobrachia pileus of 11 orthologues of Wnt signalling genes including all ctenophore Wnt ligands and Fz receptors and several members of the intracellular β-catenin pathway machinery. All genes are strongly expressed around the mouth margin at the oral pole, evoking the Wnt oral centre of cnidarians. This observation is consistent with primary axis polarisation by the Wnts being a universal metazoan feature, secondarily lost in ctenophores during early development but retained in the adult. In addition, local expression of Wnt signalling genes was seen in various anatomical structures of the body including in the locomotory comb rows, where their complex deployment suggests control by the Wnts of local comb polarity. Other important contexts of Wnt involvement which probably evolved before the ctenophore/cnidarian/bilaterian split include proliferating stem cells and progenitors irrespective of cell types, and developing as well as differentiated neuro-sensory structures.
Collapse
Affiliation(s)
- Muriel Jager
- Systématique, Adaptation, Evolution, Unité Mixte de Recherche (UMR) 7138 CNRS (Centre National de la Recherche Scientifique), Université Pierre et Marie Curie – Paris 6, Paris, France
| | - Cyrielle Dayraud
- Systématique, Adaptation, Evolution, Unité Mixte de Recherche (UMR) 7138 CNRS (Centre National de la Recherche Scientifique), Université Pierre et Marie Curie – Paris 6, Paris, France
| | - Antoine Mialot
- Systématique, Adaptation, Evolution, Unité Mixte de Recherche (UMR) 7138 CNRS (Centre National de la Recherche Scientifique), Université Pierre et Marie Curie – Paris 6, Paris, France
| | - Eric Quéinnec
- Systématique, Adaptation, Evolution, Unité Mixte de Recherche (UMR) 7138 CNRS (Centre National de la Recherche Scientifique), Université Pierre et Marie Curie – Paris 6, Paris, France
| | - Hervé le Guyader
- Systématique, Adaptation, Evolution, Unité Mixte de Recherche (UMR) 7138 CNRS (Centre National de la Recherche Scientifique), Université Pierre et Marie Curie – Paris 6, Paris, France
| | - Michaël Manuel
- Systématique, Adaptation, Evolution, Unité Mixte de Recherche (UMR) 7138 CNRS (Centre National de la Recherche Scientifique), Université Pierre et Marie Curie – Paris 6, Paris, France
| |
Collapse
|
27
|
Ryan JF, Pang K, Schnitzler CE, Nguyen AD, Moreland RT, Simmons DK, Koch BJ, Francis WR, Havlak P, Smith SA, Putnam NH, Haddock SHD, Dunn CW, Wolfsberg TG, Mullikin JC, Martindale MQ, Baxevanis AD. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 2013; 342:1242592. [PMID: 24337300 DOI: 10.1126/science.1242592] [Citation(s) in RCA: 457] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
An understanding of ctenophore biology is critical for reconstructing events that occurred early in animal evolution. Toward this goal, we have sequenced, assembled, and annotated the genome of the ctenophore Mnemiopsis leidyi. Our phylogenomic analyses of both amino acid positions and gene content suggest that ctenophores rather than sponges are the sister lineage to all other animals. Mnemiopsis lacks many of the genes found in bilaterian mesodermal cell types, suggesting that these cell types evolved independently. The set of neural genes in Mnemiopsis is similar to that of sponges, indicating that sponges may have lost a nervous system. These results present a newly supported view of early animal evolution that accounts for major losses and/or gains of sophisticated cell types, including nerve and muscle cells.
Collapse
Affiliation(s)
- Joseph F Ryan
- Genome Technology Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Yasui K, Reimer JD, Liu Y, Yao X, Kubo D, Shu D, Li Y. A diploblastic radiate animal at the dawn of cambrian diversification with a simple body plan: distinct from Cnidaria? PLoS One 2013; 8:e65890. [PMID: 23840375 PMCID: PMC3688687 DOI: 10.1371/journal.pone.0065890] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 04/28/2013] [Indexed: 12/03/2022] Open
Abstract
Background Microfossils of the genus Punctatus include developmental stages such as blastula, gastrula, and hatchlings, and represent the most complete developmental sequence of animals available from the earliest Cambrian. Despite the extremely well-preserved specimens, the evolutionary position of Punctatus has relied only on their conical remains and they have been tentatively assigned to cnidarians. We present a new interpretation of the Punctatus body plan based on the developmental reconstruction aided by recent advances in developmental biology. Results Punctatus developed from a rather large egg, gastrulated in a mode of invagination from a coeloblastura, and then formed a mouth directly from the blastopore. Spiny benthic hatchlings were distinguishable from swimming or crawling ciliate larvae found in cnidarians and sponges. A mouth appeared at the perihatching embryonic stage and was renewed periodically during growth, and old mouths transformed into the body wall, thus elongating the body. Growing animals retained a small blind gut in a large body cavity without partitioning by septa and did not form tentacles, pedal discs or holdfasts externally. A growth center at the oral pole was sufficient for body patterning throughout life, and the body patterning did not show any bias from radial symmetry. Conclusions Contrary to proposed cnidarian affinity, the Punctatus body plan has basic differences from that of cnidarians, especially concerning a spacious body cavity separating ectoderm from endoderm. The lack of many basic cnidarian characters in the body patterning of Punctatus leads us to consider its own taxonomic group, potentially outside of Cnidaria.
Collapse
Affiliation(s)
- Kinya Yasui
- Department of Biological Sciences, Graduate School of Science, Hiroshima University, Higashi-hiroshima, Hiroshima, Japan.
| | | | | | | | | | | | | |
Collapse
|
29
|
Hroudova M, Vojta P, Strnad H, Krejcik Z, Ridl J, Paces J, Vlcek C, Paces V. Diversity, phylogeny and expression patterns of Pou and Six homeodomain transcription factors in hydrozoan jellyfish Craspedacusta sowerbyi. PLoS One 2012; 7:e36420. [PMID: 22558464 PMCID: PMC3340352 DOI: 10.1371/journal.pone.0036420] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 03/31/2012] [Indexed: 01/10/2023] Open
Abstract
Formation of all metazoan bodies is controlled by a group of selector genes including homeobox genes, highly conserved across the entire animal kingdom. The homeobox genes from Pou and Six classes are key members of the regulation cascades determining development of sensory organs, nervous system, gonads and muscles. Besides using common bilaterian models, more attention has recently been targeted at the identification and characterization of these genes within the basal metazoan phyla. Cnidaria as a diploblastic sister group to bilateria with simple and yet specialized organs are suitable models for studies on the sensory organ origin and the associated role of homeobox genes. In this work, Pou and Six homeobox genes, together with a broad range of other sensory-specific transcription factors, were identified in the transcriptome of hydrozoan jellyfish Craspedacusta sowerbyi. Phylogenetic analyses of Pou and Six proteins revealed cnidarian-specific sequence motifs and contributed to the classification of individual factors. The majority of the Craspedacusta sowerbyi Pou and Six homeobox genes are predominantly expressed in statocysts, manubrium and nerve ring, the tissues with sensory and nervous activities. The described diversity and expression patterns of Pou and Six factors in hydrozoan jellyfish highlight their evolutionarily conserved functions. This study extends the knowledge of the cnidarian genome complexity and shows that the transcriptome of hydrozoan jellyfish is generally rich in homeodomain transcription factors employed in the regulation of sensory and nervous functions.
Collapse
Affiliation(s)
- Miluse Hroudova
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Simmons DK, Pang K, Martindale MQ. Lim homeobox genes in the Ctenophore Mnemiopsis leidyi: the evolution of neural cell type specification. EvoDevo 2012; 3:2. [PMID: 22239757 PMCID: PMC3283466 DOI: 10.1186/2041-9139-3-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 01/13/2012] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Nervous systems are thought to be important to the evolutionary success and diversification of metazoans, yet little is known about the origin of simple nervous systems at the base of the animal tree. Recent data suggest that ctenophores, a group of macroscopic pelagic marine invertebrates, are the most ancient group of animals that possess a definitive nervous system consisting of a distributed nerve net and an apical statocyst. This study reports on details of the evolution of the neural cell type specifying transcription factor family of LIM homeobox containing genes (Lhx), which have highly conserved functions in neural specification in bilaterian animals. RESULTS Using next generation sequencing, the first draft of the genome of the ctenophore Mnemiopsis leidyi has been generated. The Lhx genes in all animals are represented by seven subfamilies (Lhx1/5, Lhx3/4, Lmx, Islet, Lhx2/9, Lhx6/8, and LMO) of which four were found to be represented in the ctenophore lineage (Lhx1/5, Lhx3/4, Lmx, and Islet). Interestingly, the ctenophore Lhx gene complement is more similar to the sponge complement (sponges do not possess neurons) than to either the cnidarian-bilaterian or placozoan Lhx complements. Using whole mount in situ hybridization, the Lhx gene expression patterns were examined and found to be expressed around the blastopore and in cells that give rise to the apical organ and putative neural sensory cells. CONCLUSION This research gives us a first look at neural cell type specification in the ctenophore M. leidyi. Within M. leidyi, Lhx genes are expressed in overlapping domains within proposed neural cellular and sensory cell territories. These data suggest that Lhx genes likely played a conserved role in the patterning of sensory cells in the ancestor of sponges and ctenophores, and may provide a link to the expression of Lhx orthologs in sponge larval photoreceptive cells. Lhx genes were later co-opted into patterning more diversified complements of neural and non-neural cell types in later evolving animals.
Collapse
Affiliation(s)
- David K Simmons
- Kewalo Marine Laboratory, Department of Zoology, University of Hawaii at Manoa, Honolulu, HI, USA, 96813
| | - Kevin Pang
- Sars, International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway
| | - Mark Q Martindale
- Kewalo Marine Laboratory, Department of Zoology, University of Hawaii at Manoa, Honolulu, HI, USA, 96813
| |
Collapse
|
31
|
Renard E, Vacelet J, Gazave E, Lapébie P, Borchiellini C, Ereskovsky AV. Origin of the neuro-sensory system: new and expected insights from sponges. Integr Zool 2011; 4:294-308. [PMID: 21392302 DOI: 10.1111/j.1749-4877.2009.00167.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The capacity of all cells to respond to stimuli implies the conduction of information at least over short distances. In multicellular organisms, more complex systems of integration and coordination of activities are necessary. In most animals, the processing of information is performed by a nervous system. Among the most basal taxa, sponges are nerveless so that it is traditionally assumed that the integrated neuro-sensory system originated only once in Eumetazoa, a hypothesis not in agreement with some recent phylogenomic studies. The aim of this review is to show that recent data on sponges might provide clues for understanding the origin of this complex system. First, sponges are able to react to external stimuli, and some of them display spontaneous movement activities. These coordinated behaviors involve nervous system-like mechanisms, such as action potentials and/or neurotransmitters. Second, genomic analyses show that sponges possess genes orthologous to those involved in the patterning or functioning of the neuro-sensory system in Eumetazoa. Finally, some of these genes are expressed in specific cells (flask cells, choanocytes). Together with ultrastructural data, this gives rise to challenging hypotheses concerning cell types that might play neuro-sensory-like roles in sponges.
Collapse
Affiliation(s)
- Emmanuelle Renard
- Centre d'océanologie de Marseille, CNRS - Aix-Marseille Université, Marseille, France.
| | | | | | | | | | | |
Collapse
|
32
|
Röttinger E, Martindale MQ. Ventralization of an indirect developing hemichordate by NiCl₂ suggests a conserved mechanism of dorso-ventral (D/V) patterning in Ambulacraria (hemichordates and echinoderms). Dev Biol 2011; 354:173-90. [PMID: 21466800 DOI: 10.1016/j.ydbio.2011.03.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 03/07/2011] [Accepted: 03/28/2011] [Indexed: 12/16/2022]
Abstract
One of the earliest steps in embryonic development is the establishment of the future body axes. Morphological and molecular data place the Ambulacraria (echinoderms and hemichordates) within the Deuterostomia and as the sister taxon to chordates. Extensive work over the last decades in echinoid (sea urchins) echinoderms has led to the characterization of gene regulatory networks underlying germ layer specification and axis formation during embryogenesis. However, with the exception of recent studies from a direct developing hemichordate (Saccoglossus kowalevskii), very little is known about the molecular mechanism underlying early hemichordate development. Unlike echinoids, indirect developing hemichordates retain the larval body axes and major larval tissues after metamorphosis into the adult worm. In order to gain insight into dorso-ventral (D/V) patterning, we used nickel chloride (NiCl₂), a potent ventralizing agent on echinoderm embryos, on the indirect developing enteropneust hemichordate, Ptychodera flava. Our present study shows that NiCl₂ disrupts the D/V axis and induces formation of a circumferential mouth when treated before the onset of gastrulation. Molecular analysis, using newly isolated tissue-specific markers, shows that the ventral ectoderm is expanded at expense of dorsal ectoderm in treated embryos, but has little effect on germ layer or anterior-posterior markers. The resulting ventralized phenotype, the effective dose, and the NiCl₂ sensitive response period of Ptychodera flava, is very similar to the effects of nickel on embryonic development described in larval echinoderms. These strong similarities allow one to speculate that a NiCl₂ sensitive pathway involved in dorso-ventral patterning may be shared between echinoderms, hemichordates and a putative ambulacrarian ancestor. Furthermore, nickel treatments ventralize the direct developing hemichordate, S. kowalevskii indicating that a common pathway patterns both larval and adult body plans of the ambulacrarian ancestor and provides insight in to the origin of the chordate body plan.
Collapse
Affiliation(s)
- E Röttinger
- Kewalo Marine Laboratory, PBRC, University of Hawaii, Honolulu, HI, USA
| | | |
Collapse
|
33
|
Reitzel AM, Pang K, Ryan JF, Mullikin JC, Martindale MQ, Baxevanis AD, Tarrant AM. Nuclear receptors from the ctenophore Mnemiopsis leidyi lack a zinc-finger DNA-binding domain: lineage-specific loss or ancestral condition in the emergence of the nuclear receptor superfamily? EvoDevo 2011; 2:3. [PMID: 21291545 PMCID: PMC3038971 DOI: 10.1186/2041-9139-2-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 02/03/2011] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Nuclear receptors (NRs) are an ancient superfamily of metazoan transcription factors that play critical roles in regulation of reproduction, development, and energetic homeostasis. Although the evolutionary relationships among NRs are well-described in two prominent clades of animals (deuterostomes and protostomes), comparatively little information has been reported on the diversity of NRs in early diverging metazoans. Here, we identified NRs from the phylum Ctenophora and used a phylogenomic approach to explore the emergence of the NR superfamily in the animal kingdom. In addition, to gain insight into conserved or novel functions, we examined NR expression during ctenophore development. RESULTS We report the first described NRs from the phylum Ctenophora: two from Mnemiopsis leidyi and one from Pleurobrachia pileus. All ctenophore NRs contained a ligand-binding domain and grouped with NRs from the subfamily NR2A (HNF4). Surprisingly, all the ctenophore NRs lacked the highly conserved DNA-binding domain (DBD). NRs from Mnemiopsis were expressed in different regions of developing ctenophores. One was broadly expressed in the endoderm during gastrulation. The second was initially expressed in the ectoderm during gastrulation, in regions corresponding to the future tentacles; subsequent expression was restricted to the apical organ. Phylogenetic analyses of NRs from ctenophores, sponges, cnidarians, and a placozoan support the hypothesis that expansion of the superfamily occurred in a step-wise fashion, with initial radiations in NR family 2, followed by representatives of NR families 3, 6, and 1/4 originating prior to the appearance of the bilaterian ancestor. CONCLUSIONS Our study provides the first description of NRs from ctenophores, including the full complement from Mnemiopsis. Ctenophores have the least diverse NR complement of any animal phylum with representatives that cluster with only one subfamily (NR2A). Ctenophores and sponges have a similarly restricted NR complement supporting the hypothesis that the original NR was HNF4-like and that these lineages are the first two branches from the animal tree. The absence of a zinc-finger DNA-binding domain in the two ctenophore species suggests two hypotheses: this domain may have been secondarily lost within the ctenophore lineage or, if ctenophores are the first branch off the animal tree, the original NR may have lacked the canonical DBD. Phylogenomic analyses and categorization of NRs from all four early diverging animal phyla compared with the complement from bilaterians suggest the rate of NR diversification prior to the cnidarian-bilaterian split was relatively modest, with independent radiations of several NR subfamilies within the cnidarian lineage.
Collapse
Affiliation(s)
- Adam M Reitzel
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Kevin Pang
- Kewalo Marine Laboratory, Pacific Bioscience Research Center, University of Hawaii, Honolulu, HI, USA
| | - Joseph F Ryan
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - James C Mullikin
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark Q Martindale
- Kewalo Marine Laboratory, Pacific Bioscience Research Center, University of Hawaii, Honolulu, HI, USA
| | - Andreas D Baxevanis
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ann M Tarrant
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| |
Collapse
|
34
|
Developmental expression of COE across the Metazoa supports a conserved role in neuronal cell-type specification and mesodermal development. Dev Genes Evol 2010; 220:221-34. [PMID: 21069538 PMCID: PMC2990012 DOI: 10.1007/s00427-010-0343-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Accepted: 10/19/2010] [Indexed: 10/28/2022]
Abstract
The transcription factor COE (collier/olfactory-1/early B cell factor) is an unusual basic helix-loop-helix transcription factor as it lacks a basic domain and is maintained as a single copy gene in the genomes of all currently analysed non-vertebrate Metazoan genomes. Given the unique features of the COE gene, its proposed ancestral role in the specification of chemosensory neurons and the wealth of functional data from vertebrates and Drosophila, the evolutionary history of the COE gene can be readily investigated. We have examined the ways in which COE expression has diversified among the Metazoa by analysing its expression from representatives of four disparate invertebrate phyla: Ctenophora (Mnemiopsis leidyi); Mollusca (Haliotis asinina); Annelida (Capitella teleta and Chaetopterus) and Echinodermata (Strongylocentrotus purpuratus). In addition, we have studied COE function with knockdown experiments in S. purpuratus, which indicate that COE is likely to be involved in repressing serotonergic cell fate in the apical ganglion of dipleurula larvae. These analyses suggest that COE has played an important role in the evolution of ectodermally derived tissues (likely primarily nervous tissues) and mesodermally derived tissues. Our results provide a broad evolutionary foundation from which further studies aimed at the functional characterisation and evolution of COE can be investigated.
Collapse
|
35
|
Layden MJ, Meyer NP, Pang K, Seaver EC, Martindale MQ. Expression and phylogenetic analysis of the zic gene family in the evolution and development of metazoans. EvoDevo 2010; 1:12. [PMID: 21054859 PMCID: PMC2988786 DOI: 10.1186/2041-9139-1-12] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 11/05/2010] [Indexed: 11/25/2022] Open
Abstract
Background zic genes are members of the gli/glis/nkl/zic super-family of C2H2 zinc finger (ZF) transcription factors. Homologs of the zic family have been implicated in patterning neural and mesodermal tissues in bilaterians. Prior to this study, the origin of the metazoan zic gene family was unknown and expression of zic gene homologs during the development of early branching metazoans had not been investigated. Results Phylogenetic analyses of novel zic candidate genes identified a definitive zic homolog in the placozoan Trichoplax adhaerens, two gli/glis/nkl-like genes in the ctenophore Mnemiopsis leidyi, confirmed the presence of three gli/glis/nkl-like genes in Porifera, and confirmed the five previously identified zic genes in the cnidarian Nematostella vectensis. In the cnidarian N. vectensis, zic homologs are expressed in ectoderm and the gastrodermis (a bifunctional endomesoderm), in presumptive and developing tentacles, and in oral and sensory apical tuft ectoderm. The Capitella teleta zic homolog (Ct-zic) is detectable in a subset of the developing nervous system, the foregut, and the mesoderm associated with the segmentally repeated chaetae. Lastly, expression of gli and glis homologs in Mnemiopsis. leidyi is detected exclusively in neural cells in floor of the apical organ. Conclusions Based on our analyses, we propose that the zic gene family arose in the common ancestor of the Placozoa, Cnidaria and Bilateria from a gli/glis/nkl-like gene and that both ZOC and ZF-NC domains evolved prior to cnidarian-bilaterian divergence. We also conclude that zic expression in neural ectoderm and developing neurons is pervasive throughout the Metazoa and likely evolved from neural expression of an ancestral gli/glis/nkl/zic gene. zic expression in bilaterian mesoderm may be related to the expression in the gastrodermis of a cnidarian-bilaterian common ancestor.
Collapse
Affiliation(s)
- Michael J Layden
- Pacific Biosciences Research Center, Kewalo Marine Laboratory, University of Hawaii, Manoa, 41 Ahui St Honolulu, HI 96813, USA.
| | | | | | | | | |
Collapse
|
36
|
Pang K, Ryan JF, Mullikin JC, Baxevanis AD, Martindale MQ. Genomic insights into Wnt signaling in an early diverging metazoan, the ctenophore Mnemiopsis leidyi. EvoDevo 2010; 1:10. [PMID: 20920349 PMCID: PMC2959043 DOI: 10.1186/2041-9139-1-10] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 10/04/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Intercellular signaling pathways are a fundamental component of the integrating cellular behavior required for the evolution of multicellularity. The genomes of three of the four early branching animal phyla (Cnidaria, Placozoa and Porifera) have been surveyed for key components, but not the fourth (Ctenophora). Genomic data from ctenophores could be particularly relevant, as ctenophores have been proposed to be one of the earliest branching metazoan phyla. RESULTS A preliminary assembly of the lobate ctenophore Mnemiopsis leidyi genome generated using next-generation sequencing technologies were searched for components of a developmentally important signaling pathway, the Wnt/β-catenin pathway. Molecular phylogenetic analysis shows four distinct Wnt ligands (MlWnt6, MlWnt9, MlWntA and MlWntX), and most, but not all components of the receptor and intracellular signaling pathway were detected. In situ hybridization of the four Wnt ligands showed that they are expressed in discrete regions associated with the aboral pole, tentacle apparati and apical organ. CONCLUSIONS Ctenophores show a minimal (but not obviously simple) complement of Wnt signaling components. Furthermore, it is difficult to compare the Mnemiopsis Wnt expression patterns with those of other metazoans. mRNA expression of Wnt pathway components appears later in development than expected, and zygotic gene expression does not appear to play a role in early axis specification. Notably absent in the Mnemiopsis genome are most major secreted antagonists, which suggests that complex regulation of this secreted signaling pathway probably evolved later in animal evolution.
Collapse
Affiliation(s)
- Kevin Pang
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Joseph F Ryan
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - James C Mullikin
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andreas D Baxevanis
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark Q Martindale
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI, USA
| |
Collapse
|
37
|
Ryan JF, Pang K, Mullikin JC, Martindale MQ, Baxevanis AD. The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa. EvoDevo 2010; 1:9. [PMID: 20920347 PMCID: PMC2959044 DOI: 10.1186/2041-9139-1-9] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 10/04/2010] [Indexed: 11/10/2022] Open
Abstract
Background The much-debated phylogenetic relationships of the five early branching metazoan lineages (Bilateria, Cnidaria, Ctenophora, Placozoa and Porifera) are of fundamental importance in piecing together events that occurred early in animal evolution. Comparisons of gene content between organismal lineages have been identified as a potentially useful methodology for phylogenetic reconstruction. However, these comparisons require complete genomes that, until now, did not exist for the ctenophore lineage. The homeobox superfamily of genes is particularly suited for these kinds of gene content comparisons, since it is large, diverse, and features a highly conserved domain. Results We have used a next-generation sequencing approach to generate a high-quality rough draft of the genome of the ctenophore Mnemiopsis leidyi and subsequently identified a set of 76 homeobox-containing genes from this draft. We phylogenetically categorized this set into established gene families and classes and then compared this set to the homeodomain repertoire of species from the other four early branching metazoan lineages. We have identified several important classes and subclasses of homeodomains that appear to be absent from Mnemiopsis and from the poriferan Amphimedon queenslandica. We have also determined that, based on lineage-specific paralog retention and average branch lengths, it is unlikely that these missing classes and subclasses are due to extensive gene loss or unusually high rates of evolution in Mnemiopsis. Conclusions This paper provides a first glimpse of the first sequenced ctenophore genome. We have characterized the full complement of Mnemiopsis homeodomains from this species and have compared them to species from other early branching lineages. Our results suggest that Porifera and Ctenophora were the first two extant lineages to diverge from the rest of animals. Based on this analysis, we also propose a new name - ParaHoxozoa - for the remaining group that includes Placozoa, Cnidaria and Bilateria.
Collapse
Affiliation(s)
- Joseph F Ryan
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | | | | | | | | | | |
Collapse
|
38
|
Wong L, Weadick CJ, Kuo C, Chang BSW, Tropepe V. Duplicate dmbx1 genes regulate progenitor cell cycle and differentiation during zebrafish midbrain and retinal development. BMC DEVELOPMENTAL BIOLOGY 2010; 10:100. [PMID: 20860823 PMCID: PMC2954992 DOI: 10.1186/1471-213x-10-100] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 09/22/2010] [Indexed: 01/03/2023]
Abstract
Background The Dmbx1 gene is important for the development of the midbrain and hindbrain, and mouse gene targeting experiments reveal that this gene is required for mediating postnatal and adult feeding behaviours. A single Dmbx1 gene exists in terrestrial vertebrate genomes, while teleost genomes have at least two paralogs. We compared the loss of function of the zebrafish dmbx1a and dmbx1b genes in order to gain insight into the molecular mechanism by which dmbx1 regulates neurogenesis, and to begin to understand why these duplicate genes have been retained in the zebrafish genome. Results Using gene knockdown experiments we examined the function of the dmbx1 gene paralogs in zebrafish, dmbx1a and dmbx1b in regulating neurogenesis in the developing retina and midbrain. Dose-dependent loss of dmbx1a and dmbx1b function causes a significant reduction in growth of the midbrain and retina that is evident between 48-72 hpf. We show that this phenotype is not due to patterning defects or persistent cell death, but rather a deficit in progenitor cell cycle exit and differentiation. Analyses of the morphant retina or anterior hindbrain indicate that paralogous function is partially diverged since loss of dmbx1a is more severe than loss of dmbx1b. Molecular evolutionary analyses of the Dmbx1 genes suggest that while this gene family is conservative in its evolution, there was a dramatic change in selective constraint after the duplication event that gave rise to the dmbx1a and dmbx1b gene families in teleost fish, suggestive of positive selection. Interestingly, in contrast to zebrafish dmbx1a, over expression of the mouse Dmbx1 gene does not functionally compensate for the zebrafish dmbx1a knockdown phenotype, while over expression of the dmbx1b gene only partially compensates for the dmbx1a knockdown phenotype. Conclusion Our data suggest that both zebrafish dmbx1a and dmbx1b genes are retained in the fish genome due to their requirement during midbrain and retinal neurogenesis, although their function is partially diverged. At the cellular level, Dmbx1 regulates cell cycle exit and differentiation of progenitor cells. The unexpected observation of putative post-duplication positive selection of teleost Dmbx1 genes, especially dmbx1a, and the differences in functionality between the mouse and zebrafish genes suggests that the teleost Dmbx1 genes may have evolved a diverged function in the regulation of neurogenesis.
Collapse
Affiliation(s)
- Loksum Wong
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | | | | | | | | |
Collapse
|
39
|
Degnan SM, Degnan BM. The initiation of metamorphosis as an ancient polyphenic trait and its role in metazoan life-cycle evolution. Philos Trans R Soc Lond B Biol Sci 2010; 365:641-51. [PMID: 20083639 DOI: 10.1098/rstb.2009.0248] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Comparative genomics of representative basal metazoans leaves little doubt that the most recent common ancestor to all modern metazoans was morphogenetically complex. Here, we support this interpretation by demonstrating that the demosponge Amphimedon queenslandica has a biphasic pelagobenthic life cycle resembling that present in a wide range of bilaterians and anthozoan cnidarians. The A. queenslandica life cycle includes a compulsory planktonic larval phase that can end only once the larva develops competence to respond to benthic signals that induce settlement and metamorphosis. The temporal onset of competence varies between individuals as revealed by idiosyncratic responses to inductive cues. Thus, the biphasic life cycle with a dispersing larval phase of variable length appears to be a metazoan synapomorphy and may be viewed as an ancestral polyphenic trait. Larvae of a particular age that are subjected to an inductive cue either maintain the larval form or metamorphose into the post-larval/juvenile form. Variance in the development of competence dictates that only a subset of a larval cohort will settle and undergo metamorphosis at a given time, which in turn leads to variation in dispersal distance and in location of settlement. Population divergence and allopatric speciation are likely outcomes of this conserved developmental polyphenic trait.
Collapse
Affiliation(s)
- Sandie M Degnan
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | | |
Collapse
|
40
|
Deutsch JS. Homeosis and Beyond. What Is the Function of the Hox Genes? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 689:155-65. [DOI: 10.1007/978-1-4419-6673-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
41
|
Yamada A, Martindale MQ, Fukui A, Tochinai S. Highly conserved functions of the Brachyury gene on morphogenetic movements: insight from the early-diverging phylum Ctenophora. Dev Biol 2009; 339:212-22. [PMID: 20036227 DOI: 10.1016/j.ydbio.2009.12.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Revised: 10/31/2009] [Accepted: 12/14/2009] [Indexed: 12/31/2022]
Abstract
Brachyury, a member of the T-box transcription family identified in a diverse array of metazoans, was initially recognized for its function in mesoderm formation and notochord differentiation in vertebrates; however, its ancestral role has been suggested to be in control of morphogenetic movements. Here, we show that morpholino oligonucleotide knockdown of Brachyury (MlBra) in embryos of a ctenophore, one of the most ancient groups of animals, prevents the invagination of MlBra expressing stomodeal cells and is rescued with corresponding RNA injections. Injection of RNA encoding a dominant-interfering construct of MlBra causes identical phenotypes to that of RNA encoding a dominant-interfering form of Xenopus Brachyury (Xbra) in Xenopus embryos. Both injected embryos down-regulate Xbra downstream genes, Xbra itself and Xwnt11 but not axial mesodermal markers, resulting in failure to complete gastrulation due to loss of convergent extension movements. Moreover, animal cap assay reveals that MlBra induces Xwnt11 like Xbra. Overall results using Xenopus embryos show that these two genes are functionally interchangeable. These functional experiments demonstrate for the first time in a basal metazoan that the primitive role of Brachyury is to regulate morphogenetic movements, rather than to specify endomesodermal fates, and the role is conserved between non-bilaterian metazoans and vertebrates.
Collapse
Affiliation(s)
- Atsuko Yamada
- Department of Natural History Sciences, Faculty of Science, Hokkaido University, N10 W8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan.
| | | | | | | |
Collapse
|
42
|
Abstract
Analysis of the origin and evolution of neurons is crucial for revealing principles of organization of neural circuits with unexpected implications for genomic sciences, biomedical applications and regenerative medicine. This article presents an overview of some controversial ideas about the origin and evolution of neurons and nervous systems, focusing on the independent origin of complex brains and possible independent origins of neurons. First, earlier hypotheses related to the origin of neurons are summarized. Second, the diversity of nervous systems and convergent evolution of complex brains in relation to current views about animal phylogeny is discussed. Third, the lineages of molluscs and basal metazoans are used as illustrated examples of multiple origins of complex brains and neurons. Finally, a hypothesis about the independent origin of complex brains, centralized nervous systems and neurons is outlined. Injury-associated mechanisms leading to secretion of signal peptides (and related molecules) can be considered as evolutionary predecessors of inter-neuronal signaling and the major factors in the appearance of neurons in the first place.
Collapse
Affiliation(s)
- Leonid L Moroz
- Department of Neuroscience and McKnight Brain Institute, Gainesville, Fla., USA.
| |
Collapse
|
43
|
Degnan BM, Vervoort M, Larroux C, Richards GS. Early evolution of metazoan transcription factors. Curr Opin Genet Dev 2009; 19:591-9. [PMID: 19880309 DOI: 10.1016/j.gde.2009.09.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2009] [Revised: 09/16/2009] [Accepted: 09/27/2009] [Indexed: 11/29/2022]
Abstract
Analyses of recently sequenced sponge, cnidarian, placozoan, and choanoflagellate genomes have revealed that most transcription factor (TF) classes and families expressed during bilaterian development originated at the dawn of the animal kingdom, before the divergence of contemporary animal lineages. The ancestral metazoan genome included members of the bHLH, Mef2, Fox, Sox, T-box, ETS, nuclear receptor, Rel/NF-kappaB, bZIP, and Smad families, and a diversity of homeobox-containing classes, including ANTP, Prd-like, Pax, POU, LIM-HD, Six, and TALE. As many of these TF classes and families appear to be metazoan specific and not present in choanoflagellates, fungi and more distant eukaryotes, their genesis and expansion may have contributed to the evolution of animal multicellularity.
Collapse
Affiliation(s)
- Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia.
| | | | | | | |
Collapse
|
44
|
Martindale MQ, Hejnol A. A developmental perspective: changes in the position of the blastopore during bilaterian evolution. Dev Cell 2009; 17:162-74. [PMID: 19686678 DOI: 10.1016/j.devcel.2009.07.024] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Progress in resolving the phylogenetic relationships among animals and the expansion of molecular developmental studies to a broader variety of organisms has provided important insights into the evolution of developmental programs. These new studies make it possible to reevaluate old hypotheses about the evolution of animal body plans and to elaborate new ones. Here, we review recent studies that shed light on the transition from a radially organized ancestor to the last common ancestor of the Bilateria ("Urbilaterian") and present an integrative hypothesis about plausible developmental scenarios for the evolution of complex multicellular animals.
Collapse
Affiliation(s)
- Mark Q Martindale
- Kewalo Marine Laboratory, PBRC, University of Hawaii, 41 Ahui Street, Honolulu, HI, 96813, USA.
| | | |
Collapse
|
45
|
Li X, Kulkarni RP, Hill RJ, Chamberlin HM. HOM-C genes, Wnt signaling and axial patterning in the C. elegans posterior ventral epidermis. Dev Biol 2009; 332:156-65. [PMID: 19481074 DOI: 10.1016/j.ydbio.2009.05.567] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2008] [Revised: 05/14/2009] [Accepted: 05/19/2009] [Indexed: 12/27/2022]
Abstract
Wnt signaling and HOM-C/Hox genes pattern cell fate along the anterior/posterior axis in many animals. In general, Wnt signaling participates in establishing the anterior/posterior axis, whereas HOM-C genes confer regional identities to cells along the axis. However, recent work in non-bilaterial metazoans suggests that the ancestral patterning system relied on Wnts, with a later co-option of HOM-C genes to replace Wnts in regional patterning. Here we provide direct experimental support for this model from C. elegans, where a regional Wnt patterning system is uncovered in HOM-C gene mutants. Anterior/posterior patterning of P11/P12 cell fate in the C. elegans tail is normally dependent on the HOM-C gene egl-5/Abdominal-B. If the HOM-C gene mab-5/fushi tarazu is also mutant, however, a Wnt signal can promote P12 fate in the absence of egl-5. Furthermore, transcription of egl-5 in the P12.pa cell is influenced by an autoregulatory element that is essential in wild type, but not in mab-5 egl-5 double mutants, identifying regulatory parallels between P12 cell fate specification and egl-5 transcriptional regulation in the P12 lineage. Together, our results identify complex regulatory relationships among signaling pathways and HOM-C genes, and uncover a layering of patterning systems that may reflect their evolutionary history.
Collapse
Affiliation(s)
- Xin Li
- Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | | | | | | |
Collapse
|
46
|
Abstract
The genome sequence of Trichoplax adhaerens, the founding member of the enigmatic animal phylum Placozoa, has revealed that a surprising level of genetic complexity underlies its extremely simple body plan, indicating either that placozoans are secondarily simple or that there is an undiscovered morphologically complex life stage.
Collapse
|
47
|
Chiori R, Jager M, Denker E, Wincker P, Da Silva C, Le Guyader H, Manuel M, Quéinnec E. Are Hox genes ancestrally involved in axial patterning? Evidence from the hydrozoan Clytia hemisphaerica (Cnidaria). PLoS One 2009; 4:e4231. [PMID: 19156208 PMCID: PMC2626245 DOI: 10.1371/journal.pone.0004231] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Accepted: 12/05/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The early evolution and diversification of Hox-related genes in eumetazoans has been the subject of conflicting hypotheses concerning the evolutionary conservation of their role in axial patterning and the pre-bilaterian origin of the Hox and ParaHox clusters. The diversification of Hox/ParaHox genes clearly predates the origin of bilaterians. However, the existence of a "Hox code" predating the cnidarian-bilaterian ancestor and supporting the deep homology of axes is more controversial. This assumption was mainly based on the interpretation of Hox expression data from the sea anemone, but growing evidence from other cnidarian taxa puts into question this hypothesis. METHODOLOGY/PRINCIPAL FINDINGS Hox, ParaHox and Hox-related genes have been investigated here by phylogenetic analysis and in situ hybridisation in Clytia hemisphaerica, an hydrozoan species with medusa and polyp stages alternating in the life cycle. Our phylogenetic analyses do not support an origin of ParaHox and Hox genes by duplication of an ancestral ProtoHox cluster, and reveal a diversification of the cnidarian HOX9-14 genes into three groups called A, B, C. Among the 7 examined genes, only those belonging to the HOX9-14 and the CDX groups exhibit a restricted expression along the oral-aboral axis during development and in the planula larva, while the others are expressed in very specialised areas at the medusa stage. CONCLUSIONS/SIGNIFICANCE Cross species comparison reveals a strong variability of gene expression along the oral-aboral axis and during the life cycle among cnidarian lineages. The most parsimonious interpretation is that the Hox code, collinearity and conservative role along the antero-posterior axis are bilaterian innovations.
Collapse
Affiliation(s)
- Roxane Chiori
- UPMC Univ Paris 06, UMR 7138 CNRS UPMC MNHN IRD, Case 05, Paris, France
| | - Muriel Jager
- UPMC Univ Paris 06, UMR 7138 CNRS UPMC MNHN IRD, Case 05, Paris, France
| | - Elsa Denker
- Sars International Centre for Marine Molecular Biology, Bergen, Norway
| | | | | | - Hervé Le Guyader
- UPMC Univ Paris 06, UMR 7138 CNRS UPMC MNHN IRD, Case 05, Paris, France
| | - Michaël Manuel
- UPMC Univ Paris 06, UMR 7138 CNRS UPMC MNHN IRD, Case 05, Paris, France
| | - Eric Quéinnec
- UPMC Univ Paris 06, UMR 7138 CNRS UPMC MNHN IRD, Case 05, Paris, France
| |
Collapse
|
48
|
Finnerty JR, Mazza ME, Jezewski PA. Domain duplication, divergence, and loss events in vertebrate Msx paralogs reveal phylogenomically informed disease markers. BMC Evol Biol 2009; 9:18. [PMID: 19154605 PMCID: PMC2655272 DOI: 10.1186/1471-2148-9-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Accepted: 01/20/2009] [Indexed: 01/22/2023] Open
Abstract
Background Msx originated early in animal evolution and is implicated in human genetic disorders. To reconstruct the functional evolution of Msx and inform the study of human mutations, we analyzed the phylogeny and synteny of 46 metazoan Msx proteins and tracked the duplication, diversification and loss of conserved motifs. Results Vertebrate Msx sequences sort into distinct Msx1, Msx2 and Msx3 clades. The sister-group relationship between MSX1 and MSX2 reflects their derivation from the 4p/5q chromosomal paralogon, a derivative of the original "MetaHox" cluster. We demonstrate physical linkage between Msx and other MetaHox genes (Hmx, NK1, Emx) in a cnidarian. Seven conserved domains, including two Groucho repression domains (N- and C-terminal), were present in the ancestral Msx. In cnidarians, the Groucho domains are highly similar. In vertebrate Msx1, the N-terminal Groucho domain is conserved, while the C-terminal domain diverged substantially, implying a novel function. In vertebrate Msx2 and Msx3, the C-terminal domain was lost. MSX1 mutations associated with ectodermal dysplasia or orofacial clefting disorders map to conserved domains in a non-random fashion. Conclusion Msx originated from a MetaHox ancestor that also gave rise to Tlx, Demox, NK, and possibly EHGbox, Hox and ParaHox genes. Duplication, divergence or loss of domains played a central role in the functional evolution of Msx. Duplicated domains allow pleiotropically expressed proteins to evolve new functions without disrupting existing interaction networks. Human missense sequence variants reside within evolutionarily conserved domains, likely disrupting protein function. This phylogenomic evaluation of candidate disease markers will inform clinical and functional studies.
Collapse
Affiliation(s)
- John R Finnerty
- Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215, USA.
| | | | | |
Collapse
|
49
|
Pang K, Martindale MQ. Comb jellies (ctenophora): a model for Basal metazoan evolution and development. ACTA ACUST UNITED AC 2008; 2008:pdb.emo106. [PMID: 21356709 DOI: 10.1101/pdb.emo106] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
INTRODUCTIONCtenophores, or comb jellies, are a group of marine organisms whose unique biological features and phylogenetic placement make them a key taxon for understanding animal evolution. These gelatinous creatures are clearly distinct from cnidarian medusae (i.e., jellyfish). Key features present in the ctenophore body plan include biradial symmetry, an oral-aboral axis delimited by a mouth and an apical sensory organ, two tentacles, eight comb rows composed of interconnected cilia, and thick mesoglea. Other morphological features include definitive muscle cells, a nerve net, basal lamina, a sperm acrosome, and light-producing photocytes. Aspects of their development made them attractive to experimental embryologists as early as the 19th century. Recently, because of their role as an invasive species, studies on their role in ecology and fisheries-related fields have increased. Although the phylogenetic placement of ctenophores with respect to other animals has proven difficult, it is clear that, along with poriferans, placozoans, and cnidarians, ctenophores are one of the earliest diverging extant animal groups. It is important to determine if some of the complex features of ctenophores are examples of convergence or if they were lost in other animal branches. Because ctenophores are amenable to modern technical approaches, they could prove to be a highly useful emerging model.
Collapse
Affiliation(s)
- Kevin Pang
- Kewalo Marine Laboratory, University of Hawaii, Honolulu, HI 96813, USA
| | | |
Collapse
|