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Paris M, Wolff C, Patel NH, Averof M. The crustacean model Parhyale hawaiensis. Curr Top Dev Biol 2022; 147:199-230. [PMID: 35337450 DOI: 10.1016/bs.ctdb.2022.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Arthropods are the most abundant and diverse animals on earth. Among them, pancrustaceans are an ancient and morphologically diverse group, comprising a wide range of aquatic and semi-aquatic crustaceans as well as the insects, which emerged from crustacean ancestors to colonize most terrestrial habitats. Within insects, Drosophila stands out as one of the most powerful animal models, making major contributions to our understanding of development, physiology and behavior. Given these attributes, crustaceans provide a fertile ground for exploring biological diversity through comparative studies. However, beyond insects, few crustaceans are developed sufficiently as experimental models to enable such studies. The marine amphipod Parhyale hawaiensis is currently the best established crustacean system, offering year-round accessibility to developmental stages, transgenic tools, genomic resources, and established genetics and imaging approaches. The Parhyale research community is small but diverse, investigating the evolution of development, regeneration, aspects of sensory biology, chronobiology, bioprocessing and ecotoxicology.
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Affiliation(s)
- Mathilde Paris
- Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, Lyon, France; Centre National de la Recherche Scientifique (CNRS), France
| | - Carsten Wolff
- Marine Biological Laboratory, Woods Hole, MA, United States
| | - Nipam H Patel
- Marine Biological Laboratory, Woods Hole, MA, United States; Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States.
| | - Michalis Averof
- Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, Lyon, France; Centre National de la Recherche Scientifique (CNRS), France.
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The embryonic transcriptome of Parhyale hawaiensis reveals different dynamics of microRNAs and mRNAs during the maternal-zygotic transition. Sci Rep 2022; 12:174. [PMID: 34996916 PMCID: PMC8741983 DOI: 10.1038/s41598-021-03642-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/09/2021] [Indexed: 11/18/2022] Open
Abstract
Parhyale hawaiensis has emerged as the crustacean model of choice due to its tractability, ease of imaging, sequenced genome, and development of CRISPR/Cas9 genome editing tools. However, transcriptomic datasets spanning embryonic development are lacking, and there is almost no annotation of non-protein-coding RNAs, including microRNAs. We have sequenced microRNAs, together with mRNAs and long non-coding RNAs, in Parhyale using paired size-selected RNA-seq libraries at seven time-points covering important transitions in embryonic development. Focussing on microRNAs, we annotate 175 loci in Parhyale, 88 of which have no known homologs. We use these data to annotate the microRNAome of 37 crustacean genomes, and suggest a core crustacean microRNA set of around 61 sequence families. We examine the dynamic expression of microRNAs and mRNAs during the maternal-zygotic transition. Our data suggest that zygotic genome activation occurs in two waves in Parhyale with microRNAs transcribed almost exclusively in the second wave. Contrary to findings in other arthropods, we do not predict a general role for microRNAs in clearing maternal transcripts. These data significantly expand the available transcriptomics resources for Parhyale, and facilitate its use as a model organism for the study of small RNAs in processes ranging from embryonic development to regeneration.
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Cogne Y, Degli-Esposti D, Pible O, Gouveia D, François A, Bouchez O, Eché C, Ford A, Geffard O, Armengaud J, Chaumot A, Almunia C. De novo transcriptomes of 14 gammarid individuals for proteogenomic analysis of seven taxonomic groups. Sci Data 2019; 6:184. [PMID: 31562330 PMCID: PMC6764967 DOI: 10.1038/s41597-019-0192-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 08/13/2019] [Indexed: 11/17/2022] Open
Abstract
Gammarids are amphipods found worldwide distributed in fresh and marine waters. They play an important role in aquatic ecosystems and are well established sentinel species in ecotoxicology. In this study, we sequenced the transcriptomes of a male individual and a female individual for seven different taxonomic groups belonging to the two genera Gammarus and Echinogammarus: Gammarus fossarum A, G. fossarum B, G. fossarum C, Gammarus wautieri, Gammarus pulex, Echinogammarus berilloni, and Echinogammarus marinus. These taxa were chosen to explore the molecular diversity of transcribed genes of genotyped individuals from these groups. Transcriptomes were de novo assembled and annotated. High-quality assembly was confirmed by BUSCO comparison against the Arthropod dataset. The 14 RNA-Seq-derived protein sequence databases proposed here will be a significant resource for proteogenomics studies of these ecotoxicologically relevant non-model organisms. These transcriptomes represent reliable reference sequences for whole-transcriptome and proteome studies on other gammarids, for primer design to clone specific genes or monitor their specific expression, and for analyses of molecular differences between gammarid species. Measurement(s) | transcription profiling assay | Technology Type(s) | RNA sequencing | Factor Type(s) | sex • species | Sample Characteristic - Organism | Gammarus • Echinogammarus | Sample Characteristic - Environment | habitat |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9777905
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Affiliation(s)
- Yannick Cogne
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Davide Degli-Esposti
- Irstea, UR MALY Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
| | - Olivier Pible
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Duarte Gouveia
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Adeline François
- Irstea, UR MALY Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
| | - Olivier Bouchez
- GeT-PlaGe, Genotoul, INRA Auzeville, F-31320, Castanet-Tolosan, France
| | - Camille Eché
- GeT-PlaGe, Genotoul, INRA Auzeville, F-31320, Castanet-Tolosan, France
| | - Alex Ford
- School of Biological Sciences, Institute of Marine Sciences Laboratories, P04 9LY, Portsmouth, United Kingdom
| | - Olivier Geffard
- Irstea, UR MALY Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France.
| | - Arnaud Chaumot
- Irstea, UR MALY Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
| | - Christine Almunia
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
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Wittfoth C, Harzsch S, Wolff C, Sombke A. The "amphi"-brains of amphipods: new insights from the neuroanatomy of Parhyale hawaiensis (Dana, 1853). Front Zool 2019; 16:30. [PMID: 31372174 PMCID: PMC6660712 DOI: 10.1186/s12983-019-0330-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/15/2019] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Over the last years, the amphipod crustacean Parhyale hawaiensis has developed into an attractive marine animal model for evolutionary developmental studies that offers several advantages over existing experimental organisms. It is easy to rear in laboratory conditions with embryos available year-round and amenable to numerous kinds of embryological and functional genetic manipulations. However, beyond these developmental and genetic analyses, research on the architecture of its nervous system is fragmentary. In order to provide a first neuroanatomical atlas of the brain, we investigated P. hawaiensis using immunohistochemical labelings combined with laser-scanning microscopy, X-ray microcomputed tomography, histological sectioning and 3D reconstructions. RESULTS As in most amphipod crustaceans, the brain is dorsally bent out of the body axis with downward oriented lateral hemispheres of the protocerebrum. It comprises almost all prominent neuropils that are part of the suggested ground pattern of malacostracan crustaceans (except the lobula plate and projection neuron tract neuropil). Beyond a general uniformity of these neuropils, the brain of P. hawaiensis is characterized by an elaborated central complex and a modified lamina (first order visual neuropil), which displays a chambered appearance. In the light of a recent analysis on photoreceptor projections in P. hawaiensis, the observed architecture of the lamina corresponds to specialized photoreceptor terminals. Furthermore, in contrast to previous descriptions of amphipod brains, we suggest the presence of a poorly differentiated hemiellipsoid body and an inner chiasm and critically discuss these aspects. CONCLUSIONS Despite a general uniformity of amphipod brains, there is also a certain degree of variability in architecture and size of different neuropils, reflecting various ecologies and life styles of different species. In contrast to other amphipods, the brain of P. hawaiensis does not display any striking modifications or bias towards processing one particular sensory modality. Thus, we conclude that this brain represents a common type of an amphipod brain. Considering various established protocols for analyzing and manipulating P. hawaiensis, this organism is a suitable model to gain deeper understanding of brain anatomy e.g. by using connectome approaches, and this study can serve as first solid basis for following studies.
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Affiliation(s)
- Christin Wittfoth
- Department of Cytology and Evolutionary Biology, Zoological Institute and Museum, University of Greifswald, Soldmannstr. 23, 17487 Greifswald, Germany
| | - Steffen Harzsch
- Department of Cytology and Evolutionary Biology, Zoological Institute and Museum, University of Greifswald, Soldmannstr. 23, 17487 Greifswald, Germany
| | - Carsten Wolff
- Department of Biology, Comparative Zoology, Humboldt University Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Andy Sombke
- Department of Integrative Zoology, University of Vienna, Althanstr. 14, 1090 Vienna, Austria
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Sun DA, Patel NH. The amphipod crustacean Parhyale hawaiensis: An emerging comparative model of arthropod development, evolution, and regeneration. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2019; 8:e355. [PMID: 31183976 PMCID: PMC6772994 DOI: 10.1002/wdev.355] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 05/11/2019] [Indexed: 12/26/2022]
Abstract
Recent advances in genetic manipulation and genome sequencing have paved the way for a new generation of research organisms. The amphipod crustacean Parhyale hawaiensis is one such system. Parhyale are easy to rear and offer large broods of embryos amenable to injection, dissection, and live imaging. Foundational work has described Parhyale embryonic development, while advancements in genetic manipulation using CRISPR-Cas9 and other techniques, combined with genome and transcriptome sequencing, have enabled its use in studies of arthropod development, evolution, and regeneration. This study introduces Parhyale development and life history, a catalog of techniques and resources for Parhyale research, and two case studies illustrating its power as a comparative research system. This article is categorized under: Comparative Development and Evolution > Evolutionary Novelties Adult Stem Cells, Tissue Renewal, and Regeneration > Regeneration Comparative Development and Evolution > Model Systems Comparative Development and Evolution > Body Plan Evolution.
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Affiliation(s)
- Dennis A Sun
- Department of Molecular and Cell Biology, University of California, Berkeley, California
| | - Nipam H Patel
- Marine Biological Laboratory, University of Chicago, Chicago, Illinois
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Comparative transcriptome analysis explores maternal to zygotic transition during Eriocheir sinensis early embryogenesis. Gene 2019; 685:12-20. [PMID: 30321661 DOI: 10.1016/j.gene.2018.10.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 09/27/2018] [Accepted: 10/11/2018] [Indexed: 11/21/2022]
Abstract
The maternal genome directs almost all aspects of early animal development. As development proceeds, the elimination of maternal gene products and zygotic genome activation (ZGA) occur during the maternal to zygotic transition (MZT). To study the molecular mechanisms regulating this developmental event in Eriocheir sinensis, RNA-Seq technology was applied to generate comprehensive information on transcriptome dynamics during early embryonic stages. In total, 32,088 annotated unigenes were obtained from the transcriptomes of fertilized eggs and embryos at the cleavage (2-4 cell) and blastula stage. A total of 566 maternal genes and 1165 zygotic genes were isolated, among which 103 and 266 genes were predicted conserved maternal transcripts (COMATs) and conserved zygotic transcripts (COZYTs), respectively. The COMATs performed housekeeping gene functions and may be essential for initiating early embryogenesis of the Bilateria. Furthermore, 87, 76 and 117 differentially expressed genes associated with the MZT, morphogenesis and immunity were identified when compared the three transcriptomic datasets. We also unmask that the MZT takes place around the cleavage stage, when the genes involved in the clearance of maternal gene products and the ZGA were significantly up-regulated. Taken together, these datasets provide a valuable resource for understanding the mechanisms of early developmental events in E. sinensis, and facilitate further studies on molecular mechanisms of asynchronous development in crabs.
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microRNAs in Macrobrachium olfersii embryos: Identification, their biogenesis components and potential targets. Comput Biol Chem 2018; 78:205-216. [PMID: 30576966 DOI: 10.1016/j.compbiolchem.2018.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 11/24/2018] [Accepted: 12/11/2018] [Indexed: 12/21/2022]
Abstract
In embryonic development, microRNAs (miRNAs) regulate the complex gene expression associated with the complexity of embryogenesis. Today, few studies have been conducted on the identification of miRNAs and components of miRNA biogenesis on embryonic development in crustaceans, especially in prawns. In this context, the aim of this study was to identify in silico components of miRNA biogenesis, and miRNAs and potential target genes during embryonic development in the prawn Macrobrachium olfersii through small RNAs and transcriptome analyses. Using the miRDeep2 program, we identified 17 miRNA precursors in M. olfersii, which seven (miR-9, miR-10, miR-92, miR-125, miR-305, miR-1175, and miR-2788) were reported in the miRBase database, indicating high evolutionary conservation of these sequences among animals. The other 10 miRNAs of M. olfersii were novel miRNAs and only similar to Macrobrachium niponnense miRNAs, indicating genus-specific miRNAs. In addition, eight key components of miRNA biogenesis (DROSHA, PASHA/DGCR8, XPO5, RAN, DICER, TRBP2, AGO, and PIWI) were identified in M. olfersii embryos unigenes. In the annotation of miRNA targets, 516 genes were similar to known sequences in the GenBank database. Regarding the conserved miRNAs, we verified that they were differentially expressed during embryonic development in M. olfersii. In conclusion, this is the first study that identifies conserved and novel miRNAs in the prawn M. olfersii with some miRNA target genes involved in embryonic development. Our results will allow further studies on the function of these miRNAs and miRNA biogenesis components during embryonic development in M. olfersii and other prawns of commercial interest.
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Romero-Carvajal A, Turnbull MW, Baeza JA. Embryonic Development in the Peppermint Shrimp, Lysmata boggessi (Caridea: Lysmatidae). THE BIOLOGICAL BULLETIN 2018; 234:165-179. [PMID: 29949441 DOI: 10.1086/698468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
There are a limited number of model species for decapod experimental embryology. To improve our understanding of developmental pattern evolution in the Decapoda, here we describe the early embryonic development of the caridean shrimp Lysmata boggessi, from immediately after fertilization to the hatching of the zoea larva, using fluorescence microscopy and whole-mount nuclear staining with 4',6-diamidino-2-phenylindole. Lysmata boggessi follows the standard caridean pattern of early development, with early holoblastic cleavage that will later become superficial, to form a blastoderm. We found no evidence of stereotypical cleavage and the formation of blastomere interlocking bands, which suggests there is diversity in developmental patterns within the Caridea. Gastrulation starts 37 hours after fertilization, and the embryonized nauplius is formed 2 days later. Enlarged headlobes, early retinal differentiation, and delayed pereopod development are characteristics of the post-naupliar stages in this species. To facilitate comparative studies with other crustacean species, we propose a staging method based on our findings. Lysmata boggessi is a protandric simultaneous hermaphrodite that is relatively easy to breed in captivity and amenable to laboratory experimentation in studies of embryonic development.
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Artal MC, Dos Santos A, Henry TB, Umbuzeiro GDA. Development of an acute toxicity test with the tropical marine amphipod Parhyale hawaiensis. ECOTOXICOLOGY (LONDON, ENGLAND) 2018; 27:103-108. [PMID: 29138970 DOI: 10.1007/s10646-017-1875-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/26/2017] [Indexed: 06/07/2023]
Abstract
There is a lack of suitable tropical marine species for ecotoxicity tests. An attractive model organism for ecotoxicology is the marine amphipod Parhyale hawaiensis, which is already a model for genetic and developmental studies. This species is widespread, can tolerate changes in salinity, is easy to handle and is representative of circumtropical regions. The aim of this work was to describe standardized procedures for laboratory husbandry, define conditions for acute toxicity tests, and to provide acute toxicity test results for some reference toxicants. Culturing conditions for the organism in the laboratory were established in reconstituted seawater (30 ± 2 salinity), 24 ± 2 °C, photoperiod 12/12 h light/dark. Acute toxicity test procedures were developed for 96 h-exposure time, and organisms at ages <7 days. The miniaturized version of the test, based on 96-well microplates and 200 µL of exposure media provided consistent results compared to larger exposure volumes (80-mL vials protocol). Acute toxicity of Ag, Cd, Cu, Zn and ammonia determined for P. hawaiensis were consistent to previous results for other marine amphipods. We conclude that P. hawaiensis can be successfully cultured in standardized conditions and be effectively used in acute toxicity testing. Further development and use of this model will enable standardized and reproducible ecotoxicology investigations in understudied and vulnerable tropical marine ecosystems.
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Affiliation(s)
- Mariana Coletty Artal
- School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, 05508-000, Brazil
- School of Technology, University of Campinas, Limeira, 13484-332, Brazil
| | - Amanda Dos Santos
- School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, 05508-000, Brazil
- School of Technology, University of Campinas, Limeira, 13484-332, Brazil
| | - Theodore Burdick Henry
- Institute of Life and Earth Sciences, School of Energy, Geoscience, Infrastructure, and Society, Heriot-Watt University, Edinburgh, EH14 4AS, Scotland
- Center for Environmental Biotechnology, The University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN, 37996-1605, USA
| | - Gisela de Aragão Umbuzeiro
- School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, 05508-000, Brazil.
- School of Technology, University of Campinas, Limeira, 13484-332, Brazil.
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Davidson PL, Koch BJ, Schnitzler CE, Henry JQ, Martindale MQ, Baxevanis AD, Browne WE. The maternal-zygotic transition and zygotic activation of the Mnemiopsis leidyi genome occurs within the first three cleavage cycles. Mol Reprod Dev 2017; 84:1218-1229. [PMID: 29068507 DOI: 10.1002/mrd.22926] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/03/2017] [Indexed: 12/20/2022]
Abstract
The maternal-zygotic transition (MZT) describes the developmental reprogramming of gene expression marked by the degradation of maternally supplied gene products and activation of the zygotic genome. While the timing and duration of the MZT vary among taxa, little is known about early-stage transcriptional dynamics in the non-bilaterian phylum Ctenophora. We sought to better understand the extent of maternal mRNA loading and subsequent differential transcript abundance during the earliest stages of development by performing comprehensive RNA-sequencing-based analyses of mRNA abundance in single- and eight-cell stage embryos in the lobate ctenophore Mnemiopsis leidyi. We found 1,908 contigs with significant differential abundance between single- and eight-cell stages, of which 1,208 contigs were more abundant at the single-cell stage and 700 contigs were more abundant at the eight-cell stage. Of the differentially abundant contigs, 267 were exclusively present in the eight-cell samples, providing strong evidence that both the MZT and zygotic genome activation (ZGA) have commenced by the eight-cell stage. Many highly abundant transcripts encode genes involved in molecular mechanisms critical to the MZT, such as maternal transcript degradation, serine/threonine kinase activity, and chromatin remodeling. Our results suggest that chromosomal restructuring, which is critical to ZGA and the initiation of transcriptional regulation necessary for normal development, begins by the third cleavage within 1.5 hr post-fertilization in M. leidyi.
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Affiliation(s)
| | - Bernard J Koch
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Christine E Schnitzler
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, Florida.,Department of Biology, University of Florida, Gainesville, Florida
| | - Jonathan Q Henry
- Department of Cell and Developmental Biology, University of Illinois, Urbana, Illinois
| | - Mark Q Martindale
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, Florida.,Department of Biology, University of Florida, Gainesville, Florida
| | - Andreas D Baxevanis
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - William E Browne
- Department of Biology, University of Miami, Coral Gables, Florida
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Ribeiro L, Tobias-Santos V, Santos D, Antunes F, Feltran G, de Souza Menezes J, Aravind L, Venancio TM, Nunes da Fonseca R. Evolution and multiple roles of the Pancrustacea specific transcription factor zelda in insects. PLoS Genet 2017; 13:e1006868. [PMID: 28671979 PMCID: PMC5515446 DOI: 10.1371/journal.pgen.1006868] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 07/18/2017] [Accepted: 06/14/2017] [Indexed: 01/09/2023] Open
Abstract
Gene regulatory networks (GRNs) evolve as a result of the coevolutionary processes acting on transcription factors (TFs) and the cis-regulatory modules they bind. The zinc-finger TF zelda (zld) is essential for the maternal-to-zygotic transition (MZT) in Drosophila melanogaster, where it directly binds over thousand cis-regulatory modules to regulate chromatin accessibility. D. melanogaster displays a long germ type of embryonic development, where all segments are simultaneously generated along the whole egg. However, it remains unclear if zld is also involved in the MZT of short-germ insects (including those from basal lineages) or in other biological processes. Here we show that zld is an innovation of the Pancrustacea lineage, being absent in more distant arthropods (e.g. chelicerates) and other organisms. To better understand zld´s ancestral function, we thoroughly investigated its roles in a short-germ beetle, Tribolium castaneum, using molecular biology and computational approaches. Our results demonstrate roles for zld not only during the MZT, but also in posterior segmentation and patterning of imaginal disc derived structures. Further, we also demonstrate that zld is critical for posterior segmentation in the hemipteran Rhodnius prolixus, indicating this function predates the origin of holometabolous insects and was subsequently lost in long-germ insects. Our results unveil new roles of zld in different biological contexts and suggest that changes in expression of zld (and probably other major TFs) are critical in the evolution of insect GRNs. Pioneer transcription factors (TFs) are considered the first regulators of chromatin accessibility in fruit flies and vertebrates, modulating the expression of a large number of target genes. In fruit flies, zelda resembles a pioneer TF, being essential during early embryogenesis. However, the evolutionary origins and ancestral functions of zelda remain largely unknown. Through a number of gene silencing, microscopy and evolutionary analysis, the present work shows that zelda is an innovation of the Pancrustacea lineage, governing not only the MZT in the short-germ insect Tribolium castaneum, but also posterior segmentation and post-embryonic patterning of imaginal disc derived structures such as wings, legs and antennae. Further, zelda regulation of posterior segmentation predates the origin of insects with complete metamorphosis (holometabolous), as supported by gene silencing experiments in the kissing bug Rhodnius prolixus. We hypothesize that the emergence of zelda contributed to the evolution of gene regulatory networks and new morphological structures of insects.
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Affiliation(s)
- Lupis Ribeiro
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, Núcleo em Ecologia e Desenvolvimento SócioAmbiental de Macaé (NUPEM), Campus UFRJ Macaé, Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT-EM, Macaé, Brazil
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT-EM, Rio de Janeiro, Brazil
| | - Vitória Tobias-Santos
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, Núcleo em Ecologia e Desenvolvimento SócioAmbiental de Macaé (NUPEM), Campus UFRJ Macaé, Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT-EM, Macaé, Brazil
| | - Daniele Santos
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, Núcleo em Ecologia e Desenvolvimento SócioAmbiental de Macaé (NUPEM), Campus UFRJ Macaé, Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT-EM, Macaé, Brazil
| | - Felipe Antunes
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, Núcleo em Ecologia e Desenvolvimento SócioAmbiental de Macaé (NUPEM), Campus UFRJ Macaé, Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT-EM, Macaé, Brazil
| | - Geórgia Feltran
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, Núcleo em Ecologia e Desenvolvimento SócioAmbiental de Macaé (NUPEM), Campus UFRJ Macaé, Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT-EM, Macaé, Brazil
| | - Jackson de Souza Menezes
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, Núcleo em Ecologia e Desenvolvimento SócioAmbiental de Macaé (NUPEM), Campus UFRJ Macaé, Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT-EM, Macaé, Brazil
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Thiago M. Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT-EM, Rio de Janeiro, Brazil
- * E-mail: (TMV); (RNdF)
| | - Rodrigo Nunes da Fonseca
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, Núcleo em Ecologia e Desenvolvimento SócioAmbiental de Macaé (NUPEM), Campus UFRJ Macaé, Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT-EM, Macaé, Brazil
- * E-mail: (TMV); (RNdF)
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12
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Arsala D, Lynch JA. Ploidy has little effect on timing early embryonic events in the haplo-diploid wasp Nasonia. Genesis 2017; 55. [PMID: 28432826 DOI: 10.1002/dvg.23029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 02/20/2017] [Accepted: 03/06/2017] [Indexed: 12/18/2022]
Abstract
The nucleocytoplasmic (N/C) ratio plays a prominent role in the maternal-to-zygotic transition (MZT) in many animals. The effect of the N/C ratio on cell-cycle lengthening and zygotic genome activation (ZGA) has been studied extensively in Drosophila, where haploid embryos experience an additional division prior to completing cellularization and triploid embryos cellularize precociously by one division. In this study, we set out to understand how the obligate difference in ploidy in the haplodiploid wasp, Nasonia, affects the MZT and which aspects of the Drosophila MZT are conserved. While subtle differences in early embryonic development were observed in comparisons among haploid, diploid, and triploid embryos, in all cases embryos cellularize at cell cycle 12. When ZGA was inhibited, both diploid female, and haploid male, embryos went through 12 syncytial divisions and failed to cellularize before dying without further divisions. We also found that key players of the Drosophila MZT are conserved in Nasonia but have novel expression patterns. Our results suggest that zygotically expressed genes have a reduced role in determining the timing of cellularization in Nasonia relative to Drosophila, and that a stronger reliance on a maternal timer is more compatible with species where variations in embryonic ploidy are obligatory.
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Affiliation(s)
- Deanna Arsala
- University of Illinois at Chicago, Chicago, Illinois
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13
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Non-insect crustacean models in developmental genetics including an encomium to Parhyale hawaiensis. Curr Opin Genet Dev 2016; 39:149-156. [PMID: 27475080 DOI: 10.1016/j.gde.2016.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 06/25/2016] [Accepted: 07/07/2016] [Indexed: 11/23/2022]
Abstract
The impressive diversity of body plans, lifestyles and segmental specializations exhibited by crustaceans (barnacles, copepods, shrimps, crabs, lobsters and their kin) provides great material to address longstanding questions in evolutionary developmental biology. Recent advances in forward and reverse genetics and in imaging approaches applied in the amphipod Parhyale hawaiensis and other emerging crustacean model species have made it possible to probe the molecular and cellular basis of crustacean diversity. A number of biological and technical qualities like the slow tempo and holoblastic cleavage mode, the stereotypy of many cellular processes, the functional and morphological diversity of limbs along the body axis, and the availability of various experimental manipulations, have made Parhyale a powerful system to study normal development and regeneration.
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14
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Derby CD, Kozma MT, Senatore A, Schmidt M. Molecular Mechanisms of Reception and Perireception in Crustacean Chemoreception: A Comparative Review. Chem Senses 2016; 41:381-98. [PMID: 27107425 DOI: 10.1093/chemse/bjw057] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
This review summarizes our present knowledge of chemoreceptor proteins in crustaceans, using a comparative perspective to review these molecules in crustaceans relative to other metazoan models of chemoreception including mammals, insects, nematodes, and molluscs. Evolution has resulted in unique expansions of specific gene families and repurposing of them for chemosensation in various clades, including crustaceans. A major class of chemoreceptor proteins across crustaceans is the Ionotropic Receptors, which diversified from ionotropic glutamate receptors in ancient protostomes but which are not present in deuterostomes. Representatives of another major class of chemoreceptor proteins-the Grl/GR/OR family of ionotropic 7-transmembrane receptors-are diversified in insects but to date have been reported in only one crustacean species, Daphnia pulex So far, canonic 7-transmembrane G-protein coupled receptors, the principal chemoreceptors in vertebrates and reported in a few protostome clades, have not been identified in crustaceans. More types of chemoreceptors are known throughout the metazoans and might well be expected to be discovered in crustaceans. Our review also provides a comparative coverage of perireceptor events in crustacean chemoreception, including molecules involved in stimulus acquisition, stimulus delivery, and stimulus removal, though much less is known about these events in crustaceans, particularly at the molecular level.
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Affiliation(s)
| | | | - Adriano Senatore
- Present address: Biology Department, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
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15
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Chen F, Bo J, Ma X, Dong L, Shan Z, Cui Q, Chen H, Wang K. A New Membrane Lipid Raft Gene SpFLT-1 Facilitating the Endocytosis of Vibrio alginolyticus in the Crab Scylla paramamosain. PLoS One 2015; 10:e0133443. [PMID: 26186350 PMCID: PMC4506021 DOI: 10.1371/journal.pone.0133443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/26/2015] [Indexed: 11/23/2022] Open
Abstract
Pathogens can enter their host cells by way of endocytosis in which the membrane lipid raft gene flotillins are probably involved in the invasion process and this is an important way to cause infection. In this study, a new gene SpFLT-1 was identified in Scylla paramamosain, which shared high identity with the flotillin-1 of other species. The SpFLT-1 gene was widely distributed in tissues and showed the highest level of mRNA transcripts in the hemocytes. This gene might be a maternal gene based on the evident results that it was highly expressed in maternal ovaries and in the early developmental stages of the zygote and early embryo stage whereas it gradually decreased in zoea 1. SpFLT-1 positively responded to the challenge of Vibrio alginolyticus with a significantly increased level of mRNA expression in the hemocytes and gills at 3 hours post infection (hpi). The SpFLT-1 protein was detected densely in the same fraction layer where the Vibrio protein was most present in the hemocytes and gills at 3 hpi. Furthermore, it was found that the expression of SpFLT-1 decreased to the base level following disappearance of the Vibrio protein at 6 hpi in the gills. Silencing SpFLT-1 inhibited the endocytosis rate of V. alginolyticus but overexpression of the gene could facilitate bacterial entry into the epithelioma papulosum cyprinid cells. Our study indicated that SpFLT-1 may act as a key protein involved in the process of bacterial infection and this sheds light on clarifying the pathogenesis of pathogens infecting S. paramamosain.
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Affiliation(s)
- Fangyi Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Science, Xiamen University, Xiamen, Fujian, P. R. China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, Fujian, P. R. China
- Fujian Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, Fujian, P. R. China
| | - Jun Bo
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Xiaowan Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Science, Xiamen University, Xiamen, Fujian, P. R. China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, Fujian, P. R. China
- Fujian Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, Fujian, P. R. China
| | - Lixia Dong
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Science, Xiamen University, Xiamen, Fujian, P. R. China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, Fujian, P. R. China
- Fujian Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, Fujian, P. R. China
| | - Zhongguo Shan
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Science, Xiamen University, Xiamen, Fujian, P. R. China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, Fujian, P. R. China
- Fujian Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, Fujian, P. R. China
| | - Qian Cui
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Science, Xiamen University, Xiamen, Fujian, P. R. China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, Fujian, P. R. China
- Fujian Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, Fujian, P. R. China
| | - Huiyun Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Science, Xiamen University, Xiamen, Fujian, P. R. China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, Fujian, P. R. China
- Fujian Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, Fujian, P. R. China
| | - Kejian Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Science, Xiamen University, Xiamen, Fujian, P. R. China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, Fujian, P. R. China
- Fujian Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, Fujian, P. R. China
- * E-mail:
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16
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Nast AR, Extavour CG. Ablation of a single cell from eight-cell embryos of the amphipod crustacean Parhyale hawaiensis. J Vis Exp 2014. [PMID: 24686416 DOI: 10.3791/51073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The amphipod Parhyale hawaiensis is a small crustacean found in intertidal marine habitats worldwide. Over the past decade, Parhyale has emerged as a promising model organism for laboratory studies of development, providing a useful outgroup comparison to the well studied arthropod model organism Drosophila melanogaster. In contrast to the syncytial cleavages of Drosophila, the early cleavages of Parhyale are holoblastic. Fate mapping using tracer dyes injected into early blastomeres have shown that all three germ layers and the germ line are established by the eight-cell stage. At this stage, three blastomeres are fated to give rise to the ectoderm, three are fated to give rise to the mesoderm, and the remaining two blastomeres are the precursors of the endoderm and germ line respectively. However, blastomere ablation experiments have shown that Parhyale embryos also possess significant regulatory capabilities, such that the fates of blastomeres ablated at the eight-cell stage can be taken over by the descendants of some of the remaining blastomeres. Blastomere ablation has previously been described by one of two methods: injection and subsequent activation of phototoxic dyes or manual ablation. However, photoablation kills blastomeres but does not remove the dead cell body from the embryo. Complete physical removal of specific blastomeres may therefore be a preferred method of ablation for some applications. Here we present a protocol for manual removal of single blastomeres from the eight-cell stage of Parhyale embryos, illustrating the instruments and manual procedures necessary for complete removal of the cell body while keeping the remaining blastomeres alive and intact. This protocol can be applied to any Parhyale cell at the eight-cell stage, or to blastomeres of other early cleavage stages. In addition, in principle this protocol could be applicable to early cleavage stage embryos of other holoblastically cleaving marine invertebrates.
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Affiliation(s)
- Anastasia R Nast
- Department of Organismic and Evolutionary Biology, Harvard University
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17
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Gupta T, Extavour CG. Identification of a putative germ plasm in the amphipod Parhyale hawaiensis. EvoDevo 2013; 4:34. [PMID: 24314239 PMCID: PMC3878990 DOI: 10.1186/2041-9139-4-34] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 11/01/2013] [Indexed: 01/16/2023] Open
Abstract
Background Specification of the germ line is an essential event during the embryonic development of sexually reproducing animals, as germ line cells are uniquely capable of giving rise to the next generation. Animal germ cells arise through either inheritance of a specialized, maternally supplied cytoplasm called 'germ plasm’ or though inductive signaling by somatic cells. Our understanding of germ cell determination is based largely on a small number of model organisms. To better understand the evolution of germ cell specification, we are investigating this process in the amphipod crustacean Parhyale hawaiensis. Experimental evidence from previous studies demonstrated that Parhyale germ cells are specified through inheritance of a maternally supplied cytoplasmic determinant; however, this determinant has not been identified. Results Here we show that the one-cell stage Parhyale embryo has a distinct cytoplasmic region that can be identified by morphology as well as the localization of germ line-associated RNAs. Removal of this cytoplasmic region results in a loss of embryonic germ cells, supporting the hypothesis that it is required for specification of the germ line. Surprisingly, we found that removal of this distinct cytoplasm also results in aberrant somatic cell behaviors, as embryos fail to gastrulate. Conclusions Parhyale hawaiensis embryos have a specialized cytoplasm that is required for specification of the germ line. Our data provide the first functional evidence of a putative germ plasm in a crustacean and provide the basis for comparative functional analysis of germ plasm formation within non-insect arthropods.
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Affiliation(s)
- Tripti Gupta
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.
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