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Cheatle Jarvela AM, Wexler JR. Advances in genome sequencing reveal changes in gene content that contribute to arthropod macroevolution. Dev Genes Evol 2023; 233:59-76. [PMID: 37982820 DOI: 10.1007/s00427-023-00712-y] [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: 06/16/2023] [Accepted: 11/05/2023] [Indexed: 11/21/2023]
Abstract
Current sequencing technology allows for the relatively affordable generation of highly contiguous genomes. Technological advances have made it possible for researchers to investigate the consequences of diverse sorts of genomic variants, such as gene gain and loss. With the extraordinary number of high-quality genomes now available, we take stock of how these genomic variants impact phenotypic evolution. We take care to point out that the identification of genomic variants of interest is only the first step in understanding their impact. Painstaking lab or fieldwork is still required to establish causal relationships between genomic variants and phenotypic evolution. We focus mostly on arthropod research, as this phylum has an impressive degree of phenotypic diversity and is also the subject of much evolutionary genetics research. This article is intended to both highlight recent advances in the field and also to be a primer for learning about evolutionary genetics and genomics.
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Affiliation(s)
- Alys M Cheatle Jarvela
- Department of Entomology, University of Maryland, College Park, MD, USA.
- HHMI Janelia Research Campus, Ashburn, VA, USA.
| | - Judith R Wexler
- Department of Ecology, Evolution, and Behavior, The Hebrew University in Jerusalem, Jerusalem, Israel.
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2
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Li M, Kasan K, Saha Z, Yoon Y, Schmidt-Ott U. Twenty-seven ZAD-ZNF genes of Drosophila melanogaster are orthologous to the embryo polarity determining mosquito gene cucoid. PLoS One 2023; 18:e0274716. [PMID: 36595500 PMCID: PMC9810180 DOI: 10.1371/journal.pone.0274716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/16/2022] [Indexed: 01/04/2023] Open
Abstract
The C2H2 zinc finger gene cucoid establishes anterior-posterior (AP) polarity in the early embryo of culicine mosquitoes. This gene is unrelated to genes that establish embryo polarity in other fly species (Diptera), such as the homeobox gene bicoid, which serves this function in the traditional model organism Drosophila melanogaster. The cucoid gene is a conserved single copy gene across lower dipterans but nothing is known about its function in other species, and its evolution in higher dipterans, including Drosophila, is unresolved. We found that cucoid is a member of the ZAD-containing C2H2 zinc finger (ZAD-ZNF) gene family and is orthologous to 27 of the 91 members of this family in D. melanogaster, including M1BP, ranshi, ouib, nom, zaf1, odj, Nnk, trem, Zif, and eighteen uncharacterized genes. Available knowledge of the functions of cucoid orthologs in Drosophila melanogaster suggest that the progenitor of this lineage specific expansion may have played a role in regulating chromatin. We also describe many aspects of the gene duplication history of cucoid in the brachyceran lineage of D. melanogaster, thereby providing a framework for predicting potential redundancies among these genes in D. melanogaster.
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Affiliation(s)
- Muzi Li
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Koray Kasan
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Zinnia Saha
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Yoseop Yoon
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Urs Schmidt-Ott
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
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3
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Chipman AD, Edgecombe GD. Developing an integrated understanding of the evolution of arthropod segmentation using fossils and evo-devo. Proc Biol Sci 2019; 286:20191881. [PMID: 31575373 DOI: 10.1098/rspb.2019.1881] [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] [Indexed: 01/21/2023] Open
Abstract
Segmentation is fundamental to the arthropod body plan. Understanding the evolutionary steps by which arthropods became segmented is being transformed by the integration of data from evolutionary developmental biology (evo-devo), Cambrian fossils that allow the stepwise acquisition of segmental characters to be traced in the arthropod stem-group, and the incorporation of fossils into an increasingly well-supported phylogenetic framework for extant arthropods based on genomic-scale datasets. Both evo-devo and palaeontology make novel predictions about the evolution of segmentation that serve as testable hypotheses for the other, complementary data source. Fossils underpin such hypotheses as arthropodization originating in a frontal appendage and then being co-opted into other segments, and segmentation of the endodermal midgut in the arthropod stem-group. Insights from development, such as tagmatization being associated with different modes of segment generation in different body regions, and a distinct patterning of the anterior head segments, are complemented by palaeontological evidence for the pattern of tagmatization during ontogeny of exceptionally preserved fossils. Fossil and developmental data together provide evidence for a short head in stem-group arthropods and the mechanism of its formation and retention. Future breakthroughs are expected from identification of molecular signatures of developmental innovations within a phylogenetic framework, and from a focus on later developmental stages to identify the differentiation of repeated units of different systems within segmental precursors.
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Affiliation(s)
- Ariel D Chipman
- Department of Ecology, Evolution and Behavior, The Silberman Institute of Life Sciences, Edmond J. Safra Campus - Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
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4
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Verd B, Monk NAM, Jaeger J. Modularity, criticality, and evolvability of a developmental gene regulatory network. eLife 2019; 8:e42832. [PMID: 31169494 PMCID: PMC6645726 DOI: 10.7554/elife.42832] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/05/2019] [Indexed: 01/16/2023] Open
Abstract
The existence of discrete phenotypic traits suggests that the complex regulatory processes which produce them are functionally modular. These processes are usually represented by networks. Only modular networks can be partitioned into intelligible subcircuits able to evolve relatively independently. Traditionally, functional modularity is approximated by detection of modularity in network structure. However, the correlation between structure and function is loose. Many regulatory networks exhibit modular behaviour without structural modularity. Here we partition an experimentally tractable regulatory network-the gap gene system of dipteran insects-using an alternative approach. We show that this system, although not structurally modular, is composed of dynamical modules driving different aspects of whole-network behaviour. All these subcircuits share the same regulatory structure, but differ in components and sensitivity to regulatory interactions. Some subcircuits are in a state of criticality, while others are not, which explains the observed differential evolvability of the various expression features in the system.
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Affiliation(s)
- Berta Verd
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- Konrad Lorenz Institute for Evolution and Cognition Research (KLI)KlosterneuburgAustria
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Nicholas AM Monk
- School of Mathematics and StatisticsUniversity of SheffieldSheffieldUnited States
| | - Johannes Jaeger
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- Konrad Lorenz Institute for Evolution and Cognition Research (KLI)KlosterneuburgAustria
- School of Mathematics and StatisticsUniversity of SheffieldSheffieldUnited States
- Wissenschaftskolleg zu BerlinBerlinGermany
- Center for Systems Biology Dresden (CSBD)DresdenGermany
- Complexity Science Hub (CSH)ViennaAustria
- Centre de Recherches Interdisciplinaires (CRI)ParisFrance
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5
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Jiménez-Guri E, Wotton KR, Jaeger J. tarsal-less is expressed as a gap gene but has no gap gene phenotype in the moth midge Clogmia albipunctata. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180458. [PMID: 30225035 PMCID: PMC6124123 DOI: 10.1098/rsos.180458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
Gap genes are involved in segment determination during early development of the vinegar fly Drosophila melanogaster and other dipteran insects (flies, midges and mosquitoes). They are expressed in overlapping domains along the antero-posterior (A-P) axis of the blastoderm embryo. While gap domains cover the entire length of the A-P axis in Drosophila, there is a region in the blastoderm of the moth midge Clogmia albipunctata, which lacks canonical gap gene expression. Is a non-canonical gap gene functioning in this area? Here, we characterize tarsal-less (tal) in C. albipunctata. The homologue of tal in the flour beetle Tribolium castaneum (called milles-pattes, mlpt) is a bona fide gap gene. We find that Ca-tal is expressed in the region previously reported as lacking gap gene expression. Using RNA interference, we study the interaction of Ca-tal with gap genes. We show that Ca-tal is regulated by gap genes, but only has a very subtle effect on tailless (Ca-tll), while not affecting other gap genes at all. Moreover, cuticle phenotypes of Ca-tal depleted embryos do not show any gap phenotype. We conclude that Ca-tal is expressed and regulated like a gap gene, but does not function as a gap gene in C. albipunctata.
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Affiliation(s)
- Eva Jiménez-Guri
- EMBL/CRG Research Unit in Systems Biology, Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall TR10 9EZ, UK
| | - Karl R. Wotton
- EMBL/CRG Research Unit in Systems Biology, Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Johannes Jaeger
- EMBL/CRG Research Unit in Systems Biology, Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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6
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Fraire-Zamora JJ, Jaeger J, Solon J. Two consecutive microtubule-based epithelial seaming events mediate dorsal closure in the scuttle fly Megaselia abdita. eLife 2018. [PMID: 29537962 PMCID: PMC5851697 DOI: 10.7554/elife.33807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Evolution of morphogenesis is generally associated with changes in genetic regulation. Here, we report evidence indicating that dorsal closure, a conserved morphogenetic process in dipterans, evolved as the consequence of rearrangements in epithelial organization rather than signaling regulation. In Drosophila melanogaster, dorsal closure consists of a two-tissue system where the contraction of extraembryonic amnioserosa and a JNK/Dpp-dependent epidermal actomyosin cable result in microtubule-dependent seaming of the epidermis. We find that dorsal closure in Megaselia abdita, a three-tissue system comprising serosa, amnion and epidermis, differs in morphogenetic rearrangements despite conservation of JNK/Dpp signaling. In addition to an actomyosin cable, M. abdita dorsal closure is driven by the rupture and contraction of the serosa and the consecutive microtubule-dependent seaming of amnion and epidermis. Our study indicates that the evolutionary transition to a reduced system of dorsal closure involves simplification of the seaming process without changing the signaling pathways of closure progression.
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Affiliation(s)
- Juan Jose Fraire-Zamora
- Cell and Developmental Biology Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Johannes Jaeger
- Universitat Pompeu Fabra, Barcelona, Spain.,System Biology Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Konrad Lorenz Institute for Evolution and Cognition Research (KLI), Klosterneuburg, Austria
| | - Jérôme Solon
- Cell and Developmental Biology Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
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7
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Wotton KR, Alcaine-Colet A, Jaeger J, Jiménez-Guri E. Non-canonical dorsoventral patterning in the moth midge Clogmia albipunctata. EvoDevo 2017; 8:20. [PMID: 29158889 PMCID: PMC5683363 DOI: 10.1186/s13227-017-0083-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 11/03/2017] [Indexed: 11/20/2022] Open
Abstract
Background Bone morphogenetic proteins (BMPs) are of central importance for dorsal–ventral (DV) axis specification. They are core components of a signalling cascade that includes the BMP ligand decapentaplegic (DPP) and its antagonist short gastrulation (SOG) in Drosophila melanogaster. These components are very ancient, with orthologs involved in DV patterning in both protostomes and deuterostomes. Despite such strong conservation, recent comparative work in insects has revealed interesting differences in the way the patterning function of the DV system is achieved in different species. Results In this paper, we characterise the expression patterns of the principal components of the BMP DV patterning system, as well as its signalling outputs and downstream targets, in the non-cyclorrhaphan moth midge Clogmia albipunctata (Diptera: Psychodidae). We previously reported ventral expression patterns of dpp in the pole regions of C. albipunctata blastoderm embryos. Strikingly, we also find ventral sog and posteriorly restricted tkv expression, as well as expanded polar activity of pMad. We use our results from gene knock-down by embryonic RNA interference to propose a mechanism of polar morphogen shuttling in C. albipunctata. We compare these results to available data from other species and discuss scenarios for the evolution of DV signalling in the holometabolan insects. Conclusions A comparison of gene expression patterns across hemipteran and holometabolan insects reveals that expression of upstream signalling factors in the DV system is very variable, while signalling output is highly conserved. This has two major implications: first, as long as ligand shuttling and other upstream regulatory mechanisms lead to an appropriately localised activation of BMP signalling at the dorsal midline, it is of less importance exactly where the upstream components of the DV system are expressed. This, in turn, explains why the early-acting components of the DV patterning system in insects exhibit extensive amounts of developmental systems drift constrained by highly conserved downstream signalling output.
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Affiliation(s)
- Karl R Wotton
- EMBL/CRG Research Unit in Systems Biology, Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Present Address: Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall TR10 9EZ UK
| | - Anna Alcaine-Colet
- EMBL/CRG Research Unit in Systems Biology, Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Johannes Jaeger
- EMBL/CRG Research Unit in Systems Biology, Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Present Address: Complexity Science Hub Vienna, Josefstädter Straße 39, 1080 Vienna, Austria
| | - Eva Jiménez-Guri
- EMBL/CRG Research Unit in Systems Biology, Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Present Address: Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall TR10 9EZ UK
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8
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Ginzburg N, Cohen M, Chipman AD. Factors involved in early polarization of the anterior-posterior axis in the milkweed bugOncopeltus fasciatus. Genesis 2017; 55. [DOI: 10.1002/dvg.23027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 02/20/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Neta Ginzburg
- The Department of Ecology; Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus; Givat Ram Jerusalem 91904 Israel
| | - Mira Cohen
- The Department of Ecology; Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus; Givat Ram Jerusalem 91904 Israel
| | - Ariel D. Chipman
- The Department of Ecology; Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus; Givat Ram Jerusalem 91904 Israel
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9
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Urbansky S, González Avalos P, Wosch M, Lemke S. Folded gastrulation and T48 drive the evolution of coordinated mesoderm internalization in flies. eLife 2016; 5. [PMID: 27685537 PMCID: PMC5042651 DOI: 10.7554/elife.18318] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/30/2016] [Indexed: 12/17/2022] Open
Abstract
Gastrulation constitutes a fundamental yet diverse morphogenetic process of metazoan development. Modes of gastrulation range from stochastic translocation of individual cells to coordinated infolding of an epithelial sheet. How such morphogenetic differences are genetically encoded and whether they have provided specific developmental advantages is unclear. Here we identify two genes, folded gastrulation and t48, which in the evolution of fly gastrulation acted as a likely switch from an ingression of individual cells to the invagination of the blastoderm epithelium. Both genes are expressed and required for mesoderm invagination in the fruit fly Drosophila melanogaster but do not appear during mesoderm ingression of the midge Chironomus riparius. We demonstrate that early expression of either or both of these genes in C.riparius is sufficient to invoke mesoderm invagination similar to D.melanogaster. The possible genetic simplicity and a measurable increase in developmental robustness might explain repeated evolution of similar transitions in animal gastrulation. DOI:http://dx.doi.org/10.7554/eLife.18318.001 In animals, gastrulation is a period of time in early development during which a sphere of cells is reorganized into an embryo with cells arranged into three distinct layers (called germ layers). The process has changed substantially during the course of evolution and thus provides a great experimental system to investigate the genetic basis for differences in animal form and shape. As an example, true flies use at least two different mechanisms to make the middle germ layer (the mesoderm). In both cases, the mesoderm is made up of cells that move inwards from the boundary of the outer germ layer. In midges and some other flies, these cells migrate individually, while in others including fruit flies, the cells move together as a sheet. Fruit flies and midges shared their last common ancestor 250 million years ago and although the genes that make the mesoderm in fruit flies are well understood, little is known about how the mesoderm forms in midges. Urbansky, González Avalos et al. investigated which genes were responsible for the evolutionary transition between the different types of cell migration seen in flies. The experiments identified two genes – called folded gastrulation and t48 – that seem to operate as a simple switch between the two ways that mesoderm cells migrate. Both of these genes are active in fruit fly embryos and are required for the group migration of mesoderm cells. However, the genes do not appear to play a major role in the movement of individual mesoderm cells in midges. Further experiments demonstrate that switching on these genes in midge embryos is sufficient to invoke group mesoderm cell migrations similar to those seen in fruit flies. These findings show that it is possible to identify genetic changes that underlie substantial differences in animal form and shape over hundred million of years. The ease by which Urbansky, González Avalos et al. were able to switch between the two types of mesoderm migration might explain why similar transitions in gastrulation have evolved repeatedly in animals. The next step is to test this hypothesis in other animals. DOI:http://dx.doi.org/10.7554/eLife.18318.002
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Affiliation(s)
- Silvia Urbansky
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Paula González Avalos
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Maike Wosch
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Steffen Lemke
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
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10
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Surkova SY, Golubkova EV, Mamon LA, Samsonova MG. Morphogenetic networks which determine the spatial expression of zygotic genes in early Drosophila embryo. Russ J Dev Biol 2016. [DOI: 10.1134/s1062360416040093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Schmidt-Ott U, Lynch JA. Emerging developmental genetic model systems in holometabolous insects. Curr Opin Genet Dev 2016; 39:116-128. [PMID: 27399647 DOI: 10.1016/j.gde.2016.06.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/25/2016] [Accepted: 06/08/2016] [Indexed: 01/08/2023]
Abstract
The number of insect species that are amenable to functional genetic studies is growing rapidly and provides many new research opportunities in developmental and evolutionary biology. The holometabolous insects represent a disproportionate percentage of animal diversity and are thus well positioned to provide model species for a wide variety of developmental processes. Here we discuss emerging holometabolous models, and review some recent breakthroughs. For example, flies and midges were found to use structurally unrelated long-range pattern organizers, butterflies and moths revealed extensive pattern formation during oogenesis, new imaging possibilities in the flour beetle Tribolium castaneum showed how embryos break free of their extraembryonic membranes, and the complex genetics governing interspecies difference in head shape were revealed in Nasonia wasps.
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Affiliation(s)
- Urs Schmidt-Ott
- Department of Organismal Biology and Anatomy, University of Chicago, United States.
| | - Jeremy A Lynch
- Department of Biological Sciences, University of Illinois at Chicago, United States.
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12
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Crombach A, Wotton KR, Jiménez-Guri E, Jaeger J. Gap Gene Regulatory Dynamics Evolve along a Genotype Network. Mol Biol Evol 2016; 33:1293-307. [PMID: 26796549 PMCID: PMC4839219 DOI: 10.1093/molbev/msw013] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Developmental gene networks implement the dynamic regulatory mechanisms that pattern and shape the organism. Over evolutionary time, the wiring of these networks changes, yet the patterning outcome is often preserved, a phenomenon known as “system drift.” System drift is illustrated by the gap gene network—involved in segmental patterning—in dipteran insects. In the classic model organism Drosophila melanogaster and the nonmodel scuttle fly Megaselia abdita, early activation and placement of gap gene expression domains show significant quantitative differences, yet the final patterning output of the system is essentially identical in both species. In this detailed modeling analysis of system drift, we use gene circuits which are fit to quantitative gap gene expression data in M. abdita and compare them with an equivalent set of models from D. melanogaster. The results of this comparative analysis show precisely how compensatory regulatory mechanisms achieve equivalent final patterns in both species. We discuss the larger implications of the work in terms of “genotype networks” and the ways in which the structure of regulatory networks can influence patterns of evolutionary change (evolvability).
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Affiliation(s)
- Anton Crombach
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Karl R Wotton
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Eva Jiménez-Guri
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Johannes Jaeger
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
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13
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Caroti F, Urbansky S, Wosch M, Lemke S. Germ line transformation and in vivo labeling of nuclei in Diptera: report on Megaselia abdita (Phoridae) and Chironomus riparius (Chironomidae). Dev Genes Evol 2015; 225:179-86. [PMID: 26044750 PMCID: PMC4460289 DOI: 10.1007/s00427-015-0504-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 05/20/2015] [Indexed: 11/28/2022]
Abstract
To understand how and when developmental traits of the fruit fly Drosophila melanogaster originated during the course of insect evolution, similar traits are functionally studied in variably related satellite species. The experimental toolkit available for relevant fly models typically comprises gene expression and loss as well as gain-of-function analyses. Here, we extend the set of available molecular tools to piggyBac-based germ line transformation in two satellite fly models, Megaselia abdita and Chironomus riparius. As proof-of-concept application, we used a Gateway variant of the piggyBac transposon vector pBac{3xP3-eGFPafm} to generate a transgenic line that expresses His2Av-mCherry as fluorescent nuclear reporter ubiquitously in the gastrulating embryo of M. abdita. Our results open two phylogenetically important nodes of the insect order Diptera for advanced developmental evolutionary genetics.
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Affiliation(s)
- Francesca Caroti
- Centre for Organismal Studies, Universität Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Silvia Urbansky
- Centre for Organismal Studies, Universität Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Maike Wosch
- Centre for Organismal Studies, Universität Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Steffen Lemke
- Centre for Organismal Studies, Universität Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
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14
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Wotton KR, Jiménez-Guri E, Jaeger J. Maternal co-ordinate gene regulation and axis polarity in the scuttle fly Megaselia abdita. PLoS Genet 2015; 11:e1005042. [PMID: 25757102 PMCID: PMC4355411 DOI: 10.1371/journal.pgen.1005042] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 01/30/2015] [Indexed: 02/01/2023] Open
Abstract
Axis specification and segment determination in dipteran insects are an excellent model system for comparative analyses of gene network evolution. Antero-posterior polarity of the embryo is established through systems of maternal morphogen gradients. In Drosophila melanogaster, the anterior system acts through opposing gradients of Bicoid (Bcd) and Caudal (Cad), while the posterior system involves Nanos (Nos) and Hunchback (Hb) protein. These systems act redundantly. Both Bcd and Hb need to be eliminated to cause a complete loss of polarity resulting in mirror-duplicated abdomens, so-called bicaudal phenotypes. In contrast, knock-down of bcd alone is sufficient to induce double abdomens in non-drosophilid cyclorrhaphan dipterans such as the hoverfly Episyrphus balteatus or the scuttle fly Megaselia abdita. We investigate conserved and divergent aspects of axis specification in the cyclorrhaphan lineage through a detailed study of the establishment and regulatory effect of maternal gradients in M. abdita. Our results show that the function of the anterior maternal system is highly conserved in this species, despite the loss of maternal cad expression. In contrast, hb does not activate gap genes in this species. The absence of this activatory role provides a precise genetic explanation for the loss of polarity upon bcd knock-down in M. abdita, and suggests a general scenario in which the posterior maternal system is increasingly replaced by the anterior one during the evolution of the cyclorrhaphan dipteran lineage. The basic head-to-tail polarity of an animal is established very early in development. In dipteran insects (flies, midges, and mosquitoes), polarity is established with the help of so-called morphogen gradients. Morphogens are regulatory proteins that are distributed as a concentration gradient, often involving diffusion from a localised source. This graded distribution then leads to the concentration-dependent activation of different target genes along the embryo’s axis. We examine this process, which differs to a surprising extent between dipteran species, in the scuttle fly Megaselia abdita, and compare our results to the model organism Drosophila melanogaster. In this way, we not only gain insights into how the mechanisms that establish polarity function differently in different species, but also how the system has evolved since these two flies shared a common ancestor. Specifically, we pin down the main difference between Drosophila and Megaselia in the altered function of the maternal Hunchback morphogen gradient, which activates target genes in the former, but not the latter species, where it has been completely replaced by the Bicoid morphogen during evolution.
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Affiliation(s)
- Karl R. Wotton
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- * E-mail: (KW); (JJ)
| | - Eva Jiménez-Guri
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Johannes Jaeger
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- * E-mail: (KW); (JJ)
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Wotton KR, Jiménez-Guri E, Crombach A, Cicin-Sain D, Jaeger J. High-resolution gene expression data from blastoderm embryos of the scuttle fly Megaselia abdita. Sci Data 2015; 2:150005. [PMID: 25977812 PMCID: PMC4423355 DOI: 10.1038/sdata.2015.5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/03/2015] [Indexed: 12/21/2022] Open
Abstract
Gap genes are involved in segment determination during early development in dipteran insects (flies, midges, and mosquitoes). We carried out a systematic quantitative comparative analysis of the gap gene network across different dipteran species. Our work provides mechanistic insights into the evolution of this pattern-forming network. As a central component of our project, we created a high-resolution quantitative spatio-temporal data set of gap and maternal co-ordinate gene expression in the blastoderm embryo of the non-drosophilid scuttle fly, Megaselia abdita. Our data include expression patterns in both wild-type and RNAi-treated embryos. The data-covering 10 genes, 10 time points, and over 1,000 individual embryos-consist of original embryo images, quantified expression profiles, extracted positions of expression boundaries, and integrated expression patterns, plus metadata and intermediate processing steps. These data provide a valuable resource for researchers interested in the comparative study of gene regulatory networks and pattern formation, an essential step towards a more quantitative and mechanistic understanding of developmental evolution.
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Affiliation(s)
- Karl R Wotton
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Eva Jiménez-Guri
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Anton Crombach
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Damjan Cicin-Sain
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Johannes Jaeger
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
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Wotton KR, Jiménez-Guri E, Crombach A, Janssens H, Alcaine-Colet A, Lemke S, Schmidt-Ott U, Jaeger J. Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita. eLife 2015; 4:e04785. [PMID: 25560971 PMCID: PMC4337606 DOI: 10.7554/elife.04785] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 01/02/2015] [Indexed: 12/20/2022] Open
Abstract
The segmentation gene network in insects can produce equivalent phenotypic outputs despite differences in upstream regulatory inputs between species. We investigate the mechanistic basis of this phenomenon through a systems-level analysis of the gap gene network in the scuttle fly Megaselia abdita (Phoridae). It combines quantification of gene expression at high spatio-temporal resolution with systematic knock-downs by RNA interference (RNAi). Initiation and dynamics of gap gene expression differ markedly between M. abdita and Drosophila melanogaster, while the output of the system converges to equivalent patterns at the end of the blastoderm stage. Although the qualitative structure of the gap gene network is conserved, there are differences in the strength of regulatory interactions between species. We term such network rewiring 'quantitative system drift'. It provides a mechanistic explanation for the developmental hourglass model in the dipteran lineage. Quantitative system drift is likely to be a widespread mechanism for developmental evolution.
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Affiliation(s)
- Karl R Wotton
- European Molecular Biology Laboratory, CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Eva Jiménez-Guri
- European Molecular Biology Laboratory, CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Anton Crombach
- European Molecular Biology Laboratory, CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Hilde Janssens
- European Molecular Biology Laboratory, CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Anna Alcaine-Colet
- European Molecular Biology Laboratory, CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - Steffen Lemke
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, United States
| | - Urs Schmidt-Ott
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, United States
| | - Johannes Jaeger
- European Molecular Biology Laboratory, CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
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Cicin-Sain D, Pulido AH, Crombach A, Wotton KR, Jiménez-Guri E, Taly JF, Roma G, Jaeger J. SuperFly: a comparative database for quantified spatio-temporal gene expression patterns in early dipteran embryos. Nucleic Acids Res 2014; 43:D751-5. [PMID: 25404137 PMCID: PMC4383950 DOI: 10.1093/nar/gku1142] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
We present SuperFly (http://superfly.crg.eu), a relational database for quantified spatio-temporal expression data of segmentation genes during early development in different species of dipteran insects (flies, midges and mosquitoes). SuperFly has a special focus on emerging non-drosophilid model systems. The database currently includes data of high spatio-temporal resolution for three species: the vinegar fly Drosophila melanogaster, the scuttle fly Megaselia abdita and the moth midge Clogmia albipunctata. At this point, SuperFly covers up to 9 genes and 16 time points per species, with a total of 1823 individual embryos. It provides an intuitive web interface, enabling the user to query and access original embryo images, quantified expression profiles, extracted positions of expression boundaries and integrated datasets, plus metadata and intermediate processing steps. SuperFly is a valuable new resource for the quantitative comparative study of gene expression patterns across dipteran species. Moreover, it provides an interesting test set for systems biologists interested in fitting mathematical gene network models to data. Both of these aspects are essential ingredients for progress toward a more quantitative and mechanistic understanding of developmental evolution.
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Affiliation(s)
- Damjan Cicin-Sain
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | - Antonio Hermoso Pulido
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | - Anton Crombach
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | - Karl R Wotton
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | - Eva Jiménez-Guri
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | - Jean-François Taly
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | - Guglielmo Roma
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | - Johannes Jaeger
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
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Wotton KR. Heterochronic shifts in germband movements contribute to the rapid embryonic development of the coffin fly Megaselia scalaris. ARTHROPOD STRUCTURE & DEVELOPMENT 2014; 43:589-594. [PMID: 25193503 DOI: 10.1016/j.asd.2014.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 07/31/2014] [Accepted: 08/18/2014] [Indexed: 06/03/2023]
Abstract
The coffin fly, Megaselia scalaris, is a species of medical and forensic importance and is increasingly being used for the study of genetics. Postmortem interval can be estimated based on the life stage of M. scalaris recovered from corpses, therefore many studies have addressed the duration of each life stage. These studies demonstrate that embryogenesis completes significantly faster in M. scalaris than in the congener Megaselia abdita and faster even than the 24 h needed for Drosophila melanogaster embryogenesis. However, until now it has been unclear if this increased speed is achieved by reducing developmental time across all embryonic stages or by the acceleration of individual stages and processes. Here I use time-lapse imaging to create a staging scheme for M. scalaris embryogenesis. Comparison of stages between D. melanogaster and both Megaselia species reveals that heterochronic shifts, simultaneous morphogenetic movements and compression of individual stages all contribute to the rapid development of M. scalaris.
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Affiliation(s)
- Karl R Wotton
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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Wotton KR, Jiménez-Guri E, García Matheu B, Jaeger J. A staging scheme for the development of the scuttle fly Megaselia abdita. PLoS One 2014; 9:e84421. [PMID: 24409295 PMCID: PMC3883658 DOI: 10.1371/journal.pone.0084421] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 11/13/2013] [Indexed: 12/01/2022] Open
Abstract
Model organisms, such as Drosophila melanogaster, provide powerful experimental tools for the study of development. However, approaches using model systems need to be complemented by comparative studies for us to gain a deeper understanding of the functional properties and evolution of developmental processes. New model organisms need to be established to enable such comparative work. The establishment of new model system requires a detailed description of its life cycle and development. The resulting staging scheme is essential for providing morphological context for molecular studies, and allows us to homologise developmental processes between species. In this paper, we provide a staging scheme and morphological characterisation of the life cycle for an emerging non-drosophilid dipteran model system: the scuttle fly Megaselia abdita. We pay particular attention to early embryogenesis (cleavage and blastoderm stages up to gastrulation), the formation and retraction of extraembryonic tissues, and the determination and formation of germ (pole) cells. Despite the large evolutionary distance between the two species (approximately 150 million years), we find that M. abdita development is remarkably similar to D. melanogaster in terms of developmental landmarks and their relative timing.
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Affiliation(s)
- Karl R. Wotton
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Eva Jiménez-Guri
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Belén García Matheu
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Johannes Jaeger
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Barcelona, Spain
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Abstract
During the course of evolution, genomes acquire novel genetic elements as sources of functional and phenotypic diversity, including new genes that originated in recent evolution. In the past few years, substantial progress has been made in understanding the evolution and phenotypic effects of new genes. In particular, an emerging picture is that new genes, despite being present in the genomes of only a subset of species, can rapidly evolve indispensable roles in fundamental biological processes, including development, reproduction, brain function and behaviour. The molecular underpinnings of how new genes can develop these roles are starting to be characterized. These recent discoveries yield fresh insights into our broad understanding of biological diversity at refined resolution.
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MicroRNAs Act as Cofactors in Bicoid-Mediated Translational Repression. Curr Biol 2013; 23:1579-84. [DOI: 10.1016/j.cub.2013.06.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 05/14/2013] [Accepted: 06/17/2013] [Indexed: 12/31/2022]
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Jiménez-Guri E, Huerta-Cepas J, Cozzuto L, Wotton KR, Kang H, Himmelbauer H, Roma G, Gabaldón T, Jaeger J. Comparative transcriptomics of early dipteran development. BMC Genomics 2013; 14:123. [PMID: 23432914 PMCID: PMC3616871 DOI: 10.1186/1471-2164-14-123] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 02/19/2013] [Indexed: 12/24/2022] Open
Abstract
Background Modern sequencing technologies have massively increased the amount of data available for comparative genomics. Whole-transcriptome shotgun sequencing (RNA-seq) provides a powerful basis for comparative studies. In particular, this approach holds great promise for emerging model species in fields such as evolutionary developmental biology (evo-devo). Results We have sequenced early embryonic transcriptomes of two non-drosophilid dipteran species: the moth midge Clogmia albipunctata, and the scuttle fly Megaselia abdita. Our analysis includes a third, published, transcriptome for the hoverfly Episyrphus balteatus. These emerging models for comparative developmental studies close an important phylogenetic gap between Drosophila melanogaster and other insect model systems. In this paper, we provide a comparative analysis of early embryonic transcriptomes across species, and use our data for a phylogenomic re-evaluation of dipteran phylogenetic relationships. Conclusions We show how comparative transcriptomics can be used to create useful resources for evo-devo, and to investigate phylogenetic relationships. Our results demonstrate that de novo assembly of short (Illumina) reads yields high-quality, high-coverage transcriptomic data sets. We use these data to investigate deep dipteran phylogenetic relationships. Our results, based on a concatenation of 160 orthologous genes, provide support for the traditional view of Clogmia being the sister group of Brachycera (Megaselia, Episyrphus, Drosophila), rather than that of Culicomorpha (which includes mosquitoes and blackflies).
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Affiliation(s)
- Eva Jiménez-Guri
- EMBL/CRG Research Unit in Systems Biology, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain
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23
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Andrioli LP. Toward new Drosophila paradigms. Genesis 2012; 50:585-98. [DOI: 10.1002/dvg.22019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 02/07/2012] [Accepted: 02/08/2012] [Indexed: 11/07/2022]
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Jaeger J, Crombach A. Life's attractors : understanding developmental systems through reverse engineering and in silico evolution. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 751:93-119. [PMID: 22821455 DOI: 10.1007/978-1-4614-3567-9_5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We propose an approach to evolutionary systems biology which is based on reverse engineering of gene regulatory networks and in silico evolutionary simulations. We infer regulatory parameters for gene networks by fitting computational models to quantitative expression data. This allows us to characterize the regulatory structure and dynamical repertoire of evolving gene regulatory networks with a reasonable amount of experimental and computational effort. We use the resulting network models to identify those regulatory interactions that are conserved, and those that have diverged between different species. Moreover, we use the models obtained by data fitting as starting points for simulations of evolutionary transitions between species. These simulations enable us to investigate whether such transitions are random, or whether they show stereotypical series of regulatory changes which depend on the structure and dynamical repertoire of an evolving network. Finally, we present a case study-the gap gene network in dipterans (flies, midges, and mosquitoes)-to illustrate the practical application of the proposed methodology, and to highlight the kind of biological insights that can be gained by this approach.
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Rafiqi AM, Lemke S, Schmidt-Ott U. The scuttle fly Megaselia abdita (Phoridae): a link between Drosophila and Mosquito development. Cold Spring Harb Protoc 2011; 2011:pdb.emo143. [PMID: 21460041 DOI: 10.1101/pdb.emo143] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Ab Matteen Rafiqi
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
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26
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Abstract
Gap genes are involved in segment determination during the early development of the fruit fly Drosophila melanogaster as well as in other insects. This review attempts to synthesize the current knowledge of the gap gene network through a comprehensive survey of the experimental literature. I focus on genetic and molecular evidence, which provides us with an almost-complete picture of the regulatory interactions responsible for trunk gap gene expression. I discuss the regulatory mechanisms involved, and highlight the remaining ambiguities and gaps in the evidence. This is followed by a brief discussion of molecular regulatory mechanisms for transcriptional regulation, as well as precision and size-regulation provided by the system. Finally, I discuss evidence on the evolution of gap gene expression from species other than Drosophila. My survey concludes that studies of the gap gene system continue to reveal interesting and important new insights into the role of gene regulatory networks in development and evolution.
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Affiliation(s)
- Johannes Jaeger
- Centre de Regulació Genòmica, Universtitat Pompeu Fabra, Barcelona, Spain.
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27
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García-Solache M, Jaeger J, Akam M. A systematic analysis of the gap gene system in the moth midge Clogmia albipunctata. Dev Biol 2010; 344:306-18. [DOI: 10.1016/j.ydbio.2010.04.019] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2009] [Revised: 04/19/2010] [Accepted: 04/21/2010] [Indexed: 02/04/2023]
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Lemke S, Busch SE, Antonopoulos DA, Meyer F, Domanus MH, Schmidt-Ott U. Maternal activation of gap genes in the hover fly Episyrphus. Development 2010; 137:1709-19. [DOI: 10.1242/dev.046649] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The metameric organization of the insect body plan is initiated with the activation of gap genes, a set of transcription-factor-encoding genes that are zygotically expressed in broad and partially overlapping domains along the anteroposterior (AP) axis of the early embryo. The spatial pattern of gap gene expression domains along the AP axis is generally conserved, but the maternal genes that regulate their expression are not. Building on the comprehensive knowledge of maternal gap gene activation in Drosophila, we used loss- and gain-of-function experiments in the hover fly Episyrphus balteatus (Syrphidae) to address the question of how the maternal regulation of gap genes evolved. We find that, in Episyrphus, a highly diverged bicoid ortholog is solely responsible for the AP polarity of the embryo. Episyrphus bicoid represses anterior zygotic expression of caudal and activates the anterior and central gap genes orthodenticle, hunchback and Krüppel. In bicoid-deficient Episyrphus embryos, nanos is insufficient to generate morphological asymmetry along the AP axis. Furthermore, we find that torso transiently regulates anterior repression of caudal and is required for the activation of orthodenticle, whereas all posterior gap gene domains of knirps, giant, hunchback, tailless and huckebein depend on caudal. We conclude that all maternal coordinate genes have altered their specific functions during the radiation of higher flies (Cyclorrhapha).
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Affiliation(s)
- Steffen Lemke
- University of Chicago, Department of Organismal Biology and Anatomy, CLSC 921B, 920 E. 58th Street, Chicago, IL 60637, USA
| | - Stephanie E. Busch
- University of Chicago, Department of Organismal Biology and Anatomy, CLSC 921B, 920 E. 58th Street, Chicago, IL 60637, USA
| | - Dionysios A. Antonopoulos
- Argonne National Laboratory, Institute for Genomics & Systems Biology, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Folker Meyer
- Argonne National Laboratory, Institute for Genomics & Systems Biology, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Marc H. Domanus
- Argonne National Laboratory, Institute for Genomics & Systems Biology, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Urs Schmidt-Ott
- University of Chicago, Department of Organismal Biology and Anatomy, CLSC 921B, 920 E. 58th Street, Chicago, IL 60637, USA
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29
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Wilson MJ, Havler M, Dearden PK. Giant, Krüppel, and caudal act as gap genes with extensive roles in patterning the honeybee embryo. Dev Biol 2010; 339:200-11. [DOI: 10.1016/j.ydbio.2009.12.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Revised: 12/08/2009] [Accepted: 12/10/2009] [Indexed: 01/26/2023]
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30
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Lemke S, Schmidt-Ott U. Evidence for a composite anterior determinant in the hover fly Episyrphus balteatus (Syrphidae), a cyclorrhaphan fly with an anterodorsal serosa anlage. Development 2009; 136:117-27. [PMID: 19060334 DOI: 10.1242/dev.030270] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Most insect embryos develop from a monolayer of cells around the yolk, but only part of this blastoderm forms the embryonic rudiment. Another part forms extra-embryonic serosa. Size and position of the serosa anlage vary between species, and previous work raises the issue of whether such differences co-evolve with the mechanisms that establish anteroposterior (AP) polarity of the embryo. AP polarity of the Drosophila embryo depends on bicoid, which is necessary and sufficient to determine the anterior body plan. Orthologs of bicoid have been identified in various cyclorrhaphan flies and their occurrence seems to correlate with a mid-dorsal serosa or amnioserosa anlage. Here, we introduce with Episyrphus balteatus (Syrphidae) a cyclorrhaphan model for embryonic AP axis specification that features an anterodorsal serosa anlage. Current phylogenies place Episyrphus within the clade that uses bicoid mRNA as anterior determinant, but no bicoid-like sequence could be identified in this species. Using RNA interference (RNAi) and ectopic mRNA injection, we obtained evidence that pattern formation along the entire AP axis of the Episyrphus embryo relies heavily on the precise regulation of caudal, and that anterior pattern formation in particular depends on two localized factors rather than one. Early zygotic activation of orthodenticle is separated from anterior repression of caudal, two distinct functions which in Drosophila are performed jointly by bicoid, whereas hunchback appears to be regulated by both factors. Furthermore, we found that overexpression of orthodenticle is sufficient to confine the serosa anlage of Episyrphus to dorsal blastoderm. We discuss our findings in a phylogenetic context and propose that Episyrphus employs a primitive cyclorrhaphan mechanism of AP axis specification.
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Affiliation(s)
- Steffen Lemke
- University of Chicago, Department of Organismal Biology and Anatomy, CLSC 921B, 920 E. 58th Street, Chicago, IL 60637, USA
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31
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Gregor T, McGregor AP, Wieschaus EF. Shape and function of the Bicoid morphogen gradient in dipteran species with different sized embryos. Dev Biol 2008; 316:350-8. [PMID: 18328473 DOI: 10.1016/j.ydbio.2008.01.039] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Revised: 01/21/2008] [Accepted: 01/23/2008] [Indexed: 12/19/2022]
Abstract
The Bicoid morphogen evolved approximately 150 MYA from a Hox3 duplication and is only found in higher dipterans. A major difference between dipteran species, however, is the size of the embryo, which varies up to 5-fold. Although the expression of developmental factors scale with egg length, it remains unknown how this scaling is achieved. To test whether scaling is accounted for by the properties of Bicoid, we expressed eGFP fused to the coding region of bicoid from three dipteran species in transgenic Drosophila embryos using the Drosophila bicoid cis-regulatory and mRNA localization sequences. In such embryos, we find that Lucilia sericata and Calliphora vicina Bicoid produce gradients very similar to the endogenous Drosophila gradient and much shorter than what they would have produced in their own respective species. The common shape of the Drosophila, Lucilia and Calliphora Bicoid gradients appears to be a conserved feature of the Bicoid protein. Surprisingly, despite their similar distributions, we find that Bicoid from Lucilia and Calliphora do not rescue Drosophila bicoid mutants, suggesting that that Bicoid proteins have evolved species-specific functional amino acid differences. We also found that maternal expression and anteriorly localization of proteins other than Bcd does not necessarily give rise to a gradient; eGFP produced a uniform protein distribution. However, a shallow gradient was observed using eGFP-NLS, suggesting nuclear localization may be necessary but not sufficient for gradient formation.
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Affiliation(s)
- Thomas Gregor
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA
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Evolutionary origin of the amnioserosa in cyclorrhaphan flies correlates with spatial and temporal expression changes of zen. Proc Natl Acad Sci U S A 2008; 105:234-9. [PMID: 18172205 DOI: 10.1073/pnas.0709145105] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Higher cyclorrhaphan flies including Drosophila develop a single extraembryonic epithelium (amnioserosa), which closes the germband dorsally. In most other insects two extraembryonic epithelia, serosa and amnion, line the inner eggshell and the ventral germband, respectively. How the two extraembryonic epithelia evolved into one is unclear. Recent studies have shown that, in the flour beetle Tribolium and in the milkweed bug Oncopeltus, the homeobox gene zerknüllt (zen) controls the fusion of the amnion with the serosa before dorsal closure. To understand the origin of the amnioserosa in evolution, we examined the expression and function of zen in the extraembryonic tissue of lower Cyclorrhapha. We show that Megaselia abdita (Phoridae) and Episyrphus balteatus (Syrphidae) develop a serosa and a dorsal amnion, suggesting that a dorsal amnion preceded the origin of the amnioserosa in evolution. Using Krüppel (Kr) and pannier (pnr) homologues of Megaselia as markers for serosal and amniotic tissue, respectively, we show that after zen RNAi all extraembryonic tissue becomes indistinguishable from amniotic cells, like in Tribolium but unlike in Drosophila, in which zen controls all aspects of extraembryonic development. Compared with Megaselia and Episyrphus, zen expression in Drosophila is extended to cells that form the amnion in lower Cyclorrhapha and is down-regulated at the developmental stage, when serosa cells in lower Cyclorrhapha begin to expand. These expression differences between species with distinct extraembryonic tissue organizations and the conserved requirement of zen for serosa development suggest that the origin of an amnioserosa-like epithelium was accompanied by expression changes of zen.
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Simpson P, Ayyar S. Chapter 3 Evolution of Cis‐Regulatory Sequences in Drosophila. LONG-RANGE CONTROL OF GENE EXPRESSION 2008; 61:67-106. [DOI: 10.1016/s0065-2660(07)00003-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Dearden PK, Wilson MJ, Sablan L, Osborne PW, Havler M, McNaughton E, Kimura K, Milshina NV, Hasselmann M, Gempe T, Schioett M, Brown SJ, Elsik CG, Holland PW, Kadowaki T, Beye M. Patterns of conservation and change in honey bee developmental genes. Genes Dev 2006; 16:1376-84. [PMID: 17065607 PMCID: PMC1626639 DOI: 10.1101/gr.5108606] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2005] [Accepted: 05/01/2006] [Indexed: 12/16/2022]
Abstract
The current insect genome sequencing projects provide an opportunity to extend studies of the evolution of developmental genes and pathways in insects. In this paper we examine the conservation and divergence of genes and developmental processes between Drosophila and the honey bee; two holometabolous insects whose lineages separated approximately 300 million years ago, by comparing the presence or absence of 308 Drosophila developmental genes in the honey bee. Through examination of the presence or absence of genes involved in conserved pathways (cell signaling, axis formation, segmentation and homeobox transcription factors), we find that the vast majority of genes are conserved. Some genes involved in these processes are, however, missing in the honey bee. We have also examined the orthology of Drosophila genes involved in processes that differ between the honey bee and Drosophila. Many of these genes are preserved in the honey bee despite the process in which they act in Drosophila being different or absent in the honey bee. Many of the missing genes in both situations appear to have arisen recently in the Drosophila lineage, have single known functions in Drosophila, and act early in developmental pathways, while those that are preserved have pleiotropic functions. An evolutionary interpretation of these data is that either genes with multiple functions in a common ancestor are more likely to be preserved in both insect lineages, or genes that are preserved throughout evolution are more likely to co-opt additional functions.
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Affiliation(s)
- Peter K. Dearden
- Laboratory for Evolution and Development, Biochemistry Department, University of Otago, Dunedin, Aotearoa–New Zealand
| | - Megan J. Wilson
- Laboratory for Evolution and Development, Biochemistry Department, University of Otago, Dunedin, Aotearoa–New Zealand
| | - Lisha Sablan
- Laboratory for Evolution and Development, Biochemistry Department, University of Otago, Dunedin, Aotearoa–New Zealand
| | - Peter W. Osborne
- Laboratory for Evolution and Development, Biochemistry Department, University of Otago, Dunedin, Aotearoa–New Zealand
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom
| | - Melanie Havler
- Laboratory for Evolution and Development, Biochemistry Department, University of Otago, Dunedin, Aotearoa–New Zealand
| | - Euan McNaughton
- Laboratory for Evolution and Development, Biochemistry Department, University of Otago, Dunedin, Aotearoa–New Zealand
| | - Kiyoshi Kimura
- Laboratory of Apiculture, Department of Animal Breeding and Reproduction, National Institute of Livestock and Grassland Science, National Agricultural and Bio-oriented Research Organization, Tsukuba, Ibaraki, 305-0901 Japan
| | - Natalia V. Milshina
- Department of Animal Science, Texas A&M University, College Station, Texas 77843, USA
| | - Martin Hasselmann
- Heinrich-Heine Universitaet Düsseldorf, Institut fuer Genetik, 40225 Düsseldorf, Germany
| | - Tanja Gempe
- Heinrich-Heine Universitaet Düsseldorf, Institut fuer Genetik, 40225 Düsseldorf, Germany
| | - Morten Schioett
- Heinrich-Heine Universitaet Düsseldorf, Institut fuer Genetik, 40225 Düsseldorf, Germany
| | - Susan J. Brown
- Division of Biology, Kansas State University, Manhattan, Kansas 66506, USA
| | - Christine G. Elsik
- Department of Animal Science, Texas A&M University, College Station, Texas 77843, USA
| | - Peter W.H. Holland
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom
| | - Tatsuhiko Kadowaki
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601 Japan
| | - Martin Beye
- Heinrich-Heine Universitaet Düsseldorf, Institut fuer Genetik, 40225 Düsseldorf, Germany
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Olesnicky EC, Brent AE, Tonnes L, Walker M, Pultz MA, Leaf D, Desplan C. AcaudalmRNA gradient controls posterior development in the waspNasonia. Development 2006; 133:3973-82. [PMID: 16971471 DOI: 10.1242/dev.02576] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
One of the earliest steps of embryonic development is the establishment of polarity along the anteroposterior axis. Extensive studies of Drosophila embryonic development have elucidated mechanisms for establishing polarity, while studies with other model systems have found that many of these molecular components are conserved through evolution. One exception is Bicoid, the master organizer of anterior development in Drosophila and higher dipterans, which is not conserved. Thus, the study of anteroposterior patterning in insects that lack Bicoid can provide insight into the evolution of the diversity of body plan patterning networks. To this end, we have established the long germ parasitic wasp Nasonia vitripennis as a model for comparative studies with Drosophila.Here we report that, in Nasonia, a gradient of localized caudal mRNA directs posterior patterning, whereas, in Drosophila, the gradient of maternal Caudal protein is established through translational repression by Bicoid of homogeneous caudalmRNA. Loss of caudal function in Nasonia results in severe segmentation defects. We show that Nasonia caudal is an activator of gap gene expression that acts far towards the anterior of the embryo, placing it atop a cascade of early patterning. By contrast, activation of gap genes in flies relies on redundant functions of Bicoid and Caudal, leading to a lack of dramatic action on gap gene expression: caudal instead plays a limited role as an activator of pair-rule gene expression. These studies,together with studies in short germ insects, suggest that caudal is an ancestral master organizer of patterning, and that its role has been reduced in higher dipterans such as Drosophila.
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Demuth JP, Wade MJ. Maternal expression increases the rate of bicoid evolution by relaxing selective constraint. Genetica 2006; 129:37-43. [PMID: 16955333 DOI: 10.1007/s10709-006-0031-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2004] [Revised: 03/16/2005] [Accepted: 06/17/2005] [Indexed: 11/27/2022]
Abstract
Population genetic theory predicts that maternal effect genes will evolve differently than genes expressed in both sexes because selection is only half as effective on autosomal genes expressed in one sex but not the other. Here, we use sequences of the tandem gene duplicates, bicoid (bcd) and zerknüllt (zen), to test the prediction that, with similar coefficients of purifying selection, a maternal effect gene evolves more rapidly than a zygotic gene because of this reduction in selective constraint. We find that the maternal effect gene, bcd, is evolving more rapidly than zygotically expressed, zen, providing the first direct confirmation of this prediction of maternal effect theory from molecular evidence. Our results extend current explanations for the accelerated rate of bcd evolution by providing an evolutionary mechanism, relaxed selective constraint, that allows bcd the evolutionary flexibility to escape the typical functional constraints of early developmental genes. We discuss general implications of our findings for the role of maternal effect genes in early developmental patterning.
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Affiliation(s)
- Jeffery P Demuth
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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Liu PZ, Kaufman TC. Short and long germ segmentation: unanswered questions in the evolution of a developmental mode. Evol Dev 2006; 7:629-46. [PMID: 16336416 DOI: 10.1111/j.1525-142x.2005.05066.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The insect body plan is very well conserved, yet the developmental mechanisms of segmentation are surprisingly varied. Less evolutionarily derived insects undergo short germ segmentation where only the anterior segments are specified before gastrulation whereas the remaining posterior segments are formed during a later secondary growth phase. In contrast, derived long germ insects such as Drosophila specify their entire bodies essentially simultaneously. These fundamental embryological differences imply potentially divergent molecular patterning events. Numerous studies have focused on comparing the expression and function of the homologs of Drosophila segmentation genes between Drosophila and different short and long germ insects. Here we review these comparative data with special emphasis on understanding how short germ insects generate segments and how this ancestral mechanism may have been modified in derived long germ insects such as Drosophila. We break down the larger issue of short versus long germ segmentation into its component developmental problems and structure our discussion in order to highlight the unanswered questions in the evolution of insect segmentation.
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Affiliation(s)
- Paul Z Liu
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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38
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Barker MS, Demuth JP, Wade MJ. Maternal expression relaxes constraint on innovation of the anterior determinant, bicoid. PLoS Genet 2005; 1:e57. [PMID: 16299585 PMCID: PMC1283158 DOI: 10.1371/journal.pgen.0010057] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Accepted: 09/30/2005] [Indexed: 11/19/2022] Open
Abstract
The origin of evolutionary novelty is believed to involve both positive selection and relaxed developmental constraint. In flies, the redesign of anterior patterning during embryogenesis is a major developmental innovation and the rapidly evolving Hox gene, bicoid (bcd), plays a critical role. We report evidence for relaxation of selective constraint acting on bicoid as a result of its maternal pattern of gene expression. Evolutionary theory predicts 2-fold greater sequence diversity for maternal effect genes than for zygotically expressed genes, because natural selection is only half as effective acting on autosomal genes expressed in one sex as it is on genes expressed in both sexes. We sample an individual from ten populations of Drosophila melanogaster and nine populations of D. simulans for polymorphism in the tandem gene duplicates bcd, which is maternally expressed, and zerknüllt (zen), which is zygotically expressed. In both species, we find the ratio of bcd to zen nucleotide diversity to be two or more in the coding regions but one in the noncoding regions, providing the first quantitative support for the theoretical prediction of relaxed selective constraint on maternal-effect genes resulting from sex-limited expression. Our results suggest that the accelerated rate of evolution observed for bcd is owing, at least partly, to variation generated by relaxed selective constraint. How do novel structures and functions originate? This question has proven more difficult to answer than the question of how existing structures are refined to better suit the environment. Evolution by natural selection explains the latter. Ironically, it is the power of natural selection to maintain genes that are suitable for their current roles that also works against the evolution of entirely new traits. The conservation of genes controlling the early stages of embryo development, from worms, to flies, to humans, is a famous example of natural selection's power to constrain evolution and thwart the spread of evolutionary novelties. However, the gene determining which end of the fly embryo becomes the head has a relatively recent origin. How did this gene, bicoid, escape purifying selection and take on a novel function? The authors investigate the hypothesis that because bicoid is expressed only in females it experiences only half as much constraint as a gene expressed in both sexes. Comparing sequences of bicoid with its duplicate gene zerknüllt, which retains expression in both sexes, the authors show that, as expected, the variation in bicoid is twice that of zerknüllt. The findings suggest that relaxed constraint is an important step in the origin of novel function.
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Affiliation(s)
- Michael S Barker
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Jeffery P Demuth
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
- * To whom correspondence should be addressed. E-mail:
| | - Michael J Wade
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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Abstract
Most of our knowledge about the mechanisms of segmentation in arthropods comes from work on Drosophila melanogaster. In recent years it has become clear that this mechanism is far from universal, and different arthropod groups have distinct modes of segmentation that operate through divergent genetic mechanisms. We review recent data from a range of arthropods, identifying which features of the D. melanogaster segmentation cascade are present in the different groups, and discuss the evolutionary implications of their conserved and divergent aspects. A model is emerging, although slowly, for the way that arthropod segmentation mechanisms have evolved.
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Affiliation(s)
- Andrew D Peel
- University Museum of Zoology, Department of Zoology, Downing Street, Cambridge CB2 3EJ, UK
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van der Zee M, Berns N, Roth S. Distinct functions of the Tribolium zerknüllt genes in serosa specification and dorsal closure. Curr Biol 2005; 15:624-36. [PMID: 15823534 DOI: 10.1016/j.cub.2005.02.057] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2004] [Revised: 02/21/2005] [Accepted: 02/21/2005] [Indexed: 11/16/2022]
Abstract
BACKGROUND In the long-germ insect Drosophila, a single extraembryonic membrane, the amnioserosa, covers the embryo at the dorsal side. In ancestral short-germ insects, an inner membrane, the amnion, covers the embryo ventrally, and an outer membrane, the serosa, completely surrounds the embryo. An early differentiation step partitions the uniform blastoderm into the anterior-dorsal serosa and the posterior-ventral germ rudiment giving rise to amnion and embryo proper. In Drosophila, amnioserosa formation depends on the dorsoventral patterning gene zerknüllt (zen), a derived Hox3 gene. RESULTS The short-germ beetle Tribolium castaneum possesses two zen homologs, Tc-zen1 and Tc-zen2. Tc-zen1 acts early and specifies the serosa. The loss of the serosa after Tc-zen1 RNAi is compensated by an expansion of the entire germ rudiment toward the anterior. Instead of the serosa, the amnion covers the embryo at the dorsal side, and later size regulation normalizes the early fate shifts, revealing a high degree of plasticity of short-germ development. Tc-zen2 acts later and initiates the amnion and serosa fusion required for dorsal closure. After Tc-zen2 RNAi, the amnion and serosa stay apart, and the embryo closes ventrally, assuming a completely everted (inside-out) topology. CONCLUSIONS In Tribolium, the duplication of the zen genes was accompanied by subfunctionalization. One of the paralogues, Tc-zen1, acts as an early anterior-posterior patterning gene by specifying the serosa. In absence of the serosa, Tribolium embryogenesis acquires features of long-germ development with a single extraembryonic membrane. We discuss implications for the evolution of insect development including the origin of the zen-derived anterior determinant bicoid.
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Affiliation(s)
- Maurijn van der Zee
- Institut für Entwicklungsbiologie, Universität zu Köln, Gyrhofstrasse 17, D-50931 Köln, Germany
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41
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Abstract
In Drosophila, a Bcd protein gradient orchestrates patterning along the anteroposterior embryonic axis. However, studies of basal flies and other insects have revealed that bcd is a derived Hox3 gene found only in higher dipterans. To understand how bcd acquired its role in flies and how anteroposterior patterning mechanisms have evolved, I first review key features of bcd function in Drosophila: anterior localization and transcriptional and translation control of gene expression. I then discuss investigations of bcd in other higher dipterans that have provided insight into the evolution of regulatory interactions and the Bcd gradient. Finally, I review studies of Drosophila and other insects that address the evolution of bcd function and integration of bcd into ancestral regulatory mechanisms. I suggest further comparative studies may allow us to identify the intermediate steps in bcd evolution. This will make bcd a paradigm for the origin and evolution of genes and regulatory networks.
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Affiliation(s)
- Alistair P McGregor
- Department of Ecology and Evolutionary Biology, Princeton University, New Jersey 08540, USA.
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42
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Sander K, Schmidt-Ott U. Evo-devo aspects of classical and molecular data in a historical perspective. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2004; 302:69-91. [PMID: 14760654 DOI: 10.1002/jez.b.20003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We discuss the interplay between evolution and development as reflected in data and concepts since about 1800. Darwin and his "continental apostle" Haeckel put the striking similarity between early vertebrate embryos in an evolutionary context. Haeckel's partly illicit generalizations discredited evolutionary thinking among early experimental embryologists who moreover noted riddles incompatible with contemporary concepts of homology and evolution. Relevant solutions were suggested by the more recent concept of ontogenetic networks that embody complex regulatory properties and genes with partly overlapping functions. Molecular data on development increasingly reveal evolutionary opportunism, for instance when a widespread signaling chain involved in primitive immune defense was apparently recruited later on for dorso-ventral axis determination in some evolutionarily advanced insect groups. Recently, Rickettsia-related bacteria colonizing many arthropod species were found to "manipulate" the first steps of host development to the advantage of their own propagation, but by ways that could also promote host speciation. Molecular genetics can now document evolutionary steps in ontogenetic networks. In the fruit fly for instance, the novel bicoid gene has superseded a crucial patterning function within a pre-existing network--a case of "molecular caenogenesis." The expression patterns of conserved genes that antagonistically determine dorso-ventral polarity support a literal revolution envisioned almost 200 years ago. This is the dorso-ventral inversion of the body plan in some metazoans--ascribed then to the Articulata, now to the Chordata. The final section posits that the opportunistic character of evolutionary innovations is detrimental to parsimony in development.
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Affiliation(s)
- Klaus Sander
- Institut für Biologie I (Zoologie), D-79104 Freiburg, Germany.
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43
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Abstract
Evolutionary developmental genetics (evo-devo) reveals that the plasticity of development is so important that every developmental biology project should carefully take this point into consideration. The example of bicoid, the first discovered morphogen, illustrates how an essential gene can change its function during evolution. The search for bicoid homologues showed that this gene is surprisingly specific to flies (cyclorraphan diptera) and absent in other insects. In fact, recent studies demonstrate that bicoid is a very derived Hox3 homeotic gene. During insect evolution, the ancestral Hox3 gene lost its homeotic function and acquired new roles in oocytes and embryonic annexes. Then, in the lineage leading to modern flies, a duplication of this new gene, followed by functional divergence, led to the formation of bicoid and zerknüllt. Both genes are located within the Drosophila Hox complex; however, they have no homeotic function. Thanks to the power of Drosophila genetics, it is possible to suggest that torso and hunchback may constitute the insect primitive anterior organizer. The bicoid evolutionary history reveals several fundamental mechanisms of the evolution of developmental genes, such as changes of gene regulation, modifications of protein sequences and gene duplication. It also shows the need for studying a wider range of model organisms before generalisations can be made from data obtained with one particular species.
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Affiliation(s)
- François Bonneton
- Ecole Normale Supérieure de Lyon, LBMC, UMR 5161, 46, allée d'Italie, 69364 Lyon 07, France.
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Agrawal N, Dasaradhi PVN, Mohmmed A, Malhotra P, Bhatnagar RK, Mukherjee SK. RNA interference: biology, mechanism, and applications. Microbiol Mol Biol Rev 2003; 67:657-85. [PMID: 14665679 PMCID: PMC309050 DOI: 10.1128/mmbr.67.4.657-685.2003] [Citation(s) in RCA: 707] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Double-stranded RNA-mediated interference (RNAi) is a simple and rapid method of silencing gene expression in a range of organisms. The silencing of a gene is a consequence of degradation of RNA into short RNAs that activate ribonucleases to target homologous mRNA. The resulting phenotypes either are identical to those of genetic null mutants or resemble an allelic series of mutants. Specific gene silencing has been shown to be related to two ancient processes, cosuppression in plants and quelling in fungi, and has also been associated with regulatory processes such as transposon silencing, antiviral defense mechanisms, gene regulation, and chromosomal modification. Extensive genetic and biochemical analysis revealed a two-step mechanism of RNAi-induced gene silencing. The first step involves degradation of dsRNA into small interfering RNAs (siRNAs), 21 to 25 nucleotides long, by an RNase III-like activity. In the second step, the siRNAs join an RNase complex, RISC (RNA-induced silencing complex), which acts on the cognate mRNA and degrades it. Several key components such as Dicer, RNA-dependent RNA polymerase, helicases, and dsRNA endonucleases have been identified in different organisms for their roles in RNAi. Some of these components also control the development of many organisms by processing many noncoding RNAs, called micro-RNAs. The biogenesis and function of micro-RNAs resemble RNAi activities to a large extent. Recent studies indicate that in the context of RNAi, the genome also undergoes alterations in the form of DNA methylation, heterochromatin formation, and programmed DNA elimination. As a result of these changes, the silencing effect of gene functions is exercised as tightly as possible. Because of its exquisite specificity and efficiency, RNAi is being considered as an important tool not only for functional genomics, but also for gene-specific therapeutic activities that target the mRNAs of disease-related genes.
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Affiliation(s)
- Neema Agrawal
- International Center for Genetic Engineering and Biotechnology, New Delhi 110 067, India
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45
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Wittkopp PJ, Carroll SB, Kopp A. Evolution in black and white: genetic control of pigment patterns in Drosophila. Trends Genet 2003; 19:495-504. [PMID: 12957543 DOI: 10.1016/s0168-9525(03)00194-x] [Citation(s) in RCA: 214] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Patricia J Wittkopp
- Molecular Biology and Genetics, 227 Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
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46
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Abstract
Axial patterning is a fundamental event in early development, and molecules involved in determining the body axes provide a coordinate system for subsequent patterning. While orthologs of Drosophila bicoid and nanos play a conserved role in anteroposterior (AP) patterning within at least a subset of Diptera, conservation of this process has not yet been demonstrated outside of the flies. Indeed, it has been argued that bicoid, an instrumental "anterior" factor in Drosophila melanogaster, acquired this role during the evolution of more-derived dipterans. Interestingly, the interaction of Drosophila maternal nanos and maternal hunchback provides a system for patterning the AP axis that is partially redundant to the anterior system. Previous studies in grasshoppers suggest that hunchback may play a conserved role in axial patterning in this insect, but this function may be supplied solely by the zygotic component of hunchback expression. Here we provide evidence that the early pattern of zygotic grasshopper Hunchback expression is achieved through translational repression that may be mediated through the action of grasshopper nanos. This is consistent with the notion that an anterior gradient system is not necessary in all insects and that the posterior pole "probably conveys longitudinal polarity on the ensuing germ anlage".
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Affiliation(s)
- Sabbi Lall
- HHMI/Department of Organismal Biology and Anatomy, University of Chicago, 5841 South Maryland Avenue MC1028, Chicago, IL 60637, USA
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47
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Abstract
In recent years researchers have analyzed the expression patterns of the Hox genes in a multitude of arthropod species, with the hope of understanding the mechanisms at work in the evolution of the arthropod body plan. Now, with Hox expression data representing all four major groups of arthropods (chelicerates, myriapods, crustaceans, and insects), it seems appropriate to summarize the results and take stock of what has been learned. In this review we summarize the expression and functional data regarding the 10 arthropod Hox genes: labial proboscipedia, Hox3/zen, Deformed, Sex combs reduced, fushi tarazu, Antennapedia, Ultrabithorax, abdominal-A, and Abdominal-B. In addition, we discuss mechanisms of developmental evolutionary change thought to be important for the emergence of novel morphological features within the arthropods.
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Affiliation(s)
- Cynthia L Hughes
- Howard Hughes Medical Institute, Department of Biology, Indiana University, Bloomington, IN 47405, USA
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48
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Abstract
Genomics is the study of the structure and function of the genome: the set of genetic information encoded in the DNA of the nucleus and organelles of an organism. It is a dynamic field that combines traditional paths of inquiry with new approaches that would have been impossible without recent technological developments. Much of the recent focus has been on obtaining the sequence of entire genomes, determining the order and organization of the genes, and developing libraries that provide immediate physical access to any desired DNA fragment. This has enabled functional studies on a genome-wide level, including analysis of the genetic basis of complex traits, quantification of global patterns of gene expression, and systematic gene disruption projects. The successful contribution of genomics to problems in applied entomology requires the cooperation of the private and public sectors to build upon the knowledge derived from the Drosophila genome and effectively develop models for other insect Orders.
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Affiliation(s)
- David G Heckel
- Centre for Environmental Stress and Adaptation Research, Department of Genetics, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Hughes CL, Kaufman TC. Exploring the myriapod body plan: expression patterns of the ten Hox genes in a centipede. Development 2002; 129:1225-38. [PMID: 11874918 DOI: 10.1242/dev.129.5.1225] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The diversity of the arthropod body plan has long been a fascinating subject of study. A flurry of recent research has analyzed Hox gene expression in various arthropod groups, with hopes of gaining insight into the mechanisms that underlie their evolution. The Hox genes have been analyzed in insects, crustaceans and chelicerates. However, the expression patterns of the Hox genes have not yet been comprehensively analyzed in a myriapod. We present the expression patterns of the ten Hox genes in a centipede, Lithobius atkinsoni, and compare our results to those from studies in other arthropods. We have three major findings. First, we find that Hox gene expression is remarkably dynamic across the arthropods. The expression patterns of the Hox genes in the centipede are in many cases intermediate between those of the chelicerates and those of the insects and crustaceans, consistent with the proposed intermediate phylogenetic position of the Myriapoda. Second, we found two ‘extra’ Hox genes in the centipede compared with those in Drosophila. Based on its pattern of expression, Hox3 appears to have a typical Hox-like role in the centipede, suggesting that the novel functions of the Hox3 homologs zen and bicoid were adopted somewhere in the crustacean-insect clade. In the centipede, the expression of the gene fushi tarazu suggests that it has both a Hox-like role (as in the mite), as well as a role in segmentation (as in insects). This suggests that this dramatic change in function was achieved via a multifunctional intermediate, a condition maintained in the centipede. Last, we found that Hox expression correlates with tagmatic boundaries, consistent with the theory that changes in Hox genes had a major role in evolution of the arthropod body plan.
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Affiliation(s)
- Cynthia L Hughes
- Howard Hughes Medical Institute, Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Abstract
Genetic screens in Drosophila melanogaster have helped elucidate the process of axis formation during early embryogenesis. Axis formation in the D. melanogaster embryo involves the use of two fundamentally different mechanisms for generating morphogenetic activity: patterning the anteroposterior axis by diffusion of a transcription factor within the syncytial embryo and specification of the dorsoventral axis through a signal transduction cascade. Identification of Drosophila genes involved in axis formation provides a launch-pad for comparative studies that examine the evolution of axis specification in different insects. Additionally, there is similarity between axial patterning mechanisms elucidated genetically in Drosophila and those demonstrated for chordates such as Xenopus. In this review we examine the postfertilization mechanisms underlying axis specification in Drosophila. Comparative data are then used to ask whether aspects of axis formation might be derived or ancestral.
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Affiliation(s)
- S Lall
- Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois 60637, USA
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