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Zand M, Ruan J. Spatial mapping of single cells in the Drosophila embryo from transcriptomic data based on topological consistency. F1000Res 2020; 9:1014. [PMID: 33824719 PMCID: PMC7993407 DOI: 10.12688/f1000research.24163.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/05/2020] [Indexed: 04/01/2024] Open
Abstract
The advancement in single-cell RNA sequencing technologies allow us to obtain transcriptome at single cell resolution. However, the original spatial context of cells, a crucial knowledge for understanding cellular and tissue-level functions, is often lost during sequencing. To address this issue, the DREAM Single Cell Transcriptomics Challenge launched a community-wide effort to seek computational solutions for spatial mapping of single cells in tissues using single-cell RNAseq (scRNA-seq) data and a reference atlas obtained from in situ hybridization data. As a top-performing team in this competition, we approach this problem in three steps. The first step involves identifying a set of most informative genes based on the consistency between gene expression similarity and cell proximity. For this step, we propose two different approaches, i.e., an unsupervised approach that does not utilize the gold standard location of the cells provided by the challenge organizers, and a supervised approach that relies on the gold standard locations. In the second step, a Particle Swarm Optimization algorithm is used to optimize the weights of different genes in order to maximize matches between the predicted locations and the gold standard locations. Finally, the information embedded in the cell topology is used to improve the predicted cell-location scores by weighted averaging of scores from neighboring locations. Evaluation results based on DREAM scores show that our method accurately predicts the location of single cells, and the predictions lead to successful recovery of the spatial expression patterns for most of landmark genes. In addition, investigating the selected genes demonstrates that most predictive genes are cluster specific, and stable across our supervised and unsupervised gene selection frameworks. Overall, the promising results obtained by our methods in DREAM challenge demonstrated that topological consistency is a useful concept in identifying marker genes and constructing predictive models for spatial mapping of single cells.
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Affiliation(s)
- Maryam Zand
- Computer science, University of Texas at San Antonio, San Antonio, Texas, 78249, USA
| | - Jianhua Ruan
- Computer science, University of Texas at San Antonio, San Antonio, Texas, 78249, USA
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2
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Zand M, Ruan J. Spatial mapping of single cells in the Drosophila embryo from transcriptomic data based on topological consistency. F1000Res 2020; 9:1014. [PMID: 33824719 PMCID: PMC7993407 DOI: 10.12688/f1000research.24163.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/05/2021] [Indexed: 11/30/2022] Open
Abstract
The advancement in single-cell RNA sequencing technologies allow us to obtain transcriptome at single cell resolution. However, the original spatial context of cells, a crucial knowledge for understanding cellular and tissue-level functions, is often lost during sequencing. To address this issue, the DREAM Single Cell Transcriptomics Challenge launched a community-wide effort to seek computational solutions for spatial mapping of single cells in tissues using single-cell RNAseq (scRNA-seq) data and a reference atlas obtained from in situ hybridization data. As a top-performing team in this competition, we approach this problem in three steps. The first step involves identifying a set of most informative genes based on the consistency between gene expression similarity and cell proximity. For this step, we propose two different approaches, i.e., an unsupervised approach that does not utilize the gold standard location of the cells provided by the challenge organizers, and a supervised approach that relies on the gold standard locations. In the second step, a Particle Swarm Optimization algorithm is used to optimize the weights of different genes in order to maximize matches between the predicted locations and the gold standard locations. Finally, the information embedded in the cell topology is used to improve the predicted cell-location scores by weighted averaging of scores from neighboring locations. Evaluation results based on DREAM scores show that our method accurately predicts the location of single cells, and the predictions lead to successful recovery of the spatial expression patterns for most of landmark genes. In addition, investigating the selected genes demonstrates that most predictive genes are cluster specific, and stable across our supervised and unsupervised gene selection frameworks. Overall, the promising results obtained by our methods in DREAM challenge demonstrated that topological consistency is a useful concept in identifying marker genes and constructing predictive models for spatial mapping of single cells.
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Affiliation(s)
- Maryam Zand
- Computer science, University of Texas at San Antonio, San Antonio, Texas, 78249, USA
| | - Jianhua Ruan
- Computer science, University of Texas at San Antonio, San Antonio, Texas, 78249, USA
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3
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Williams TA, Nagy LM. Linking gene regulation to cell behaviors in the posterior growth zone of sequentially segmenting arthropods. ARTHROPOD STRUCTURE & DEVELOPMENT 2017; 46:380-394. [PMID: 27720841 DOI: 10.1016/j.asd.2016.10.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 10/03/2016] [Indexed: 06/06/2023]
Abstract
Virtually all arthropods all arthropods add their body segments sequentially, one by one in an anterior to posterior progression. That process requires not only segment specification but typically growth and elongation. Here we review the functions of some of the key genes that regulate segmentation: Wnt, caudal, Notch pathway, and pair-rule genes, and discuss what can be inferred about their evolution. We focus on how these regulatory factors are integrated with growth and elongation and discuss the importance and challenges of baseline measures of growth and elongation. We emphasize a perspective that integrates the genetic regulation of segment patterning with the cellular mechanisms of growth and elongation.
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Affiliation(s)
| | - Lisa M Nagy
- Department of Molecular and Cellular Biology, The University of Arizona, Tucson, AZ 85721, USA.
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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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5
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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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6
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Klomp J, Athy D, Kwan CW, Bloch NI, Sandmann T, Lemke S, Schmidt-Ott U. Embryo development. A cysteine-clamp gene drives embryo polarity in the midge Chironomus. Science 2015; 348:1040-2. [PMID: 25953821 DOI: 10.1126/science.aaa7105] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 04/27/2015] [Indexed: 12/19/2022]
Abstract
In the fruit fly Drosophila, head formation is driven by a single gene, bicoid, which generates head-to-tail polarity of the main embryonic axis. Bicoid deficiency results in embryos with tail-to-tail polarity and no head. However, most insects lack bicoid, and the molecular mechanism for establishing head-to-tail polarity is poorly understood. We have identified a gene that establishes head-to-tail polarity of the mosquito-like midge, Chironomus riparius. This gene, named panish, encodes a cysteine-clamp DNA binding domain and operates through a different mechanism than bicoid. This finding, combined with the observation that the phylogenetic distributions of panish and bicoid are limited to specific families of flies, reveals frequent evolutionary changes of body axis determinants and a remarkable opportunity to study gene regulatory network evolution.
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Affiliation(s)
- Jeff Klomp
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
| | - Derek Athy
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
| | - Chun Wai Kwan
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
| | - Natasha I Bloch
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
| | - Thomas Sandmann
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Steffen Lemke
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
| | - Urs Schmidt-Ott
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA.
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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, 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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Chang CC, Hsiao YM, Huang TY, Cook CE, Shigenobu S, Chang TH. Noncanonical expression of caudal during early embryogenesis in the pea aphid Acyrthosiphon pisum: maternal cad-driven posterior development is not conserved. INSECT MOLECULAR BIOLOGY 2013; 22:442-455. [PMID: 23683148 DOI: 10.1111/imb.12035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Previously we identified anterior localization of hunchback (Aphb) mRNA in oocytes and early embryos of the parthenogenetic and viviparous pea aphid Acyrthosiphon pisum, suggesting that the breaking of anterior asymmetry in the oocytes leads to the formation of the anterior axis in embryos. In order to study posterior development in the asexual pea aphid, we cloned and analysed the developmental expression of caudal (Apcad), a posterior gene highly conserved in many animal phyla. We found that transcripts of Apcad were not detected in germaria, oocytes and embryos prior to the formation of the blastoderm in the asexual (viviparous) pea aphid. This unusual expression pattern differs from that of the existing insect models, including long- and short-germ insects, where maternal cad mRNA is passed to the early embryos and forms a posterior-anterior gradient. The first detectable Apcad expression occurred in the newly formed primordial germ cells and their adjacent blastodermal cells during late blastulation. From gastrulation onward, and as in other insects, Apcad mRNA is restricted to the posteriormost region of the germ band. Similarly, in the sexual (oviparous) oocytes we were able to identify anterior localization of Aphb mRNA but posterior localization of Apcad was not detected. This suggests that cad-driven posterior development is not conserved during early embryogenesis in asexual and sexual pea aphids.
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Affiliation(s)
- C-C Chang
- Laboratory for Genetics and Development, Department of Entomology/Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan.
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Clayton AM, Cirimotich CM, Dong Y, Dimopoulos G. Caudal is a negative regulator of the Anopheles IMD pathway that controls resistance to Plasmodium falciparum infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 39:323-332. [PMID: 23178401 PMCID: PMC3892953 DOI: 10.1016/j.dci.2012.10.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 10/11/2012] [Accepted: 10/12/2012] [Indexed: 06/02/2023]
Abstract
Malaria parasite transmission depends upon the successful development of Plasmodium in its Anopheles mosquito vector. The mosquito's innate immune system constitutes a major bottleneck for parasite population growth. We show here that in Anopheles gambiae, the midgut-specific transcription factor Caudal acts as a negative regulator in the Imd pathway-mediated immune response against the human malaria parasite Plasmodium falciparum. Caudal also modulates the mosquito midgut bacterial flora. RNAi-mediated silencing of Caudal enhanced the mosquito's resistance to bacterial infections and increased the transcriptional abundance of key immune effector genes. Interestingly, Caudal's silencing resulted in an increased lifespan of the mosquito, while it impaired reproductive fitness with respect to egg laying and hatching.
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Affiliation(s)
| | | | | | - George Dimopoulos
- Corresponding author. Address: W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, MD 21205, USA. Tel.: 1-443-287-0128. Fax: 1-410-955-0105.
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13
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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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14
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Nakao H. Anterior and posterior centers jointly regulate Bombyx embryo body segmentation. Dev Biol 2012; 371:293-301. [DOI: 10.1016/j.ydbio.2012.08.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 08/28/2012] [Indexed: 11/29/2022]
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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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16
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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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17
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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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18
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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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19
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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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Schmidt-Ott U, Rafiqi AM, Lemke S. Hox3/zen and the evolution of extraembryonic epithelia in insects. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 689:133-44. [PMID: 20795328 DOI: 10.1007/978-1-4419-6673-5_10] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Insects have undergone dramatic evolutionary changes in extraembryonic development, which correlate with changes in the expression of the class-3 Hox gene zen. Here, we review the evolution of this gene in insects and point out how changes in zen expression may have affected extraembryonic development at the morphological and the genetic level.
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Affiliation(s)
- Urs Schmidt-Ott
- University of Chicago, Department of Organismal Biology and Anatomy, 920 E. 58th Street, Chicago, IL 60637, USA.
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21
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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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