1
|
Cano‐Fernández H, Brun‐Usan M, Tissot T, Salazar‐Ciudad I. A Morphospace Exploration Using a General Model of Development Reveals a Basic Set of Morphologies for Early Animal Development and Evolution. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2025; 344:45-58. [PMID: 39711075 PMCID: PMC11788879 DOI: 10.1002/jez.b.23279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 10/16/2024] [Accepted: 11/01/2024] [Indexed: 12/24/2024]
Abstract
What morphologies are more likely to appear during evolution is a central question in zoology. Here we offer a novel approach to this question based on first developmental principles. We assumed that morphogenesis results from the genetic regulation of cell properties and behaviors (adhesion, contraction, etc.). We used EmbryoMaker, a general model of development that can simulate any gene network regulating cell properties and behaviors, the mechanical interactions and signaling between cells and the morphologies arising from those. We created spherical initial conditions with anterior and dorsal territories. We performed simulations changing the cell properties and behaviors regulated in these territories to explore which morphologies may have been possible. Thus, we obtained a set of the most basic animal morphologies that can be developmentally possible assuming very simple induction and morphogenesis. Our simulations suggest that elongation, invagination, evagination, condensation and anisotropic growth are the morphogenetic transformations more likely to appear from changes in cell properties and behaviors. We also found some parallels between our simulations and the morphologies of simple animals, some early stages of animal development and fossils attributed to early animals.
Collapse
Affiliation(s)
- Hugo Cano‐Fernández
- Genomics, Bioinformatics and Evolution Group, Departament de Genètica I MicrobiologiaUniversitat Autònoma de BarcelonaCerdanyola del VallèsSpain
| | - Miguel Brun‐Usan
- Departamento de Paleobiología, Center for the Integration of PaleobiologyUniversidad Autónoma de MadridMadridSpain
| | - Tazzio Tissot
- Electronics and Computer Science DepartmentUniversity of SouthamptonSouthamptonUK
| | - Isaac Salazar‐Ciudad
- Genomics, Bioinformatics and Evolution Group, Departament de Genètica I MicrobiologiaUniversitat Autònoma de BarcelonaCerdanyola del VallèsSpain
- Centre de Recerca Matemàtica (CRM)Cerdanyola del VallèsSpain
| |
Collapse
|
2
|
Olivetta M, Bhickta C, Chiaruttini N, Burns J, Dudin O. A multicellular developmental program in a close animal relative. Nature 2024; 635:382-389. [PMID: 39506108 DOI: 10.1038/s41586-024-08115-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 09/25/2024] [Indexed: 11/08/2024]
Abstract
All animals develop from a single-celled zygote into a complex multicellular organism through a series of precisely orchestrated processes1,2. Despite the remarkable conservation of early embryogenesis across animals, the evolutionary origins of how and when this process first emerged remain elusive. Here, by combining time-resolved imaging and transcriptomic profiling, we show that single cells of the ichthyosporean Chromosphaera perkinsii-a close relative that diverged from animals about 1 billion years ago3,4-undergo symmetry breaking and develop through cleavage divisions to produce a prolonged multicellular colony with distinct co-existing cell types. Our findings about the autonomous and palintomic developmental program of C. perkinsii hint that such multicellular development either is much older than previously thought or evolved convergently in ichthyosporeans.
Collapse
Affiliation(s)
- Marine Olivetta
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Chandni Bhickta
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Nicolas Chiaruttini
- Bioimaging and Optics Core Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - John Burns
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA.
| | - Omaya Dudin
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- Department of Biochemistry, University of Geneva, Geneva, Switzerland.
| |
Collapse
|
3
|
Cano-Fernández H, Tissot T, Brun-Usan M, Salazar-Ciudad I. On the origins of developmental robustness: modeling buffering mechanisms against cell-level noise. Development 2023; 150:dev201911. [PMID: 38032004 DOI: 10.1242/dev.201911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023]
Abstract
During development, cells are subject to stochastic fluctuations in their positions (i.e. cell-level noise) that can potentially lead to morphological noise (i.e. stochastic differences between morphologies that are expected to be equal, e.g. the right and left sides of bilateral organisms). In this study, we explore new and existing hypotheses on buffering mechanisms against cell-level noise. Many of these hypotheses focus on how the boundaries between territories of gene expression remain regular and well defined, despite cell-level noise and division. We study these hypotheses and how irregular territory boundaries lead to morphological noise. To determine the consistency of the different hypotheses, we use a general computational model of development: EmbryoMaker. EmbryoMaker can implement arbitrary gene networks regulating basic cell behaviors (contraction, adhesion, etc.), signaling and tissue biomechanics. We found that buffering mechanisms based on the orientation of cell divisions cannot lead to regular boundaries but that other buffering mechanisms can (homotypic adhesion, planar contraction, non-dividing boundaries, constant signaling and majority rule hypotheses). We also explore the effects of the shape and size of the territories on morphological noise.
Collapse
Affiliation(s)
- Hugo Cano-Fernández
- Genomics, Bioinformatics and Evolution group, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona 08193, Spain
| | - Tazzio Tissot
- Electronics and Computer Science Department, University of Southampton, Southampton SO17 1BJ, UK
| | - Miguel Brun-Usan
- Departamento de Biologia, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Isaac Salazar-Ciudad
- Genomics, Bioinformatics and Evolution group, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona 08193, Spain
- Centre de Recerca Matemàtica (CRM), Cerdanyola del Vallès 08193, Spain
| |
Collapse
|
4
|
Peluffo RD, Hernández JA. The Na +,K +-ATPase and its stoichiometric ratio: some thermodynamic speculations. Biophys Rev 2023; 15:539-552. [PMID: 37681108 PMCID: PMC10480117 DOI: 10.1007/s12551-023-01082-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/18/2023] [Indexed: 09/09/2023] Open
Abstract
Almost seventy years after its discovery, the sodium-potassium adenosine triphosphatase (the sodium pump) located in the cell plasma membrane remains a source of novel mechanistic and physiologic findings. A noteworthy feature of this enzyme/transporter is its robust stoichiometric ratio under physiological conditions: it sequentially counter-transports three sodium ions and two potassium ions against their electrochemical potential gradients per each hydrolyzed ATP molecule. Here we summarize some present knowledge about the sodium pump and its physiological roles, and speculate whether energetic constraints may have played a role in the evolutionary selection of its characteristic stoichiometric ratio.
Collapse
Affiliation(s)
- R. Daniel Peluffo
- Group of Biophysical Chemistry, Department of Biological Sciences, CENUR Litoral Norte, Universidad de La República, Rivera 1350, CP: 50000 Salto, Uruguay
| | - Julio A. Hernández
- Biophysics and Systems Biology Section, Department of Cell and Molecular Biology, Facultad de Ciencias, Universidad de La República, Iguá 4225, CP: 11400 Montevideo, Uruguay
| |
Collapse
|
5
|
Fan X, Zhang W. Genome-wide identification of FAR gene family and functional analysis of NlFAR10 during embryogenesis in the brown planthopper Nilaparvata lugens. Int J Biol Macromol 2022; 223:798-811. [PMID: 36375673 DOI: 10.1016/j.ijbiomac.2022.11.075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/02/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022]
Abstract
Fatty acyl-CoA reductases (FARs) catalyze the synthesis of fatty alcohols from corresponding fatty acid precursors in organisms. However, the function of FARs in insect fecundity and embryogenesis remains largely unclear. Here, a total of 22 putative FAR proteins were identified in the brown planthopper Nilaparvata lugens, a hemipteran insect pest of rice, and most of them were highly expressed in embryonic stages. Among them, NlFAR10 was specifically and highly expressed in the later embryogenesis, but was promiscuously expressed in tissues of adults. The heterologously expressed NlFAR10 was able to produce the intermediate fatty acid alcohols from the corresponding acyl-CoA precursors. When NlFAR10 was silenced through RNAi in vivo, the embryogenesis was obviously inhibited, resulting in low hatching rates. Moreover, the metabolome analyses indicated that loss of NlFAR10 affected lipid metabolism and purine metabolism during embryogenesis. To the best of our knowledge, this is the first report of a FAR member affecting insect embryogenesis, thus providing a new target for future pest management.
Collapse
Affiliation(s)
- Xiaobin Fan
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Institute of Zoology, Chinese Academy of Science, No. 1 Beichen WestRoad, Chaoyang District, Beijing, 100101, China
| | - Wenqing Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| |
Collapse
|
6
|
Abstract
The study of developmental processes in Rhodnius prolixus has recently advanced with the sequencing of the genome. In this work, we analyze the maternal gene expression driving oogenesis and early embryogenesis in R. prolixus. We examined the transcriptional profile of mRNAs to establish the genes expressed across the ovary, unfertilized eggs and different embryonic stages of R. prolixus until the formation of the germ band anlage (0, 12, 24, and 48 h post egg laying). We identified 81 putative maternal and ovary-related genes and validated their expression by qRT-PCR. We validate the function of the ortholog gene Bicaudal-D (Rp-BicD) by in situ hybridization and parental RNAi. Consistent with a role in oogenesis and early development of R. prolixus, we show that lack of Rp-BicD does not significantly affect oogenesis but impairs the formation of the blastoderm. Based on our findings, we propose three times of action for maternal genes during oogenesis and embryogenesis in R. prolixus.
Collapse
|
7
|
Tata A, Chow RD, Tata PR. Epithelial cell plasticity: breaking boundaries and changing landscapes. EMBO Rep 2021; 22:e51921. [PMID: 34096150 DOI: 10.15252/embr.202051921] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 05/08/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022] Open
Abstract
Epithelial tissues respond to a wide variety of environmental and genotoxic stresses. As an adaptive mechanism, cells can deviate from their natural paths to acquire new identities, both within and across lineages. Under extreme conditions, epithelial tissues can utilize "shape-shifting" mechanisms whereby they alter their form and function at a tissue-wide scale. Mounting evidence suggests that in order to acquire these alternate tissue identities, cells follow a core set of "tissue logic" principles based on developmental paradigms. Here, we review the terminology and the concepts that have been put forward to describe cell plasticity. We also provide insights into various cell intrinsic and extrinsic factors, including genetic mutations, inflammation, microbiota, and therapeutic agents that contribute to cell plasticity. Additionally, we discuss recent studies that have sought to decode the "syntax" of plasticity-i.e., the cellular and molecular principles through which cells acquire new identities in both homeostatic and malignant epithelial tissues-and how these processes can be manipulated for developing novel cancer therapeutics.
Collapse
Affiliation(s)
- Aleksandra Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Ryan D Chow
- Department of Genetics, Systems Biology Institute, Medical Scientist Training Program, Yale University School of Medicine, New Haven, CT, USA
| | - Purushothama Rao Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA.,Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA.,Regeneration Next, Duke University, Durham, NC, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| |
Collapse
|
8
|
Abstract
The concept of developmental constraints has been central to understand the role of development in morphological evolution. Developmental constraints are classically defined as biases imposed by development on the distribution of morphological variation. This opinion article argues that the concepts of developmental constraints and developmental biases do not accurately represent the role of development in evolution. The concept of developmental constraints was coined to oppose the view that natural selection is all-capable and to highlight the importance of development for understanding evolution. In the modern synthesis, natural selection was seen as the main factor determining the direction of morphological evolution. For that to be the case, morphological variation needs to be isotropic (i.e. equally possible in all directions). The proponents of the developmental constraint concept argued that development makes that some morphological variation is more likely than other (i.e. variation is not isotropic), and that, thus, development constraints evolution by precluding natural selection from being all-capable. This article adds to the idea that development is not compatible with the isotropic expectation by arguing that, in fact, it could not be otherwise: there is no actual reason to expect that development could lead to isotropic morphological variation. It is then argued that, since the isotropic expectation is untenable, the role of development in evolution should not be understood as a departure from such an expectation. The role of development in evolution should be described in an exclusively positive way, as the process determining which directions of morphological variation are possible, instead of negatively, as a process precluding the existence of morphological variation we have no actual reason to expect. This article discusses that this change of perspective is not a mere question of semantics: it leads to a different interpretation of the studies on developmental constraints and to a different research program in evolution and development. This program does not ask whether development constrains evolution. Instead it asks questions such as, for example, how different types of development lead to different types of morphological variation and, together with natural selection, determine the directions in which different lineages evolve.
Collapse
|
9
|
Milocco L, Salazar‐Ciudad I. Is evolution predictable? Quantitative genetics under complex genotype‐phenotype maps. Evolution 2020; 74:230-244. [DOI: 10.1111/evo.13907] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Lisandro Milocco
- Institute of BiotechnologyUniversity of Helsinki 00014 Helsinki Finland
| | - Isaac Salazar‐Ciudad
- Institute of BiotechnologyUniversity of Helsinki 00014 Helsinki Finland
- Centre de Recerca Matemàtica 08193 Barcelona Spain
- Genomics, Bioinformatics and Evolution. Departament de Genètica i MicrobiologiaUniversitat Autònoma de Barcelona 08193 Barcelona Spain
| |
Collapse
|
10
|
Jaeger J, Verd B. Dynamic positional information: Patterning mechanism versus precision in gradient-driven systems. Curr Top Dev Biol 2019; 137:219-246. [PMID: 32143744 DOI: 10.1016/bs.ctdb.2019.11.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There is much talk about information in biology. In developmental biology, this takes the form of "positional information," especially in the context of morphogen-based pattern formation. Unfortunately, the concept of "information" is rarely defined in any precise manner. Here, we provide two alternative interpretations of "positional information," and examine the complementary meanings and uses of each concept. Positional information defined as Shannon information helps us understand decoding and error propagation in patterning systems. General relativistic positional information, in contrast, provides a metric to assess the output of pattern-forming mechanisms. Both interpretations provide powerful conceptual tools that do not compete, but are best used in combination to gain a proper mechanistic understanding of robust patterning.
Collapse
Affiliation(s)
- Johannes Jaeger
- Complexity Science Hub (CSH), Vienna, Austria; Department of Molecular Evolution & Development, University of Vienna, Vienna, Austria.
| | - Berta Verd
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
11
|
Hagolani PF, Zimm R, Marin-Riera M, Salazar-Ciudad I. Cell signaling stabilizes morphogenesis against noise. Development 2019; 146:146/20/dev179309. [PMID: 31628213 DOI: 10.1242/dev.179309] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/12/2019] [Indexed: 01/02/2023]
Abstract
Embryonic development involves gene networks, extracellular signaling, cell behaviors (cell division, adhesion, etc.) and mechanical interactions. How should these be coordinated to lead to complex and robust morphologies? To explore this question, we randomly wired genes and cell behaviors into a huge number of networks in EmbryoMaker. EmbryoMaker is a computational model of animal development that simulates how the 3D positions of cells, i.e. morphology, change over time due to such networks. We found that any gene network can lead to complex morphologies if this activates cell behaviors over large regions of the embryo. Importantly, however, for such complex morphologies to be robust to noise, gene networks should include cell signaling that compartmentalizes the embryo into small regions where cell behaviors are regulated differently. If, instead, cell behaviors are equally regulated over large regions, complex but non-robust morphologies arise. We explain how compartmentalization enhances robustness and why it is a general feature of animal development. Our results are consistent with theories proposing that robustness evolved by the co-option of gene networks and extracellular cell signaling in early animal evolution.
Collapse
Affiliation(s)
- Pascal F Hagolani
- Evo-devo Helsinki community, Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, 00014, Helsinki, Finland
| | - Roland Zimm
- Evo-devo Helsinki community, Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, 00014, Helsinki, Finland.,Institut de Génomique Fonctionnelle de Lyon, UMR 5242, CNRS, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69364 Lyon, France
| | - Miquel Marin-Riera
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; European Molecular Biology Laboratory, 08003 Barcelona, Spain.,Pompeu Fabra University, 08002 Barcelona, Spain
| | - Isaac Salazar-Ciudad
- Evo-devo Helsinki community, Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, 00014, Helsinki, Finland .,Genomics, Bioinformatics and Evolution. Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain.,Centre de Rercerca Matemàtica, 08193, Cerdanyola del Vallès, Spain
| |
Collapse
|
12
|
Coronado-Zamora M, Salvador-Martínez I, Castellano D, Barbadilla A, Salazar-Ciudad I. Adaptation and Conservation throughout the Drosophila melanogaster Life-Cycle. Genome Biol Evol 2019; 11:1463-1482. [PMID: 31028390 PMCID: PMC6535812 DOI: 10.1093/gbe/evz086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2019] [Indexed: 01/09/2023] Open
Abstract
Previous studies of the evolution of genes expressed at different life-cycle stages of Drosophila melanogaster have not been able to disentangle adaptive from nonadaptive substitutions when using nonsynonymous sites. Here, we overcome this limitation by combining whole-genome polymorphism data from D. melanogaster and divergence data between D. melanogaster and Drosophila yakuba. For the set of genes expressed at different life-cycle stages of D. melanogaster, as reported in modENCODE, we estimate the ratio of substitutions relative to polymorphism between nonsynonymous and synonymous sites (α) and then α is discomposed into the ratio of adaptive (ωa) and nonadaptive (ωna) substitutions to synonymous substitutions. We find that the genes expressed in mid- and late-embryonic development are the most conserved, whereas those expressed in early development and postembryonic stages are the least conserved. Importantly, we found that low conservation in early development is due to high rates of nonadaptive substitutions (high ωna), whereas in postembryonic stages it is due, instead, to high rates of adaptive substitutions (high ωa). By using estimates of different genomic features (codon bias, average intron length, exon number, recombination rate, among others), we also find that genes expressed in mid- and late-embryonic development show the most complex architecture: they are larger, have more exons, more transcripts, and longer introns. In addition, these genes are broadly expressed among all stages. We suggest that all these genomic features are related to the conservation of mid- and late-embryonic development. Globally, our study supports the hourglass pattern of conservation and adaptation over the life-cycle.
Collapse
Affiliation(s)
- Marta Coronado-Zamora
- Genomics, Bioinformatics and Evolution, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Irepan Salvador-Martínez
- Evo-Devo Helsinki Community, Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, Finland.,Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | | | - Antonio Barbadilla
- Genomics, Bioinformatics and Evolution, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Isaac Salazar-Ciudad
- Genomics, Bioinformatics and Evolution, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Evo-Devo Helsinki Community, Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, Finland.,Centre de Recerca Matemàtica, Cerdanyola del Vallès, Spain
| |
Collapse
|
13
|
Hu X, Ke L, Wang Z, Zeng Z. Dynamic transcriptome landscape of Asian domestic honeybee (Apis cerana) embryonic development revealed by high-quality RNA sequencing. BMC DEVELOPMENTAL BIOLOGY 2018; 18:11. [PMID: 29653508 PMCID: PMC5899340 DOI: 10.1186/s12861-018-0169-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/03/2018] [Indexed: 12/18/2022]
Abstract
Background Honeybee development consists of four stages: embryo, larva, pupa and adult. Embryogenesis, a key process of cell division and differentiation, takes 3 days in honeybees. However, the embryonic transcriptome and the dynamic regulation of embryonic transcription are still largely uncharacterized in honeybees, especially in the Asian honeybee (Apis cerana). Here, we employed high-quality RNA-seq to explore the transcriptome of Asian honeybee embryos at three ages, approximately 24, 48 and 72 h (referred to as Day1, Day2 and Day3, respectively). Results Nine embryo samples, three from each age, were collected for RNA-seq. According to the staging scheme of honeybee embryos and the morphological features we observed, our Day1, Day2 and Day3 embryos likely corresponded to the late stage four, stage eight and stage ten development stages, respectively. Hierarchical clustering and principal component analysis showed that same-age samples were grouped together, and the Day2 samples had a closer relationship with the Day3 samples than the Day1 samples. Finally, a total of 18,284 genes harboring 55,646 transcripts were detected in the A. cerana embryos, of which 44.5% consisted of the core transcriptome shared by all three ages of embryos. A total of 4088 upregulated and 3046 downregulated genes were identified among the three embryo ages, of which 2010, 3177 and 1528 genes were upregulated and 2088, 2294 and 303 genes were downregulated from Day1 to Day2, from Day1 to Day3 and from Day2 to Day3, respectively. The downregulated genes were mostly involved in cellular, biosynthetic and metabolic processes, gene expression and protein localization, and macromolecule modification; the upregulated genes mainly participated in cell development and differentiation, tissue, organ and system development, and morphogenesis. Interestingly, several biological processes related to the response to and detection of light stimuli were enriched in the first-day A. cerana embryogenesis but not in the Apis mellifera embryogenesis, which was valuable for further investigations. Conclusions Our transcriptomic data substantially expand the number of known transcribed elements in the A. cerana genome and provide a high-quality view of the transcriptome dynamics of A. cerana embryonic development. Electronic supplementary material The online version of this article (10.1186/s12861-018-0169-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xiaofen Hu
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Li Ke
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Zilong Wang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Zhijiang Zeng
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China.
| |
Collapse
|
14
|
Zimm R, Bentley BP, Wyneken J, Moustakas-Verho JE. Environmental Causation of Turtle Scute Anomalies in ovo and in silico. Integr Comp Biol 2017; 57:1303-1311. [DOI: 10.1093/icb/icx066] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
|
15
|
Brun-Usan M, Marín-Riera M, Grande C, Truchado-Garcia M, Salazar-Ciudad I. A set of simple cell processes is sufficient to model spiral cleavage. Development 2016; 144:54-62. [PMID: 27888194 DOI: 10.1242/dev.140285] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 11/14/2016] [Indexed: 11/20/2022]
Abstract
During cleavage, different cellular processes cause the zygote to become partitioned into a set of cells with a specific spatial arrangement. These processes include the orientation of cell division according to: an animal-vegetal gradient; the main axis (Hertwig's rule) of the cell; and the contact areas between cells or the perpendicularity between consecutive cell divisions (Sachs' rule). Cell adhesion and cortical rotation have also been proposed to be involved in spiral cleavage. We use a computational model of cell and tissue biomechanics to account for the different existing hypotheses about how the specific spatial arrangement of cells in spiral cleavage arises during development. Cell polarization by an animal-vegetal gradient, a bias to perpendicularity between consecutive cell divisions (Sachs' rule), cortical rotation and cell adhesion, when combined, reproduce the spiral cleavage, whereas other combinations of processes cannot. Specifically, cortical rotation is necessary at the 8-cell stage to direct all micromeres in the same direction. By varying the relative strength of these processes, we reproduce the spatial arrangement of cells in the blastulae of seven different invertebrate species.
Collapse
Affiliation(s)
- Miguel Brun-Usan
- Genomics, Bioinformatics and Evolution, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain.,Evo-devo Helsinki community, Centre of Excellence in Computational and Experimental Developmental Biology, Institute of Biotechnology, University of Helsinki, PO Box 56, Helsinki FIN-00014, Finland
| | - Miquel Marín-Riera
- Genomics, Bioinformatics and Evolution, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain.,Evo-devo Helsinki community, Centre of Excellence in Computational and Experimental Developmental Biology, Institute of Biotechnology, University of Helsinki, PO Box 56, Helsinki FIN-00014, Finland
| | - Cristina Grande
- Departamento de Biología Molecular and Centro de Biología Molecular, 'Severo Ochoa' (CSIC, Universidad Autónoma de Madrid), Madrid, Spain.,Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain
| | - Marta Truchado-Garcia
- Departamento de Biología Molecular and Centro de Biología Molecular, 'Severo Ochoa' (CSIC, Universidad Autónoma de Madrid), Madrid, Spain.,Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain
| | - Isaac Salazar-Ciudad
- Genomics, Bioinformatics and Evolution, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain .,Evo-devo Helsinki community, Centre of Excellence in Computational and Experimental Developmental Biology, Institute of Biotechnology, University of Helsinki, PO Box 56, Helsinki FIN-00014, Finland
| |
Collapse
|
16
|
Newman SA. 'Biogeneric' developmental processes: drivers of major transitions in animal evolution. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150443. [PMID: 27431521 PMCID: PMC4958937 DOI: 10.1098/rstb.2015.0443] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2016] [Indexed: 02/07/2023] Open
Abstract
Using three examples drawn from animal systems, I advance the hypothesis that major transitions in multicellular evolution often involved the constitution of new cell-based materials with unprecedented morphogenetic capabilities. I term the materials and formative processes that arise when highly evolved cells are incorporated into mesoscale matter 'biogeneric', to reflect their commonality with, and distinctiveness from, the organizational properties of non-living materials. The first transition arose by the innovation of classical cell-adhesive cadherins with transmembrane linkage to the cytoskeleton and the appearance of the morphogen Wnt, transforming some ancestral unicellular holozoans into 'liquid tissues', and thereby originating the metazoans. The second transition involved the new capabilities, within a basal metazoan population, of producing a mechanically stable basal lamina, and of planar cell polarization. This gave rise to the eumetazoans, initially diploblastic (two-layered) forms, and then with the addition of extracellular matrices promoting epithelial-mesenchymal transformation, three-layered triploblasts. The last example is the fin-to-limb transition. Here, the components of a molecular network that promoted the development of species-idiosyncratic endoskeletal elements in gnathostome ancestors are proposed to have evolved to a dynamical regime in which they constituted a Turing-type reaction-diffusion system capable of organizing the stereotypical arrays of elements of lobe-finned fish and tetrapods. The contrasting implications of the biogeneric materials-based and neo-Darwinian perspectives for understanding major evolutionary transitions are discussed.This article is part of the themed issue 'The major synthetic evolutionary transitions'.
Collapse
Affiliation(s)
- Stuart A Newman
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY 10595, USA
| |
Collapse
|
17
|
Dowling A, Doroba C, Maier JA, Cohen L, VandeBerg J, Sears KE. Cellular and molecular drivers of differential organ growth: insights from the limbs of Monodelphis domestica. Dev Genes Evol 2016; 226:235-43. [PMID: 27194412 DOI: 10.1007/s00427-016-0549-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/03/2016] [Indexed: 10/21/2022]
Abstract
A fundamental question in biology is "how is growth differentially regulated during development to produce organs of particular sizes?" We used a new model system for the study of differential organ growth, the limbs of the opossum (Monodelphis domestica), to investigate the cellular and molecular basis of differential organ growth in mammals. Opossum forelimbs grow much faster than hindlimbs, making opossum limbs an exceptional system with which to study differential growth. We first used the great differences in opossum forelimb and hindlimb growth to identify cellular processes and molecular signals that underlie differential limb growth. We then used organ culture and pharmacological addition of FGF ligands and inhibitors to test the role of the Fgf/Mitogen-activated protein kinases (MAPK) signaling pathway in driving these cellular processes. We found that molecular signals from within the limb drive differences in cell proliferation that contribute to the differential growth of the forelimb and hindlimbs of opossums. We also found that alterations in the Fgf/MAPK pathway can generate differences in cell proliferation that mirror those observed between wild-type forelimb and hindlimbs of opossums and that manipulation of Fgf/MAPK signaling affects downstream focal adhesion-extracellular matrix (FA-ECM) and Wnt signaling in opossum limbs. Taken together, these findings suggest that evolutionary changes in the Fgf/MAPK pathway could help drive the observed differences in cell behaviors and growth in opossum forelimb and hindlimbs.
Collapse
Affiliation(s)
- Anna Dowling
- School of Integrative Biology, University of Illinois, 505 S Goodwin Avenue, Urbana, IL, 61801, USA
| | - Carolyn Doroba
- School of Integrative Biology, University of Illinois, 505 S Goodwin Avenue, Urbana, IL, 61801, USA
| | - Jennifer A Maier
- School of Integrative Biology, University of Illinois, 505 S Goodwin Avenue, Urbana, IL, 61801, USA
| | - Lorna Cohen
- School of Integrative Biology, University of Illinois, 505 S Goodwin Avenue, Urbana, IL, 61801, USA
| | - John VandeBerg
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Karen E Sears
- School of Integrative Biology, University of Illinois, 505 S Goodwin Avenue, Urbana, IL, 61801, USA.
- Institute for Genomic Biology, University of Illinois, 1206 W Gregory Drive, Urbana, IL, 61801, USA.
| |
Collapse
|
18
|
Mora Van Cauwelaert E, Arias Del Angel JA, Benítez M, Azpeitia EM. Development of cell differentiation in the transition to multicellularity: a dynamical modeling approach. Front Microbiol 2015; 6:603. [PMID: 26157427 PMCID: PMC4477168 DOI: 10.3389/fmicb.2015.00603] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 06/01/2015] [Indexed: 12/16/2022] Open
Abstract
Multicellularity has emerged and continues to emerge in a variety of lineages and under diverse environmental conditions. In order to attain individuality and integration, multicellular organisms must exhibit spatial cell differentiation, which in turn allows cell aggregates to robustly generate traits and behaviors at the multicellular level. Nevertheless, the mechanisms that may lead to the development of cellular differentiation and patterning in emerging multicellular organisms remain unclear. We briefly review two conceptual frameworks that have addressed this issue: the cooperation-defection framework and the dynamical patterning modules (DPMs) framework. Then, situating ourselves in the DPM formalism first put forward by S. A. Newman and collaborators, we state a hypothesis for cell differentiation and arrangement in cellular masses of emerging multicellular organisms. Our hypothesis is based on the role of the generic cell-to-cell communication and adhesion patterning mechanisms, which are two fundamental mechanisms for the evolution of multicellularity, and whose molecules seem to be well-conserved in extant multicellular organisms and their unicellular relatives. We review some fundamental ideas underlying this hypothesis and contrast them with empirical and theoretical evidence currently available. Next, we use a mathematical model to illustrate how the mechanisms and assumptions considered in the hypothesis we postulate may render stereotypical arrangements of differentiated cells in an emerging cellular aggregate and may contribute to the variation and recreation of multicellular phenotypes. Finally, we discuss the potential implications of our approach and compare them to those entailed by the cooperation-defection framework in the study of cell differentiation in the transition to multicellularity.
Collapse
Affiliation(s)
- Emilio Mora Van Cauwelaert
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de MéxicoMexico, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de MéxicoMexico, Mexico
| | - Juan A. Arias Del Angel
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de MéxicoMexico, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de MéxicoMexico, Mexico
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de MéxicoMexico, Mexico
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de MéxicoMexico, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de MéxicoMexico, Mexico
| | - Eugenio M. Azpeitia
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de MéxicoMexico, Mexico
- Institut National de Recherche en Informatique et en Automatique Project-Team Virtual Plants joint with CIRAD and INRAMontpellier, France
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de MéxicoMexico, Mexico
| |
Collapse
|
19
|
Clark RM, Fewell JH. Transitioning from unstable to stable colony growth in the desert leafcutter ant Acromyrmex versicolor. Behav Ecol Sociobiol 2013. [DOI: 10.1007/s00265-013-1632-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
20
|
Salazar-Ciudad I. Tooth patterning and evolution. Curr Opin Genet Dev 2012; 22:585-92. [PMID: 23266218 DOI: 10.1016/j.gde.2012.10.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 09/28/2012] [Accepted: 10/24/2012] [Indexed: 11/28/2022]
Abstract
Teeth are a good system for studying development and evolution. Tooth development is largely independent of the rest of the body and teeth can be grown in culture to attain almost normal morphology. Their development is not affected by the patterns of movement or sensorial perception in the embryo. Teeth are hard and easily preserved. Thus, there is plenty of easily accessible information about the patterns of morphological variation occurring between and within species. This review summarises recent work and describes how tooth development can be understood as the coupling between a reaction-diffusion system and differential growth produced by diffusible growth factors: which growth factors are involved, how they affect each other's expression and how they affect the spatial patterns of proliferation that lead to final morphology. There are some aspects of tooth development, however, that do not conform to some common assumptions in many reaction-diffusion models. Those are discussed here since they provide clues about how reaction-diffusion systems may work in actual developmental systems. Mathematical models implementing what we know about tooth development are discussed.
Collapse
Affiliation(s)
- Isaac Salazar-Ciudad
- Evolutionary Phenomics Group, Developmental Biology Program, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
21
|
Jaeger J, Irons D, Monk N. The inheritance of process: a dynamical systems approach. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2012; 318:591-612. [PMID: 23060018 DOI: 10.1002/jez.b.22468] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 06/12/2012] [Accepted: 07/01/2012] [Indexed: 11/11/2022]
Abstract
A central unresolved problem of evolutionary biology concerns the way in which evolution at the genotypic level relates to the evolution of phenotypes. This genotype-phenotype map involves developmental and physiological processes, which are complex and not well understood. These processes co-determine the rate and direction of adaptive change by shaping the distribution of phenotypic variability on which selection can act. In this study, we argue-expanding on earlier ideas by Goodwin, Oster, and Alberch-that an explicit treatment of this map in terms of dynamical systems theory can provide an integrated understanding of evolution and development. We describe a conceptual framework, which demonstrates how development determines the probability of possible phenotypic transitions-and hence the evolvability of a biological system. We use a simple conceptual model to illustrate how the regulatory dynamics of the genotype-phenotype map can be passed on from generation to generation, and how heredity itself can be treated as a dynamic process. Our model yields explanations for punctuated evolutionary dynamics, the difference between micro- and macroevolution, and for the role of the environment in major phenotypic transitions. We propose a quantitative research program in evolutionary developmental systems biology-combining experimental methods with mathematical modeling-which aims at elaborating our conceptual framework by applying it to a wide range of evolving developmental systems. This requires a large and sustained effort, which we believe is justified by the significant potential benefits of an extended evolutionary theory that uses dynamic molecular genetic data to reintegrate development and evolution.
Collapse
Affiliation(s)
- Johannes Jaeger
- EMBL/CRG Research Unit in Systems Biology, Centre de Regulació Genòmica, Universtitat Pompeu Fabra, Barcelona, Spain.
| | | | | |
Collapse
|
22
|
The evolution of early animal embryos: conservation or divergence? Trends Ecol Evol 2012; 27:385-93. [DOI: 10.1016/j.tree.2012.03.007] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 03/14/2012] [Accepted: 03/20/2012] [Indexed: 12/17/2022]
|
23
|
Hallgrímsson B, Jamniczky HA, Young NM, Rolian C, Schmidt-Ott U, Marcucio RS. The generation of variation and the developmental basis for evolutionary novelty. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2012; 318:501-17. [PMID: 22649039 DOI: 10.1002/jez.b.22448] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 01/31/2012] [Accepted: 02/02/2012] [Indexed: 01/07/2023]
Abstract
Organisms exhibit an incredible diversity of form, a fact that makes the evolution of novelty seemingly self-evident. However, despite the "obvious" case for novelty, defining this concept in evolutionary terms is highly problematic, so much so that some have suggested discarding it altogether. Approaches to this problem tend to take either an adaptation- or development-based perspective, but we argue here that an exclusive focus on either of these misses the original intent of the novelty concept and undermines its practical utility. We propose instead that for a feature to be novel, it must have evolved both by a transition between adaptive peaks on the fitness landscape and that this transition must have overcome a previous developmental constraint. This definition focuses novelty on the explanation of apparently difficult or low-probability evolutionary transitions and highlights how the integration of developmental and functional considerations are necessary to evolutionary explanation. It further reinforces that novelty is a central concern not just of evolutionary developmental biology (i.e., "evo-devo") but of evolutionary biology more generally. We explore this definition of novelty in light of four examples that range from the obvious to subtle.
Collapse
Affiliation(s)
- Benedikt Hallgrímsson
- Department of Cell Biology & Anatomy, McCaig Bone and Joint Institute, University of Calgary, Calgary, Alberta, Canada.
| | | | | | | | | | | |
Collapse
|
24
|
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: 1.5] [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.
Collapse
|
25
|
Newman SA. Animal egg as evolutionary innovation: a solution to the “embryonic hourglass” puzzle. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2011; 316:467-83. [DOI: 10.1002/jez.b.21417] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Revised: 04/01/2011] [Accepted: 04/07/2011] [Indexed: 12/26/2022]
|