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Abstract
The goal of comparative developmental biology is identifying mechanistic differences in embryonic development between different taxa and how these evolutionary changes have led to morphological and organizational differences in adult body plans. Much of this work has focused on direct-developing species in which the adult forms straight from the embryo and embryonic modifications have direct effects on the adult. However, most animal lineages are defined by indirect development, in which the embryo gives rise to a larval body plan and the adult forms by transformation of the larva. Historically, much of our understanding of complex life cycles is viewed through the lenses of ecology and zoology. In this review, we discuss the importance of establishing developmental rather than morphological or ecological criteria for defining developmental mode and explicitly considering the evolutionary implications of incorporating complex life cycles into broad developmental comparisons of embryos across metazoans.
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Affiliation(s)
- Laurent Formery
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California, USA;
- Department of Cell and Molecular Biology, University of California, Berkeley, California, USA
| | - Christopher J Lowe
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California, USA;
- Chan Zuckerberg BioHub, San Francisco, California, USA
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2
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Kyomen S, Murillo-Rincón AP, Kaucká M. Evolutionary mechanisms modulating the mammalian skull development. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220080. [PMID: 37183900 PMCID: PMC10184257 DOI: 10.1098/rstb.2022.0080] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Mammals possess impressive craniofacial variation that mirrors their adaptation to diverse ecological niches, feeding behaviour, physiology and overall lifestyle. The spectrum of craniofacial geometries is established mainly during embryonic development. The formation of the head represents a sequence of events regulated on genomic, molecular, cellular and tissue level, with each step taking place under tight spatio-temporal control. Even minor variations in timing, position or concentration of the molecular drivers and the resulting events can affect the final shape, size and position of the skeletal elements and the geometry of the head. Our knowledge of craniofacial development increased substantially in the last decades, mainly due to research using conventional vertebrate model organisms. However, how developmental differences in head formation arise specifically within mammals remains largely unexplored. This review highlights three evolutionary mechanisms acknowledged to modify ontogenesis: heterochrony, heterotopy and heterometry. We present recent research that links changes in developmental timing, spatial organization or gene expression levels to the acquisition of species-specific skull morphologies. We highlight how these evolutionary modifications occur on the level of the genes, molecules and cellular processes, and alter conserved developmental programmes to generate a broad spectrum of skull shapes characteristic of the class Mammalia. This article is part of the theme issue 'The mammalian skull: development, structure and function'.
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Affiliation(s)
- Stella Kyomen
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, Plön 24306, Germany
| | - Andrea P Murillo-Rincón
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, Plön 24306, Germany
| | - Markéta Kaucká
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, Plön 24306, Germany
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3
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Cutter AD. Speciation and development. Evol Dev 2023; 25:289-327. [PMID: 37545126 DOI: 10.1111/ede.12454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/13/2023] [Accepted: 07/20/2023] [Indexed: 08/08/2023]
Abstract
Understanding general principles about the origin of species remains one of the foundational challenges in evolutionary biology. The genomic divergence between groups of individuals can spawn hybrid inviability and hybrid sterility, which presents a tantalizing developmental problem. Divergent developmental programs may yield either conserved or divergent phenotypes relative to ancestral traits, both of which can be responsible for reproductive isolation during the speciation process. The genetic mechanisms of developmental evolution involve cis- and trans-acting gene regulatory change, protein-protein interactions, genetic network structures, dosage, and epigenetic regulation, all of which also have roots in population genetic and molecular evolutionary processes. Toward the goal of demystifying Darwin's "mystery of mysteries," this review integrates microevolutionary concepts of genetic change with principles of organismal development, establishing explicit links between population genetic process and developmental mechanisms in the production of macroevolutionary pattern. This integration aims to establish a more unified view of speciation that binds process and mechanism.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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4
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Rothier PS, Fabre AC, Clavel J, Benson RBJ, Herrel A. Mammalian forelimb evolution is driven by uneven proximal-to-distal morphological diversity. eLife 2023; 12:81492. [PMID: 36700542 PMCID: PMC9908075 DOI: 10.7554/elife.81492] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 01/24/2023] [Indexed: 01/27/2023] Open
Abstract
Vertebrate limb morphology often reflects the environment due to variation in locomotor requirements. However, proximal and distal limb segments may evolve differently from one another, reflecting an anatomical gradient of functional specialization that has been suggested to be impacted by the timing of development. Here, we explore whether the temporal sequence of bone condensation predicts variation in the capacity of evolution to generate morphological diversity in proximal and distal forelimb segments across more than 600 species of mammals. Distal elements not only exhibit greater shape diversity, but also show stronger within-element integration and, on average, faster evolutionary responses than intermediate and upper limb segments. Results are consistent with the hypothesis that late developing distal bones display greater morphological variation than more proximal limb elements. However, the higher integration observed within the autopod deviates from such developmental predictions, suggesting that functional specialization plays an important role in driving within-element covariation. Proximal and distal limb segments also show different macroevolutionary patterns, albeit not showing a perfect proximo-distal gradient. The high disparity of the mammalian autopod, reported here, is consistent with the higher potential of development to generate variation in more distal limb structures, as well as functional specialization of the distal elements.
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Affiliation(s)
- Priscila S Rothier
- Département Adaptations du Vivant, Muséum National d'Histoire NaturelleParisFrance
| | - Anne-Claire Fabre
- Naturhistorisches Museum BernBernSwitzerland
- Institute of Ecology and Evolution, University of BernBernSwitzerland
- Life Sciences Department, Vertebrates Division, Natural History MuseumLondonUnited Kingdom
| | - Julien Clavel
- Life Sciences Department, Vertebrates Division, Natural History MuseumLondonUnited Kingdom
- Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023VilleurbanneFrance
| | - Roger BJ Benson
- Department of Earth Sciences, University of OxfordOxfordUnited Kingdom
| | - Anthony Herrel
- Département Adaptations du Vivant, Muséum National d'Histoire NaturelleParisFrance
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5
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Liu J, Huang T, Chen W, Ding C, Zhao T, Zhao X, Cai B, Zhang Y, Li S, Zhang L, Xue M, He X, Ge W, Zhou C, Xu Y, Zhang R. Developmental mRNA m 5C landscape and regulatory innovations of massive m 5C modification of maternal mRNAs in animals. Nat Commun 2022; 13:2484. [PMID: 35513466 PMCID: PMC9072368 DOI: 10.1038/s41467-022-30210-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 04/06/2022] [Indexed: 11/09/2022] Open
Abstract
m5C is one of the longest-known RNA modifications, however, its developmental dynamics, functions, and evolution in mRNAs remain largely unknown. Here, we generate quantitative mRNA m5C maps at different stages of development in 6 vertebrate and invertebrate species and find convergent and unexpected massive methylation of maternal mRNAs mediated by NSUN2 and NSUN6. Using Drosophila as a model, we reveal that embryos lacking maternal mRNA m5C undergo cell cycle delays and fail to timely initiate maternal-to-zygotic transition, implying the functional importance of maternal mRNA m5C. From invertebrates to the lineage leading to humans, two waves of m5C regulatory innovations are observed: higher animals gain cis-directed NSUN2-mediated m5C sites at the 5' end of the mRNAs, accompanied by the emergence of more structured 5'UTR regions; humans gain thousands of trans-directed NSUN6-mediated m5C sites enriched in genes regulating the mitotic cell cycle. Collectively, our studies highlight the existence and regulatory innovations of a mechanism of early embryonic development and provide key resources for elucidating the role of mRNA m5C in biology and disease. mRNAs are known to be decorated with m5C at a low-to-medium level. Here, the authors generate atlases of mRNA m5C during animal development in 6 species and identify convergent and unexpected massive methylation of maternal mRNAs by NSUN2 and NSUN6.
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Affiliation(s)
- Jianheng Liu
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Tao Huang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Wanying Chen
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Chenhui Ding
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Tianxuan Zhao
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Xueni Zhao
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Bing Cai
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Yusen Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Song Li
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Ling Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Maoguang Xue
- Division of Human Reproduction and Developmental Genetics, Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Xiuju He
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Wanzhong Ge
- Division of Human Reproduction and Developmental Genetics, Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China. .,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China. .,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Canquan Zhou
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China.
| | - Yanwen Xu
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China.
| | - Rui Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China.
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6
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Uchida Y, Shigenobu S, Takeda H, Furusawa C, Irie N. Potential contribution of intrinsic developmental stability toward body plan conservation. BMC Biol 2022; 20:82. [PMID: 35399082 PMCID: PMC8996622 DOI: 10.1186/s12915-022-01276-5] [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] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite the morphological diversity of animals, their basic anatomical patterns-the body plans in each animal phylum-have remained highly conserved over hundreds of millions of evolutionary years. This is attributed to conservation of the body plan-establishing developmental period (the phylotypic period) in each lineage. However, the evolutionary mechanism behind this phylotypic period conservation remains under debate. A variety of hypotheses based on the concept of modern synthesis have been proposed, such as negative selection in the phylotypic period through its vulnerability to embryonic lethality. Here we tested a new hypothesis that the phylotypic period is developmentally stable; it has less potential to produce phenotypic variations than the other stages, and this has most likely led to the evolutionary conservation of body plans. RESULTS By analyzing the embryos of inbred Japanese medaka embryos raised under the same laboratory conditions and measuring the whole embryonic transcriptome as a phenotype, we found that the phylotypic period has greater developmental stability than other stages. Comparison of phenotypic differences between two wild medaka populations indicated that the phylotypic period and its genes in this period remained less variational, even after environmental and mutational modifications accumulated during intraspecies evolution. Genes with stable expression levels were enriched with those involved in cell-cell signalling and morphological specification such as Wnt and Hox, implying possible involvement in body plan development of these genes. CONCLUSIONS This study demonstrated the correspondence between the developmental stage with low potential to produce phenotypic variations and that with low diversity in micro- and macroevolution, namely the phylotypic period. Whereas modern synthesis explains evolution as a process of shaping of phenotypic variations caused by mutations, our results highlight the possibility that phenotypic variations are readily limited by the intrinsic nature of organisms, namely developmental stability, thus biasing evolutionary outcomes.
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Affiliation(s)
- Yui Uchida
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, 444-8585, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Chikara Furusawa
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
- Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Naoki Irie
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
- Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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7
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Cornejo-Paramo P, Roper K, Degnan S, Degnan B, Wong ES. Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis. Genome Res 2022; 32:474-487. [PMID: 35045977 PMCID: PMC8896464 DOI: 10.1101/gr.275864.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/12/2022] [Indexed: 11/25/2022]
Abstract
The chromatin environment plays a central role in regulating developmental gene expression in metazoans. Yet, the ancestral regulatory landscape of metazoan embryogenesis is unknown. Here, we generate chromatin accessibility profiles for six embryonic, plus larval and adult stages in the sponge Amphimedon queenslandica. These profiles are reproducible within stages, reflect histone modifications, and identify transcription factor (TF) binding sequence motifs predictive of cis-regulatory elements operating during embryogenesis in other metazoans, but not the unicellular relative Capsaspora. Motif analysis of chromatin accessibility profiles across Amphimedon embryogenesis identifies three major developmental periods. As in bilaterian embryogenesis, early development in Amphimedon involves activating and repressive chromatin in regions both proximal and distal to transcription start sites. Transcriptionally repressive elements (“silencers”) are prominent during late embryogenesis. They coincide with an increase in cis-regulatory regions harboring metazoan TF binding motifs, as well as an increase in the expression of metazoan-specific genes. Changes in chromatin state and gene expression in Amphimedon suggest the conservation of distal enhancers, dynamically silenced chromatin, and TF-DNA binding specificity in animal embryogenesis.
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8
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Anlas K, Trivedi V. Studying evolution of the primary body axis in vivo and in vitro. eLife 2021; 10:e69066. [PMID: 34463611 PMCID: PMC8456739 DOI: 10.7554/elife.69066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/27/2021] [Indexed: 02/06/2023] Open
Abstract
The metazoan body plan is established during early embryogenesis via collective cell rearrangements and evolutionarily conserved gene networks, as part of a process commonly referred to as gastrulation. While substantial progress has been achieved in terms of characterizing the embryonic development of several model organisms, underlying principles of many early patterning processes nevertheless remain enigmatic. Despite the diversity of (pre-)gastrulating embryo and adult body shapes across the animal kingdom, the body axes, which are arguably the most fundamental features, generally remain identical between phyla. Recently there has been a renewed appreciation of ex vivo and in vitro embryo-like systems to model early embryonic patterning events. Here, we briefly review key examples and propose that similarities in morphogenesis and associated gene expression dynamics may reveal an evolutionarily conserved developmental mode as well as provide further insights into the role of external or extraembryonic cues in shaping the early embryo. In summary, we argue that embryo-like systems can be employed to inform previously uncharted aspects of animal body plan evolution as well as associated patterning rules.
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Affiliation(s)
| | - Vikas Trivedi
- EMBL BarcelonaBarcelonaSpain
- EMBL Heidelberg, Developmental BiologyHeidelbergGermany
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9
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Liu J, Viales RR, Khoueiry P, Reddington JP, Girardot C, Furlong E, Robinson-Rechavi M. The hourglass model of evolutionary conservation during embryogenesis extends to developmental enhancers with signatures of positive selection. Genome Res 2021; 31:1573-1581. [PMID: 34266978 PMCID: PMC8415374 DOI: 10.1101/gr.275212.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 06/02/2021] [Indexed: 11/24/2022]
Abstract
Inter-species comparisons of both morphology and gene expression within a phylum have revealed a period in the middle of embryogenesis with more similarity between species compared to earlier and later time-points. This "developmental hourglass" pattern has been observed in many phyla, yet the evolutionary constraints on gene expression, and underlying mechanisms of how this is regulated, remains elusive. Moreover, the role of positive selection on gene regulation in the more diverged earlier and later stages of embryogenesis remains unknown. Here, using DNase-seq to identify regulatory regions in two distant Drosophila species (D. melanogaster and D. virilis), we assessed the evolutionary conservation and adaptive evolution of enhancers throughout multiple stages of embryogenesis. This revealed a higher proportion of conserved enhancers at the phylotypic period, providing a regulatory basis for the hourglass expression pattern. Using an in silico mutagenesis approach, we detect signatures of positive selection on developmental enhancers at early and late stages of embryogenesis, with a depletion at the phylotypic period, suggesting positive selection as one evolutionary mechanism underlying the hourglass pattern of animal evolution.
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10
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Seligmann H, Vuillerme N, Demongeot J. Unpredictable, Counter-Intuitive Geoclimatic and Demographic Correlations of COVID-19 Spread Rates. BIOLOGY 2021; 10:623. [PMID: 34356478 PMCID: PMC8301123 DOI: 10.3390/biology10070623] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/16/2021] [Accepted: 06/29/2021] [Indexed: 11/17/2022]
Abstract
We present spread parameters for first and second waves of the COVID-19 pandemic for USA states, and for consecutive nonoverlapping periods of 20 days for the USA and 51 countries across the globe. We studied spread rates in the USA states and 51 countries, and analyzed associations between spread rates at different periods, and with temperature, elevation, population density and age. USA first/second wave spread rates increase/decrease with population density, and are uncorrelated with temperature and median population age. Spread rates are systematically inversely proportional to those estimated 80-100 days later. Ascending/descending phases of the same wave only partially explain this. Directions of correlations with factors such as temperature and median age flip. Changes in environmental trends of the COVID-19 pandemic remain unpredictable; predictions based on classical epidemiological knowledge are highly uncertain. Negative associations between population density and spread rates, observed in independent samples and at different periods, are most surprising. We suggest that systematic negative associations between spread rates 80-100 days apart could result from confinements selecting for greater contagiousness, a potential double-edged sword effect of confinements.
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Affiliation(s)
- Hervé Seligmann
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France;
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem 91404, Israel;
| | - Nicolas Vuillerme
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France;
| | - Jacques Demongeot
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem 91404, Israel;
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11
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Lineweaver CH, Bussey KJ, Blackburn AC, Davies PCW. Cancer progression as a sequence of atavistic reversions. Bioessays 2021; 43:e2000305. [PMID: 33984158 DOI: 10.1002/bies.202000305] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 12/27/2022]
Abstract
It has long been recognized that cancer onset and progression represent a type of reversion to an ancestral quasi-unicellular phenotype. This general concept has been refined into the atavistic model of cancer that attempts to provide a quantitative analysis and testable predictions based on genomic data. Over the past decade, support for the multicellular-to-unicellular reversion predicted by the atavism model has come from phylostratigraphy. Here, we propose that cancer onset and progression involve more than a one-off multicellular-to-unicellular reversion, and are better described as a series of reversionary transitions. We make new predictions based on the chronology of the unicellular-eukaryote-to-multicellular-eukaryote transition. We also make new predictions based on three other evolutionary transitions that occurred in our lineage: eukaryogenesis, oxidative phosphorylation and the transition to adaptive immunity. We propose several modifications to current phylostratigraphy to improve age resolution to test these predictions. Also see the video abstract here: https://youtu.be/3unEu5JYJrQ.
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Affiliation(s)
- Charles H Lineweaver
- Planetary Science Institute, Research School of Astronomy and Astrophysics & Research School of Earth Sciences, The Australian National University, Canberra, ACT, Australia.,Mt Stromlo Observatory, Canberra, ACT, Australia
| | - Kimberly J Bussey
- Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, Arizona, USA.,Precision Medicine, Midwestern University, Glendale, Arizona, USA
| | - Anneke C Blackburn
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Paul C W Davies
- Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, Arizona, USA
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12
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Xu Z, Kang Q, Yu Z, Tian L, Zhang J, Wang T. Research on the Species Difference of the Hepatotoxicity of Medicine Based on Transcriptome. Front Pharmacol 2021; 12:647084. [PMID: 33995060 PMCID: PMC8115263 DOI: 10.3389/fphar.2021.647084] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/08/2021] [Indexed: 12/18/2022] Open
Abstract
In recent years, several drugs have been withdrawn from use by regulatory bodies owing to hepatotoxicity; therefore, studies on drug-induced liver injury (DILI) are being actively pursued. Most studies evaluating DILI use rats or mice as animal models to determine drug toxicity; however, the toxicity of a drug can vary between rats or mice. These inconsistencies in in vivo studies among different animal models affect the extrapolation of experimental results to humans. Thus, it is particularly important to choose the most suitable animal model to determine drug hepatotoxicity owing to the genomic differences between rats and mice resulting from evolution. In this study, genome-wide transcriptome analysis was used to explore hepatotoxicity caused by differences in species. Our findings provide the preclinical basis to further study the mechanisms of drug hepatotoxicity and aid in the selection of animal models to determine drug safety. We used murine models (Sprague-Dawley and Wistar rats, ICR and Kunming mice) in this study and by using transcriptome sequencing with the differentially expressed genes in rat and mouse livers as the entry point, we explored the mechanism of oxidative stress and the difference in gene expression in the lipid-metabolism pathway between rats and mice. The clinically established hepatotoxic drugs, fructus psoraleae and acetaminophen were used to validate our study. Using pathological studies, we confirmed that oxidative stress in mice was more serious than that in rats, and that Kunming mice were more suited for the study of oxidative stress-related DILI. The validity of our findings was further verified based on gene expression. Thus, our study could serve as a valuable reference for the evaluation of potential preclinical hepatotoxicity. Moreover, it could be used in the prediction and early diagnosis of drug-induced liver injury caused by traditional Chinese medicine or synthetic drugs, thereby providing a new avenue for drug-toxicity studies.
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Affiliation(s)
- Ziying Xu
- Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Qianjun Kang
- Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Zihui Yu
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Lichun Tian
- Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Jingxuan Zhang
- Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Ting Wang
- Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
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13
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Fujimoto S, Yamanaka K, Tanegashima C, Nishimura O, Kuraku S, Kuratani S, Irie N. Measuring potential effects of the developmental burden associated with the vertebrate notochord. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 338:129-136. [PMID: 33689235 PMCID: PMC9291948 DOI: 10.1002/jez.b.23032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 01/11/2021] [Accepted: 01/27/2021] [Indexed: 01/20/2023]
Abstract
The notochord functions primarily as a supporting tissue to maintain the anteroposterior axis of primitive chordates, a function that is replaced entirely by the vertebral column in many vertebrates. The notochord still appears during vertebrate embryogenesis and plays a crucial role in the developmental pattern formation of surrounding structures, such as the somites and neural tube, providing the basis for the vertebrate body plan. The indispensable role of the notochord has often been referred to as the developmental burden and used to explain the evolutionary conservation of notochord; however, the existence of this burden has not been successfully exemplified so far. Since the adaptive value of target tissues appears to result in the evolutionary conservation of upstream structures through the developmental burden, we performed comparative gene expression profiling of the notochord, somites, and neural tube during the mid‐embryonic stages in turtles and chicken to measure their evolutionary conservation. When compared with the somites and neural tube, overall gene expression profiles in the notochord showed significantly lower or merely comparable levels of conservation. However, genes involved in inductive signalings, such as the sonic hedgehog (Shh) cascade and the formation of functional primary cilia, showed relatively higher levels of conservation in all the three structures analyzed. Collectively, these results suggest that shh signals are critical as the inductive source and receiving structures, possibly constituting the inter‐dependencies of developmental burden. Potential evolutionary effects toward notochord by developmental burden was evaluated by Laser Micro Dissection RNAseq (LMDseq). Notochord was less conserved than neural tube and somites; however, genes in sonic hedgehog (shh) signaling cascade was found to be evolutionarily conserved (not only in notochord but also in somites and neural tube). These results suggest that Shh signals are critical as the inductive source and receiving structures, possibly constituting the inter‐dependencies of developmental burden. Further studies that directly measure the burden required to verify the hypothesis are awaited.
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Affiliation(s)
| | | | | | | | | | | | - Naoki Irie
- Department of Biological SciencesThe University of TokyoTokyoJapan
- Universal Biology InstituteThe University of TokyoTokyoJapan
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14
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Kaczmarek P, Metscher B, Rupik W. Embryology of the naso-palatal complex in Gekkota based on detailed 3D analysis in Lepidodactylus lugubris and Eublepharis macularius. J Anat 2021; 238:249-287. [PMID: 33169847 PMCID: PMC7812140 DOI: 10.1111/joa.13312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/10/2020] [Accepted: 08/26/2020] [Indexed: 02/03/2023] Open
Abstract
The vomeronasal organ (VNO), nasal cavity, lacrimal duct, choanal groove, and associated parts of the superficial (soft tissue) palate are called the naso-palatal complex. Despite the morphological diversity of the squamate noses, little is known about the embryological basis of this variation. Moreover, developmental data might be especially interesting in light of the morpho-molecular discordance of squamate phylogeny, since a 'molecular scenario' implies an occurrence of unexpected scale of homoplasy also in olfactory systems. In this study, we used X-ray microtomography and light microscopy to describe morphogenesis of the naso-palatal complex in two gekkotans: Lepidodactylus lugubris (Gekkonidae) and Eublepharis macularius (Eublepharidae). Our embryological data confirmed recent findings about the nature of some developmental processes in squamates, for example, involvement of the lateral nasal prominence in the formation of the choanal groove. Moreover, our study revealed previously unknown differences between the studied gekkotans and allows us to propose redefinition of the anterior concha of Sphenodon. Interpretation of some described conditions might be problematic in the phylogenetic context, since they represent unknown: squamate, nonophidian squamate, or gekkotan features.
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Affiliation(s)
- Paweł Kaczmarek
- Institute of Biology, Biotechnology and Environmental ProtectionFaculty of Natural SciencesUniversity of Silesia in KatowiceKatowicePoland
| | - Brian Metscher
- Department of Evolutionary BiologyUniversity of ViennaViennaAustria
| | - Weronika Rupik
- Institute of Biology, Biotechnology and Environmental ProtectionFaculty of Natural SciencesUniversity of Silesia in KatowiceKatowicePoland
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15
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Uesaka M, Kuratani S, Irie N. The developmental hourglass model and recapitulation: An attempt to integrate the two models. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 338:76-86. [PMID: 33503326 PMCID: PMC9292893 DOI: 10.1002/jez.b.23027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 12/18/2022]
Abstract
Recapitulation is a hypothetical concept that assumes embryogenesis of an animal parallels its own phylogenetic history, sequentially developing from more ancestral features to more derived ones. This concept predicts that the earliest developmental stage of various animals should represent the most evolutionarily conserved patterns. Recent transcriptome‐based studies, on the other hand, have reported that mid‐embryonic, organogenetic periods show the highest level of conservation (the developmental hourglass model). This, however, does not rule out the possibility that recapitulation would still be detected after the mid‐embryonic period. In accordance with this, recapitulation‐like morphological features are enriched in late developmental stages. Moreover, our recent chromatin accessibility‐based study provided molecular evidence for recapitulation in the mid‐to‐late embryogenesis of vertebrates, as newly evolved gene regulatory elements tended to be activated at late embryonic stages. In this review, we revisit the recapitulation hypothesis, together with recent molecular‐based studies that support the developmental hourglass model. We contend that the recapitulation hypothesis does not entirely contradict the developmental hourglass model and that these two may even coexist in later embryonic stages of vertebrates. Finally, we review possible mechanisms underlying the recapitulation pattern of chromatin accessibility together with the hourglass‐like evolutionary conservation in vertebrate embryogenesis. Recapitulation pattern has been reported for chromatin accessibility during the mid‐to‐late embryogenesis. The observed recapitulation pattern and the developmental hourglass model may coexist. The possible evolutionary mechanisms underlying tendencies of embryonic evolution were discussed.
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Affiliation(s)
- Masahiro Uesaka
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,Laboratory for Evolutionary Morphology, RIKEN Cluster for Pioneering Research, Kobe, Japan
| | - Naoki Irie
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
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16
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Futo M, Opašić L, Koska S, Čorak N, Široki T, Ravikumar V, Thorsell A, Lenuzzi M, Kifer D, Domazet-Lošo M, Vlahoviček K, Mijakovic I, Domazet-Lošo T. Embryo-Like Features in Developing Bacillus subtilis Biofilms. Mol Biol Evol 2021; 38:31-47. [PMID: 32871001 PMCID: PMC7783165 DOI: 10.1093/molbev/msaa217] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Correspondence between evolution and development has been discussed for more than two centuries. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure. For instance, it has been increasingly recognized that multicellular behavior underlies biofilm formation in bacteria. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed toward later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants, and fungi. Given that most cells on Earth reside in the form of biofilms and that biofilms represent the oldest known fossils, we anticipate that the widely adopted vision of the first life as a single-cell and free-living organism needs rethinking.
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Affiliation(s)
- Momir Futo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Luka Opašić
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Sara Koska
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Nina Čorak
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Tin Široki
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Vaishnavi Ravikumar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Annika Thorsell
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maša Lenuzzi
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Domagoj Kifer
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Mirjana Domazet-Lošo
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Kristian Vlahoviček
- Bioinformatics Group, Division of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
- School of Biosciences, University of Skövde, Skövde, Sweden
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tomislav Domazet-Lošo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Catholic University of Croatia, Zagreb, Croatia
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17
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How to build a larval body with less than a hundred cells? Insights from the early development of a stalked jellyfish (Staurozoa, Cnidaria). ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-020-00459-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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Liu J, Frochaux M, Gardeux V, Deplancke B, Robinson-Rechavi M. Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo. BMC Biol 2020; 18:129. [PMID: 32950053 PMCID: PMC7502200 DOI: 10.1186/s12915-020-00842-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/07/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The evolution of embryological development has long been characterized by deep conservation. In animal development, the phylotypic stage in mid-embryogenesis is more conserved than either early or late stages among species within the same phylum. Hypotheses to explain this hourglass pattern have focused on purifying the selection of gene regulation. Here, we propose an alternative-genes are regulated in different ways at different stages and have different intrinsic capacities to respond to perturbations on gene expression. RESULTS To eliminate the influence of natural selection, we quantified the expression variability of isogenetic single embryo transcriptomes throughout fly Drosophila melanogaster embryogenesis. We found that the expression variability is lower at the phylotypic stage, supporting that the underlying regulatory architecture in this stage is more robust to stochastic variation on gene expression. We present evidence that the phylotypic stage is also robust to genetic variations on gene expression. Moreover, chromatin regulation appears to play a key role in the variation and evolution of gene expression. CONCLUSIONS We suggest that a phylum-level pattern of embryonic conservation can be explained by the intrinsic difference of gene regulatory mechanisms in different stages.
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Affiliation(s)
- Jialin Liu
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
| | - Michael Frochaux
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Vincent Gardeux
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bart Deplancke
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
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19
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Abstract
New species arise as the genomes of populations diverge. The developmental 'alarm clock' of speciation sounds off when sufficient divergence in genetic control of development leads hybrid individuals to infertility or inviability, the world awoken to the dawn of new species with intrinsic post-zygotic reproductive isolation. Some developmental stages will be more prone to hybrid dysfunction due to how molecular evolution interacts with the ontogenetic timing of gene expression. Considering the ontogeny of hybrid incompatibilities provides a profitable connection between 'evo-devo' and speciation genetics to better link macroevolutionary pattern, microevolutionary process, and molecular mechanisms. Here, we explore speciation alongside development, emphasizing their mutual dependence on genetic network features, fitness landscapes, and developmental system drift. We assess models for how ontogenetic timing of reproductive isolation can be predictable. Experiments and theory within this synthetic perspective can help identify new rules of speciation as well as rules in the molecular evolution of development.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of TorontoTorontoCanada
| | - Joanna D Bundus
- Department of Integrative Biology, University of Wisconsin – MadisonMadisonUnited States
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20
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Gutiérrez-Ramos X, Vázquez M, Dorantes-Acosta AE, Díaz-Fleischer F, Peralta-Alvarez CA, Nuñez-Martínez HN, Arzate-Mejía RG, Recillas-Targa F, Arteaga-Vázquez MA, Zurita M. Novel tephritid-specific features revealed from cytological and transcriptomic analysis of Anastrepha ludens embryonic development. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 122:103412. [PMID: 32417415 DOI: 10.1016/j.ibmb.2020.103412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Anastrepha ludens is a major pest of fruits including citrus and mangoes in Mexico and Central America with major economic and social impacts. Despite its importance, our knowledge on its embryonic development is scarce. Here, we report the first cytological study of embryonic development in A. ludens and provide a transcriptional landscape during key embryonic stages. We established 17 stages of A. ludens embryogenesis that closely resemble the morphological events observed in Drosophila. In addition to the extended duration of embryonic development, we observed notable differences including yolk extrusion at both poles of the embryo, distinct nuclear division waves in the syncytial blastoderm and a heterochronic change during the involution of the head. Characterization of the transcriptional dynamics during syncytial blastoderm, cellular blastoderm and gastrulation, showed that approximately 9000 different transcripts are present at each stage. Even though we identified most of the transcripts with a role during embryonic development present in Drosophila, including sex determination genes, a number of transcripts were absent not only in A. ludens but in other tephritids such as Ceratitis capitata and Bactrocera dorsalis. Intriguingly, some A. ludens embryo transcripts encode proteins present in other organisms but not in other flies. Furthermore, we developed an RNA in situ hybridization protocol that allowed us to obtain the expression patterns of genes whose functions are important in establishing the embryonic body pattern. Our results revealed novel tephritid-specific features during A. ludens embryonic development and open new avenues for strategies aiming to control this important pest.
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Affiliation(s)
- Ximena Gutiérrez-Ramos
- Departamento de Genética Del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico; Group of Epigenetics and Developmental Biology, INBIOTECA, Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Mexico
| | - Martha Vázquez
- Departamento de Genética Del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico
| | - Ana E Dorantes-Acosta
- Group of Epigenetics and Developmental Biology, INBIOTECA, Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Mexico
| | - Francisco Díaz-Fleischer
- Group of Epigenetics and Developmental Biology, INBIOTECA, Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Mexico
| | - Carlos A Peralta-Alvarez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico
| | - Hober N Nuñez-Martínez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico
| | - Rodrigo G Arzate-Mejía
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico
| | - Félix Recillas-Targa
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico
| | - Mario A Arteaga-Vázquez
- Group of Epigenetics and Developmental Biology, INBIOTECA, Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Mexico.
| | - Mario Zurita
- Departamento de Genética Del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico.
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21
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Demongeot J, Seligmann H. Comparisons between small ribosomal RNA and theoretical minimal RNA ring secondary structures confirm phylogenetic and structural accretion histories. Sci Rep 2020; 10:7693. [PMID: 32376895 PMCID: PMC7203183 DOI: 10.1038/s41598-020-64627-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/01/2020] [Indexed: 12/16/2022] Open
Abstract
Ribosomal RNAs are complex structures that presumably evolved by tRNA accretions. Statistical properties of tRNA secondary structures correlate with genetic code integration orders of their cognate amino acids. Ribosomal RNA secondary structures resemble those of tRNAs with recent cognates. Hence, rRNAs presumably evolved from ancestral tRNAs. Here, analyses compare secondary structure subcomponents of small ribosomal RNA subunits with secondary structures of theoretical minimal RNA rings, presumed proto-tRNAs. Two independent methods determined different accretion orders of rRNA structural subelements: (a) classical comparative homology and phylogenetic reconstruction, and (b) a structural hypothesis assuming an inverted onion ring growth where the three-dimensional ribosome's core is most ancient and peripheral elements most recent. Comparisons between (a) and (b) accretions orders with RNA ring secondary structure scales show that recent rRNA subelements are: 1. more like RNA rings with recent cognates, indicating ongoing coevolution between tRNA and rRNA secondary structures; 2. less similar to theoretical minimal RNA rings with ancient cognates. Our method fits (a) and (b) in all examined organisms, more with (a) than (b). Results stress the need to integrate independent methods. Theoretical minimal RNA rings are potential evolutionary references for any sequence-based evolutionary analyses, independent of the focal data from that study.
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Affiliation(s)
- Jacques Demongeot
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, F-38700, La Tronche, France.
| | - Hervé Seligmann
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, F-38700, La Tronche, France
- The National Natural History Collections, The Hebrew University of Jerusalem, 91404, Jerusalem, Israel
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22
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Peng G, Cui G, Ke J, Jing N. Using Single-Cell and Spatial Transcriptomes to Understand Stem Cell Lineage Specification During Early Embryo Development. Annu Rev Genomics Hum Genet 2020; 21:163-181. [PMID: 32339035 DOI: 10.1146/annurev-genom-120219-083220] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Embryonic development and stem cell differentiation provide a paradigm to understand the molecular regulation of coordinated cell fate determination and the architecture of tissue patterning. Emerging technologies such as single-cell RNA sequencing and spatial transcriptomics are opening new avenues to dissect cell organization, the divergence of morphological and molecular properties, and lineage allocation. Rapid advances in experimental and computational tools have enabled researchers to make many discoveries and revisit old hypotheses. In this review, we describe the use of single-cell RNA sequencing in studies of molecular trajectories and gene regulation networks for stem cell lineages, while highlighting the integratedexperimental and computational analysis of single-cell and spatial transcriptomes in the molecular annotation of tissue lineages and development during postimplantation gastrulation.
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Affiliation(s)
- Guangdun Peng
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; .,Center for Cell Lineage and Atlas, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Guizhong Cui
- Center for Cell Lineage and Atlas, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
| | - Jincan Ke
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China;
| | - Naihe Jing
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; .,Center for Cell Lineage and Atlas, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China;
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23
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Ereskovsky AV. In Search of the Ancestral Organization and Phylotypic Stage of Porifera. Russ J Dev Biol 2020. [DOI: 10.1134/s1062360419060031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Sarmah S, Srivastava R, McClintick JN, Janga SC, Edenberg HJ, Marrs JA. Embryonic ethanol exposure alters expression of sox2 and other early transcripts in zebrafish, producing gastrulation defects. Sci Rep 2020; 10:3951. [PMID: 32127575 PMCID: PMC7054311 DOI: 10.1038/s41598-020-59043-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/21/2020] [Indexed: 01/10/2023] Open
Abstract
Ethanol exposure during prenatal development causes fetal alcohol spectrum disorder (FASD), the most frequent preventable birth defect and neurodevelopmental disability syndrome. The molecular targets of ethanol toxicity during development are poorly understood. Developmental stages surrounding gastrulation are very sensitive to ethanol exposure. To understand the effects of ethanol on early transcripts during embryogenesis, we treated zebrafish embryos with ethanol during pre-gastrulation period and examined the transcripts by Affymetrix GeneChip microarray before gastrulation. We identified 521 significantly dysregulated genes, including 61 transcription factors in ethanol-exposed embryos. Sox2, the key regulator of pluripotency and early development was significantly reduced. Functional annotation analysis showed enrichment in transcription regulation, embryonic axes patterning, and signaling pathways, including Wnt, Notch and retinoic acid. We identified all potential genomic targets of 25 dysregulated transcription factors and compared their interactions with the ethanol-dysregulated genes. This analysis predicted that Sox2 targeted a large number of ethanol-dysregulated genes. A gene regulatory network analysis showed that many of the dysregulated genes are targeted by multiple transcription factors. Injection of sox2 mRNA partially rescued ethanol-induced gene expression, epiboly and gastrulation defects. Additional studies of this ethanol dysregulated network may identify therapeutic targets that coordinately regulate early development.
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Affiliation(s)
- Swapnalee Sarmah
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Rajneesh Srivastava
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jeanette N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Sarath C Janga
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - James A Marrs
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA.
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25
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Yamazaki A, Morino Y, Urata M, Yamaguchi M, Minokawa T, Furukawa R, Kondo M, Wada H. pmar1/ phb homeobox genes and the evolution of the double-negative gate for endomesoderm specification in echinoderms. Development 2020; 147:dev.182139. [PMID: 32001441 DOI: 10.1242/dev.182139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 01/20/2020] [Indexed: 12/18/2022]
Abstract
In several model animals, the earliest phases of embryogenesis are regulated by lineage-specific genes, such as Drosophila bicoid Sea urchin (echinoid) embryogenesis is initiated by zygotic expression of pmar1, a paired-class homeobox gene that has been considered to be present only in the lineage of modern urchins (euechinoids). In euechinoids, Pmar1 promotes endomesoderm specification by repressing the hairy and enhancer of split C (hesC) gene. Here, we have identified the basal echinoid (cidaroid) pmar1 gene, which also promotes endomesoderm specification but not by repressing hesC A further search for related genes demonstrated that other echinoderms have pmar1-related genes named phb Functional analyses of starfish Phb proteins indicated that, similar to cidaroid Pmar1, they promote activation of endomesoderm regulatory gene orthologs via an unknown repressor that is not HesC. Based on these results, we propose that Pmar1 may have recapitulated the regulatory function of Phb during the early diversification of echinoids and that the additional repressor HesC was placed under the control of Pmar1 in the euechinoid lineage. This case provides an exceptional model for understanding how early developmental processes diverge.
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Affiliation(s)
- Atsuko Yamazaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan
| | - Yoshiaki Morino
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan
| | - Makoto Urata
- Noto Marine Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Ogi, Noto-cho, Ishikawa 927-0553, Japan.,Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan
| | - Masaaki Yamaguchi
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan
| | - Takuya Minokawa
- Research Center for Marine Biology, Tohoku University, Sakamoto 9, Asamushi, Aomori 039-3501, Japan
| | - Ryohei Furukawa
- Department of Biology, Research and Education Center for Natural Sciences, Keio University, Hiyoshi, Kouhoku-ku, Yokohama, Kanagawa 223-8521, Japan
| | - Mariko Kondo
- Misaki Marine Biological Station, Graduate School of Science, The University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa 238-0225, Japan
| | - Hiroshi Wada
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan
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26
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Demongeot J, Seligmann H. Accretion history of large ribosomal subunits deduced from theoretical minimal RNA rings is congruent with histories derived from phylogenetic and structural methods. Gene 2020; 738:144436. [PMID: 32027954 DOI: 10.1016/j.gene.2020.144436] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/24/2020] [Accepted: 02/01/2020] [Indexed: 12/17/2022]
Abstract
Accretions of tRNAs presumably formed the large complex ribosomal RNA structures. Similarities of tRNA secondary structures with rRNA secondary structures increase with the integration order of their cognate amino acid in the genetic code, indicating tRNA evolution towards rRNA-like structures. Here analyses rank secondary structure subelements of three large ribosomal RNAs (Prokaryota: Archaea: Thermus thermophilus; Bacteria: Escherichia coli; Eukaryota: Saccharomyces cerevisiae) in relation to their similarities with secondary structures formed by presumed proto-tRNAs, represented by 25 theoretical minimal RNA rings. These ranks are compared to those derived from two independent methods (ranks provide a relative evolutionary age to the rRNA substructure), (a) cladistic phylogenetic analyses and (b) 3D-crystallography where core subelements are presumed ancient and peripheral ones recent. Comparisons of rRNA secondary structure subelements with RNA ring secondary structures show congruence between ranks deduced by this method and both (a) and (b) (more with (a) than (b)), especially for RNA rings with predicted ancient cognate amino acid. Reconstruction of accretion histories of large rRNAs will gain from adequately integrating information from independent methods. Theoretical minimal RNA rings, sequences deterministically designed in silico according to specific coding constraints, might produce adequate scales for prebiotic and early life molecular evolution.
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Affiliation(s)
- Jacques Demongeot
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, F-38700 La Tronche, France.
| | - Hervé Seligmann
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, F-38700 La Tronche, France; The National Natural History Collections, The Hebrew University of Jerusalem, 91404 Jerusalem, Israel.
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27
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Vianello S, Lutolf MP. Understanding the Mechanobiology of Early Mammalian Development through Bioengineered Models. Dev Cell 2019; 48:751-763. [PMID: 30913407 DOI: 10.1016/j.devcel.2019.02.024] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/13/2019] [Accepted: 02/26/2019] [Indexed: 12/21/2022]
Abstract
Research in developmental biology has been recently enriched by a multitude of in vitro models recapitulating key milestones of mammalian embryogenesis. These models obviate the challenge posed by the inaccessibility of implanted embryos, multiply experimental opportunities, and favor approaches traditionally associated with organoids and tissue engineering. Here, we provide a perspective on how these models can be applied to study the mechano-geometrical contributions to early mammalian development, which still escape direct verification in species that develop in utero. We thus outline new avenues for robust and scalable perturbation of geometry and mechanics in ways traditionally limited to non-implanting developmental models.
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Affiliation(s)
- Stefano Vianello
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences (SV) and School of Engineering (STI), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Matthias P Lutolf
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences (SV) and School of Engineering (STI), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Institute of Chemical Sciences and Engineering, School of Basic Science (SB), EPFL, Lausanne, Switzerland.
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28
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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: 1.8] [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.
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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
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29
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Cutter AD, Garrett RH, Mark S, Wang W, Sun L. Molecular evolution across developmental time reveals rapid divergence in early embryogenesis. Evol Lett 2019; 3:359-373. [PMID: 31388446 PMCID: PMC6675142 DOI: 10.1002/evl3.122] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/30/2019] [Indexed: 12/16/2022] Open
Abstract
Ontogenetic development hinges on the changes in gene expression in time and space within an organism, suggesting that the demands of ontogenetic growth can impose or reveal predictable pattern in the molecular evolution of genes expressed dynamically across development. Here, we characterize coexpression modules of the Caenorhabditis elegans transcriptome, using a time series of 30 points from early embryo to adult. By capturing the functional form of expression profiles with quantitative metrics, we find fastest evolution in the distinctive set of genes with transcript abundance that declines through development from a peak in young embryos. These genes are highly enriched for oogenic function and transient early zygotic expression, are nonrandomly distributed in the genome, and correspond to a life stage especially prone to inviability in interspecies hybrids. These observations conflict with the "early conservation model" for the evolution of development, although expression-weighted sequence divergence analysis provides some support for the "hourglass model." Genes in coexpression modules that peak toward adulthood also evolve fast, being hyper-enriched for roles in spermatogenesis, implicating a history of sexual selection and relaxation of selection on sperm as key factors driving rapid change to ontogenetically distinguishable coexpression modules of genes. We propose that these predictable trends of molecular evolution for dynamically expressed genes across ontogeny predispose particular life stages, early embryogenesis in particular, to hybrid dysfunction in the speciation process.
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Affiliation(s)
- Asher D. Cutter
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONM6G1W3Canada
| | - Rose H. Garrett
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONM6G1W3Canada
- Division of Biostatistics, Dalla Lana School of Public HealthUniversity of TorontoTorontoONM6G1W3Canada
- Department of Statistical SciencesUniversity of TorontoTorontoONM6G1W3Canada
| | - Stephanie Mark
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONM6G1W3Canada
| | - Wei Wang
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONM6G1W3Canada
| | - Lei Sun
- Division of Biostatistics, Dalla Lana School of Public HealthUniversity of TorontoTorontoONM6G1W3Canada
- Department of Statistical SciencesUniversity of TorontoTorontoONM6G1W3Canada
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30
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Liu J, Robinson-Rechavi M. Adaptive Evolution of Animal Proteins over Development: Support for the Darwin Selection Opportunity Hypothesis of Evo-Devo. Mol Biol Evol 2019; 35:2862-2872. [PMID: 30184095 PMCID: PMC6278863 DOI: 10.1093/molbev/msy175] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A driving hypothesis of evolutionary developmental biology is that animal morphological diversity is shaped both by adaptation and by developmental constraints. Here, we have tested Darwin’s “selection opportunity” hypothesis, according to which high evolutionary divergence in late development is due to strong positive selection. We contrasted it to a “developmental constraint” hypothesis, according to which late development is under relaxed negative selection. Indeed, the highest divergence between species, both at the morphological and molecular levels, is observed late in embryogenesis and postembryonically. To distinguish between adaptation and relaxation hypotheses, we investigated the evidence of positive selection on protein-coding genes in relation to their expression over development, in fly Drosophila melanogaster, zebrafish Danio rerio, and mouse Mus musculus. First, we found that genes specifically expressed in late development have stronger signals of positive selection. Second, over the full transcriptome, genes with evidence for positive selection trend to be expressed in late development. Finally, genes involved in pathways with cumulative evidence of positive selection have higher expression in late development. Overall, there is a consistent signal that positive selection mainly affects genes and pathways expressed in late embryonic development and in adult. Our results imply that the evolution of embryogenesis is mostly conservative, with most adaptive evolution affecting some stages of postembryonic gene expression, and thus postembryonic phenotypes. This is consistent with the diversity of environmental challenges to which juveniles and adults are exposed.
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Affiliation(s)
- Jialin Liu
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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31
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Cardoso-Moreira M, Halbert J, Valloton D, Velten B, Chen C, Shao Y, Liechti A, Ascenção K, Rummel C, Ovchinnikova S, Mazin PV, Xenarios I, Harshman K, Mort M, Cooper DN, Sandi C, Soares MJ, Ferreira PG, Afonso S, Carneiro M, Turner JMA, VandeBerg JL, Fallahshahroudi A, Jensen P, Behr R, Lisgo S, Lindsay S, Khaitovich P, Huber W, Baker J, Anders S, Zhang YE, Kaessmann H. Gene expression across mammalian organ development. Nature 2019; 571:505-509. [PMID: 31243369 PMCID: PMC6658352 DOI: 10.1038/s41586-019-1338-5] [Citation(s) in RCA: 382] [Impact Index Per Article: 76.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/31/2019] [Indexed: 01/08/2023]
Abstract
The evolution of gene expression in mammalian organ development remains largely uncharacterized. Here we report the transcriptomes of seven organs (cerebrum, cerebellum, heart, kidney, liver, ovary and testis) across developmental time points from early organogenesis to adulthood for human, rhesus macaque, mouse, rat, rabbit, opossum and chicken. Comparisons of gene expression patterns identified correspondences of developmental stages across species, and differences in the timing of key events during the development of the gonads. We found that the breadth of gene expression and the extent of purifying selection gradually decrease during development, whereas the amount of positive selection and expression of new genes increase. We identified differences in the temporal trajectories of expression of individual genes across species, with brain tissues showing the smallest percentage of trajectory changes, and the liver and testis showing the largest. Our work provides a resource of developmental transcriptomes of seven organs across seven species, and comparative analyses that characterize the development and evolution of mammalian organs.
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Affiliation(s)
- Margarida Cardoso-Moreira
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
| | - Jean Halbert
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Delphine Valloton
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Britta Velten
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Chunyan Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yi Shao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Angélica Liechti
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Kelly Ascenção
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Coralie Rummel
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | | | - Pavel V Mazin
- Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute) RAS, Moscow, Russia
- Faculty of Computer Science, HSE University, Moscow, Russia
| | - Ioannis Xenarios
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Keith Harshman
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Matthew Mort
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - Carmen Sandi
- Laboratory of Behavioral Genetics, Brain Mind Institute, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Michael J Soares
- Institute for Reproduction and Perinatal Research, Departments of Pathology and Laboratory Medicine and Pediatrics, University of Kansas Medical Center, Kansas City, MO, USA
- Center for Perinatal Research, Children's Research Institute, Children's Mercy, Kansas City, MO, USA
| | - Paula G Ferreira
- Departamento de Anatomia, Universidade do Porto, Porto, Portugal
- ICBAS (Instituto de Ciências Biomédicas Abel Salazar), UMIB (Unidade Multidisciplinar de Investigação Biomédica), Universidade do Porto, Porto, Portugal
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Universidade do Porto, Porto, Portugal
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Universidade do Porto, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - James M A Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - John L VandeBerg
- South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, Harlingen and Edinburg, TX, USA
- The Department of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, Harlingen and Edinburg, TX, USA
| | - Amir Fallahshahroudi
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | - Per Jensen
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | - Rüdiger Behr
- Platform Degenerative Diseases, German Primate Center, Leibniz Institute for Primate Research (DPZ), Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany
| | - Steven Lisgo
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle, UK
| | - Susan Lindsay
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle, UK
| | - Philipp Khaitovich
- Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, Russia
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Julie Baker
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Simon Anders
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
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32
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Wu L, Ferger KE, Lambert JD. Gene Expression Does Not Support the Developmental Hourglass Model in Three Animals with Spiralian Development. Mol Biol Evol 2019; 36:1373-1383. [DOI: 10.1093/molbev/msz065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
It has been proposed that animals have a pattern of developmental evolution resembling an hourglass because the most conserved development stage—often called the phylotypic stage—is always in midembryonic development. Although the topic has been debated for decades, recent studies using molecular data such as RNA-seq gene expression data sets have largely supported the existence of periods of relative evolutionary conservation in middevelopment, consistent with the phylotypic stage and the hourglass concepts. However, so far this approach has only been applied to a limited number of taxa across the tree of life. Here, using established phylotranscriptomic approaches, we found a surprising reverse hourglass pattern in two molluscs and a polychaete annelid, representatives of the Spiralia, an understudied group that contains a large fraction of metazoan body plan diversity. These results suggest that spiralians have a divergent midembryonic stage, with more conserved early and late development, which is the inverse of the pattern seen in almost all other organisms where these phylotranscriptomic approaches have been reported. We discuss our findings in light of proposed reasons for the phylotypic stage and hourglass model in other systems.
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Affiliation(s)
- Longjun Wu
- Department of Biology, University of Rochester, Rochester, NY
| | - Kailey E Ferger
- Department of Biology, University of Rochester, Rochester, NY
| | - J David Lambert
- Department of Biology, University of Rochester, Rochester, NY
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33
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Uesaka M, Kuratani S, Takeda H, Irie N. Recapitulation-like developmental transitions of chromatin accessibility in vertebrates. ZOOLOGICAL LETTERS 2019; 5:33. [PMID: 31807314 PMCID: PMC6857340 DOI: 10.1186/s40851-019-0148-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/06/2019] [Indexed: 05/09/2023]
Abstract
The relationship between development and evolution has been a central theme in evolutionary developmental biology. Across the vertebrates, the most highly conserved gene expression profiles are found at mid-embryonic, organogenesis stages, whereas those at earlier and later stages are more diverged. This hourglass-like pattern of divergence does not necessarily rule out the possibility that gene expression profiles that are more evolutionarily derived appear at later stages of development; however, no molecular-level evidence of such a phenomenon has been reported. To address this issue, we compared putative gene regulatory elements among different species within a phylum. We made a genome-wide assessment of accessible chromatin regions throughout embryogenesis in three vertebrate species (mouse, chicken, and medaka) and estimated the evolutionary ages of these regions to define their evolutionary origins on the phylogenetic tree. In all the three species, we found that genomic regions tend to become accessible in an order that parallels their phylogenetic history, with evolutionarily newer gene regulations activated at later developmental stages. This tendency was restricted only after the mid-embryonic, phylotypic periods. Our results imply a phylogenetic hierarchy of putative regulatory regions, in which their activation parallels the phylogenetic order of their appearance. One evolutionary mechanism that may explain this phenomenon is that newly introduced regulatory elements are more likely to survive if activated at later stages of embryogenesis. Possible relationships between this phenomenon and the so-called recapitulation are discussed.
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Affiliation(s)
- Masahiro Uesaka
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
- Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Kobe, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
- Universal Biology Institute, The University of Tokyo, Tokyo, Japan
| | - Naoki Irie
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
- Universal Biology Institute, The University of Tokyo, Tokyo, Japan
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34
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Feltes BC, Grisci BI, Poloni JDF, Dorn M. Perspectives and applications of machine learning for evolutionary developmental biology. Mol Omics 2018; 14:289-306. [PMID: 30168572 DOI: 10.1039/c8mo00111a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Evolutionary Developmental Biology (Evo-Devo) is an ever-expanding field that aims to understand how development was modulated by the evolutionary process. In this sense, "omic" studies emerged as a powerful ally to unravel the molecular mechanisms underlying development. In this scenario, bioinformatics tools become necessary to analyze the growing amount of information. Among computational approaches, machine learning stands out as a promising field to generate knowledge and trace new research perspectives for bioinformatics. In this review, we aim to expose the current advances of machine learning applied to evolution and development. We draw clear perspectives and argue how evolution impacted machine learning techniques.
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Affiliation(s)
- Bruno César Feltes
- Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.
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35
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Yang D, Xu A, Shen P, Gao C, Zang J, Qiu C, Ouyang H, Jiang Y, He F. A two-level model for the role of complex and young genes in the formation of organism complexity and new insights into the relationship between evolution and development. EvoDevo 2018; 9:22. [PMID: 30455862 PMCID: PMC6231269 DOI: 10.1186/s13227-018-0111-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 10/25/2018] [Indexed: 11/14/2022] Open
Abstract
Background How genome complexity affects organismal phenotypic complexity is a fundamental question in evolutionary developmental biology. Previous studies proposed various contributing factors of genome complexity and tried to find the connection between genomic complexity and organism complexity. However, a general model to answer this question is lacking. Here, we introduce a ‘two-level’ model for the realization of genome complexity at phenotypic level. Results Five representative species across Protostomia and Deuterostomia were involved in this study. The intrinsic gene properties contributing to genome complexity were classified into two generalized groups: the complexity and age degree of both protein-coding and noncoding genes. We found that young genes tend to be simpler; however, the mid-age genes, rather than the oldest genes, show the highest proportion of high complexity. Complex genes tend to be utilized preferentially in each stage of embryonic development, with maximum representation during the late stage of organogenesis. This trend is mainly attributed to mid-age complex genes. In contrast, young genes tend to be expressed in specific spatiotemporal states. An obvious correlation between the time point of the change in over- and under-representation and the order of gene age was observed, which supports the funnel-like model of the conservation pattern of development. In addition, we found some probable causes for the seemingly contradictory ‘funnel-like’ or ‘hourglass’ model. Conclusions These results indicate that complex and young genes contribute to organismal complexity at two different levels: Complex genes contribute to the complexity of individual proteomes in certain states, whereas young genes contribute to the diversity of proteomes in different spatiotemporal states. This conclusion is valid across the five species investigated, indicating it is a conserved model across Protostomia and Deuterostomia. The results in this study also support ‘funnel-like model’ from a new viewpoint and explain why there are different evo–devo relation models. Electronic supplementary material The online version of this article (10.1186/s13227-018-0111-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dong Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206 The People's Republic of China
| | - Aishi Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206 The People's Republic of China
| | - Pan Shen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206 The People's Republic of China
| | - Chao Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206 The People's Republic of China
| | - Jiayin Zang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206 The People's Republic of China
| | - Chen Qiu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206 The People's Republic of China
| | - Hongsheng Ouyang
- 2Animal Sciences College of Jilin University, Changchun, 130062 The People's Republic of China
| | - Ying Jiang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206 The People's Republic of China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206 The People's Republic of China
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Stone R, Portegys T, Mikhailovsky G, Alicea B. Origins of the Embryo: Self-organization through cybernetic regulation. Biosystems 2018; 173:73-82. [DOI: 10.1016/j.biosystems.2018.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/13/2018] [Accepted: 08/13/2018] [Indexed: 12/12/2022]
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Liu J, Robinson-Rechavi M. Developmental Constraints on Genome Evolution in Four Bilaterian Model Species. Genome Biol Evol 2018; 10:2266-2277. [PMID: 30137380 PMCID: PMC6130771 DOI: 10.1093/gbe/evy177] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2018] [Indexed: 12/12/2022] Open
Abstract
Developmental constraints on genome evolution have been suggested to follow either an early conservation model or an "hourglass" model. Both models agree that late development strongly diverges between species, but debate on which developmental period is the most conserved. Here, based on a modified "Transcriptome Age Index" approach, that is, weighting trait measures by expression level, we analyzed the constraints acting on three evolutionary traits of protein coding genes (strength of purifying selection on protein sequences, phyletic age, and duplicability) in four species: Nematode worm Caenorhabditis elegans, fly Drosophila melanogaster, zebrafish Danio rerio, and mouse Mus musculus. In general, we found that both models can be supported by different genomic properties. Sequence evolution follows an hourglass model, but the evolution of phyletic age and of duplicability follow an early conservation model. Further analyses indicate that stronger purifying selection on sequences in the middle development are driven by temporal pleiotropy of these genes. In addition, we report evidence that expression in late development is enriched with retrogenes, which usually lack efficient regulatory elements. This implies that expression in late development could facilitate transcription of new genes, and provide opportunities for acquisition of function. Finally, in C. elegans, we suggest that dosage imbalance could be one of the main factors that cause depleted expression of high duplicability genes in early development.
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Affiliation(s)
- Jialin Liu
- Department of Ecology and Evolution, University of Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Seligmann H. Protein Sequences Recapitulate Genetic Code Evolution. Comput Struct Biotechnol J 2018; 16:177-189. [PMID: 30002789 PMCID: PMC6040577 DOI: 10.1016/j.csbj.2018.05.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/16/2022] Open
Abstract
Several hypotheses predict ranks of amino acid assignments to genetic code's codons. Analyses here show that average positions of amino acid species in proteins correspond to assignment ranks, in particular as predicted by Juke's neutral mutation hypothesis for codon assignments. In all tested protein groups, including co- and post-translationally folding proteins, 'recent' amino acids are on average closer to gene 5' extremities than 'ancient' ones. Analyses of pairwise residue contact energies matrices suggest that early amino acids stereochemically selected late ones that stablilize residue interactions within protein cores, presumably producing 5'-late-to-3'-early amino acid protein sequence gradients. The gradient might reduce protein misfolding, also after mutations, extending principles of neutral mutations to protein folding. Presumably, in self-perpetuating and self-correcting systems like the genetic code, initial conditions produce similarities between evolution of the process (the genetic code) and 'ontogeny' of resulting structures (here proteins), producing apparent teleonomy between process and product.
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Affiliation(s)
- Hervé Seligmann
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR MEPHI, Aix-Marseille Université, IRD, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France.
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TFAP2C regulates transcription in human naive pluripotency by opening enhancers. Nat Cell Biol 2018; 20:553-564. [PMID: 29695788 PMCID: PMC5926822 DOI: 10.1038/s41556-018-0089-0] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 03/20/2018] [Indexed: 02/08/2023]
Abstract
Naïve and primed pluripotent hESCs bear transcriptional similarity to pre- and post-implantation epiblast and thus constitute a developmental model for understanding the earliest pluripotent stages in human embryo development. To identify new transcription factors that differentially regulate the unique pluripotent stages, we mapped open chromatin using ATAC-Seq and found enrichment of the AP2 transcription factor binding motif at naïve-specific open chromatin. We determined that the AP2 family member TFAP2C is upregulated during primed to naïve reversion and becomes widespread at naïve-specific enhancers. TFAP2C functions to maintain pluripotency and repress neuroectodermal differentiation during the transition from primed to naïve by facilitating the opening of enhancers proximal to pluripotency factors. Additionally, we identify a previously undiscovered naïve-specific POU5F1 (OCT4) enhancer enriched for TFAP2C binding. Taken together, TFAP2C establishes and maintains naïve human pluripotency and regulates OCT4 expression by mechanisms that are distinct from mouse.
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Schiffer PH, Polsky AL, Cole AG, Camps JIR, Kroiher M, Silver DH, Grishkevich V, Anavy L, Koutsovoulos G, Hashimshony T, Yanai I. The gene regulatory program of Acrobeloides nanus reveals conservation of phylum-specific expression. Proc Natl Acad Sci U S A 2018; 115:4459-4464. [PMID: 29626130 PMCID: PMC5924915 DOI: 10.1073/pnas.1720817115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The evolution of development has been studied through the lens of gene regulation by examining either closely related species or extremely distant animals of different phyla. In nematodes, detailed cell- and stage-specific expression analyses are focused on the model Caenorhabditis elegans, in part leading to the view that the developmental expression of gene cascades in this species is archetypic for the phylum. Here, we compared two species of an intermediate evolutionary distance: the nematodes C. elegans (clade V) and Acrobeloides nanus (clade IV). To examine A. nanus molecularly, we sequenced its genome and identified the expression profiles of all genes throughout embryogenesis. In comparison with C. elegans, A. nanus exhibits a much slower embryonic development and has a capacity for regulative compensation of missing early cells. We detected conserved stages between these species at the transcriptome level, as well as a prominent middevelopmental transition, at which point the two species converge in terms of their gene expression. Interestingly, we found that genes originating at the dawn of the Ecdysozoa supergroup show the least expression divergence between these two species. This led us to detect a correlation between the time of expression of a gene and its phylogenetic age: evolutionarily ancient and young genes are enriched for expression in early and late embryogenesis, respectively, whereas Ecdysozoa-specific genes are enriched for expression during the middevelopmental transition. Our results characterize the developmental constraints operating on each individual embryo in terms of developmental stages and genetic evolutionary history.
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Affiliation(s)
- Philipp H Schiffer
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
| | - Avital L Polsky
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Alison G Cole
- Department of Molecular Evolution and Development, University of Vienna, 1090 Vienna, Austria
| | - Julia I R Camps
- Molecular Cell Biology, Institute I for Anatomy University Clinic Cologne, University of Cologne, 50937 Cologne, Germany
| | - Michael Kroiher
- Zoological Institute, Cologne Biocenter, University of Cologne, 50674 Cologne, Germany
| | - David H Silver
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | | | - Leon Anavy
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Georgios Koutsovoulos
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JW, United Kingdom
| | - Tamar Hashimshony
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Itai Yanai
- Institute for Computational Medicine, NYU School of Medicine, New York, NY 10016
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Uchida Y, Uesaka M, Yamamoto T, Takeda H, Irie N. Embryonic lethality is not sufficient to explain hourglass-like conservation of vertebrate embryos. EvoDevo 2018; 9:7. [PMID: 29568479 PMCID: PMC5855935 DOI: 10.1186/s13227-018-0095-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/09/2018] [Indexed: 12/13/2022] Open
Abstract
Background Understanding the general trends in developmental changes during animal evolution, which are often associated with morphological diversification, has long been a central issue in evolutionary developmental biology. Recent comparative transcriptomic studies revealed that gene expression profiles of mid-embryonic period tend to be more evolutionarily conserved than those in earlier or later periods. While the hourglass-like divergence of developmental processes has been demonstrated in a variety of animal groups such as vertebrates, arthropods, and nematodes, the exact mechanism leading to this mid-embryonic conservation remains to be clarified. One possibility is that the mid-embryonic period (pharyngula period in vertebrates) is highly prone to embryonic lethality, and the resulting negative selections lead to evolutionary conservation of this phase. Here, we tested this “mid-embryonic lethality hypothesis” by measuring the rate of lethal phenotypes of three different species of vertebrate embryos subjected to two kinds of perturbations: transient perturbations and genetic mutations. Results By subjecting zebrafish (Danio rerio), African clawed frog (Xenopus laevis), and chicken (Gallus gallus) embryos to transient perturbations, namely heat shock and inhibitor treatments during three developmental periods [early (represented by blastula and gastrula), pharyngula, and late], we found that the early stages showed the highest rate of lethal phenotypes in all three species. This result was corroborated by perturbation with genetic mutations. By tracking the survival rate of wild-type embryos and embryos with genetic mutations induced by UV irradiation in zebrafish and African clawed frogs, we found that the highest decrease in survival rate was at the early stages particularly around gastrulation in both these species. Conclusion In opposition to the “mid-embryonic lethality hypothesis,” our results consistently showed that the stage with the highest lethality was not around the conserved pharyngula period, but rather around the early period in all the vertebrate species tested. These results suggest that negative selection by embryonic lethality could not explain hourglass-like conservation of animal embryos. This highlights the potential contribution of alternative mechanisms such as the diversifying effect of positive selections against earlier and later stages, and developmental constraints which lead to conservation of mid-embryonic stages. Electronic supplementary material The online version of this article (10.1186/s13227-018-0095-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yui Uchida
- 1Department of Biological Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Masahiro Uesaka
- 1Department of Biological Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Takayoshi Yamamoto
- 1Department of Biological Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Hiroyuki Takeda
- 1Department of Biological Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan.,2Universal Biology Institute, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Naoki Irie
- 1Department of Biological Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan.,2Universal Biology Institute, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
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Kuo DH, Hsiao YH. Duplicated FoxA genes in the leech Helobdella: Insights into the evolution of direct development in clitellate annelids. Dev Dyn 2018; 247:763-778. [PMID: 29396890 DOI: 10.1002/dvdy.24621] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/25/2018] [Accepted: 01/26/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND As an adaptation to the land, the clitellate annelid had reorganized its embryogenesis to develop "directly" without the ancestral planktonic larval stage. To study the evolution of gut development in the directly developing clitellates, we characterized the expression pattern of the conserved gut gene, FoxA, in the embryonic development of the leech. RESULTS The leech has three FoxA paralogs. Hau-FoxA1 is first expressed in a subset of endoderm cells and then in the foregut and the midgut. Hau-FoxA2 is expressed in the stomodeum, which is secondarily derived from the anterior ectoderm in the clitellates rather than the tissue around the blastopore, the ancestral site of mouth formation in Phylum Annelida. Hau-FoxA3 is expressed during the morphogenesis of segmental ganglia from the ectodermal teloblast lineages, a clitellate-specific trait. Hau-FoxA1 and Hau-FoxA2 are also expressed during the morphogenesis of the leech-specific front sucker. CONCLUSIONS The expression patterns suggested that Hau-FoxA1 carries out most of the conserved function in the endoderm and gut development, while the other two duplicates appear to have evolved unique novel functions in the directly developing clitellate embryos. Therefore, neofunctionalization and co-option of FoxA might have made a significant contribution to the evolution of direct development in Clitellata. Developmental Dynamics 247:763-778, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Dian-Han Kuo
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Hsiang Hsiao
- Department of Life Science, National Taiwan University, Taipei, Taiwan
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43
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Niven JE, Frasnelli E. Insights into the evolution of lateralization from the insects. PROGRESS IN BRAIN RESEARCH 2018; 238:3-31. [DOI: 10.1016/bs.pbr.2018.06.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Constrained vertebrate evolution by pleiotropic genes. Nat Ecol Evol 2017; 1:1722-1730. [PMID: 28963548 DOI: 10.1038/s41559-017-0318-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 08/16/2017] [Indexed: 02/06/2023]
Abstract
Despite morphological diversification of chordates over 550 million years of evolution, their shared basic anatomical pattern (or 'bodyplan') remains conserved by unknown mechanisms. The developmental hourglass model attributes this to phylum-wide conserved, constrained organogenesis stages that pattern the bodyplan (the phylotype hypothesis); however, there has been no quantitative testing of this idea with a phylum-wide comparison of species. Here, based on data from early-to-late embryonic transcriptomes collected from eight chordates, we suggest that the phylotype hypothesis would be better applied to vertebrates than chordates. Furthermore, we found that vertebrates' conserved mid-embryonic developmental programmes are intensively recruited to other developmental processes, and the degree of the recruitment positively correlates with their evolutionary conservation and essentiality for normal development. Thus, we propose that the intensively recruited genetic system during vertebrates' organogenesis period imposed constraints on its diversification through pleiotropic constraints, which ultimately led to the common anatomical pattern observed in vertebrates.
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Malik A, Gildor T, Sher N, Layous M, Ben-Tabou de-Leon S. Parallel embryonic transcriptional programs evolve under distinct constraints and may enable morphological conservation amidst adaptation. Dev Biol 2017; 430:202-213. [PMID: 28780048 DOI: 10.1016/j.ydbio.2017.07.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/13/2017] [Accepted: 07/26/2017] [Indexed: 12/27/2022]
Abstract
Embryonic development evolves by balancing stringent morphological constraints with genetic and environmental variation. The design principle that allows developmental transcriptional programs to conserve embryonic morphology while adapting to environmental changes is still not fully understood. To address this fundamental challenge, we compare developmental transcriptomes of two sea urchin species, Paracentrotus lividus and Strongylocentrotus purpuratus, that shared a common ancestor about 40 million years ago and are geographically distant yet show similar morphology. We find that both developmental and housekeeping genes show highly dynamic and strongly conserved temporal expression patterns. The expression of other gene sets, including homeostasis and response genes, show divergent expression which could result from either evolutionary drift or adaptation to local environmental conditions. The interspecies correlations of developmental gene expressions are highest between morphologically similar developmental time points whereas the interspecies correlations of housekeeping gene expression are high between all the late zygotic time points. Relatedly, the position of the phylotypic stage varies between these two groups of genes: developmental gene expression shows highest conservation at mid-developmental stage, in agreement with the hourglass model while the conservation of housekeeping genes keeps increasing with developmental time. When all genes are combined, the relationship between conservation of gene expression and morphological similarity is partially masked by housekeeping genes and genes with diverged expression. Our study illustrates various transcriptional programs that coexist in the developing embryo and evolve under different constraints. Apparently, morphological constraints underlie the conservation of developmental gene expression while embryonic fitness requires the conservation of housekeeping gene expression and the species-specific adjustments of homeostasis gene expression. The distinct evolutionary forces acting on these transcriptional programs enable the conservation of similar body plans while allowing adaption.
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Affiliation(s)
- Assaf Malik
- Bionformatics Core Unit, University of Haifa, Haifa 31905, Israel
| | - Tsvia Gildor
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 31905, Israel
| | - Noa Sher
- Bionformatics Core Unit, University of Haifa, Haifa 31905, Israel
| | - Majed Layous
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 31905, Israel
| | - Smadar Ben-Tabou de-Leon
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 31905, Israel
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Maier JA, Rivas-Astroza M, Deng J, Dowling A, Oboikovitz P, Cao X, Behringer RR, Cretekos CJ, Rasweiler JJ, Zhong S, Sears KE. Transcriptomic insights into the genetic basis of mammalian limb diversity. BMC Evol Biol 2017; 17:86. [PMID: 28335721 PMCID: PMC5364624 DOI: 10.1186/s12862-017-0902-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 02/03/2017] [Indexed: 12/28/2022] Open
Abstract
Background From bat wings to whale flippers, limb diversification has been crucial to the evolutionary success of mammals. We performed the first transcriptome-wide study of limb development in multiple species to explore the hypothesis that mammalian limb diversification has proceeded through the differential expression of conserved shared genes, rather than by major changes to limb patterning. Specifically, we investigated the manner in which the expression of shared genes has evolved within and among mammalian species. Results We assembled and compared transcriptomes of bat, mouse, opossum, and pig fore- and hind limbs at the ridge, bud, and paddle stages of development. Results suggest that gene expression patterns exhibit larger variation among species during later than earlier stages of limb development, while within species results are more mixed. Consistent with the former, results also suggest that genes expressed at later developmental stages tend to have a younger evolutionary age than genes expressed at earlier stages. A suite of key limb-patterning genes was identified as being differentially expressed among the homologous limbs of all species. However, only a small subset of shared genes is differentially expressed in the fore- and hind limbs of all examined species. Similarly, a small subset of shared genes is differentially expressed within the fore- and hind limb of a single species and among the forelimbs of different species. Conclusions Taken together, results of this study do not support the existence of a phylotypic period of limb development ending at chondrogenesis, but do support the hypothesis that the hierarchical nature of development translates into increasing variation among species as development progresses. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0902-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jennifer A Maier
- School of Integrative Biology, University of Illinois, 505 S Goodwin Avenue, Urbana, IL, 61801, USA
| | - Marcelo Rivas-Astroza
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Jenny Deng
- Department of Genetics, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Anna Dowling
- School of Integrative Biology, University of Illinois, 505 S Goodwin Avenue, Urbana, IL, 61801, USA
| | - Paige Oboikovitz
- School of Integrative Biology, University of Illinois, 505 S Goodwin Avenue, Urbana, IL, 61801, USA
| | - Xiaoyi Cao
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Richard R Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Chris J Cretekos
- Department of Biological Sciences, Idaho State University, 921 South 8th Avenue, Pocatello, ID, 83209, USA
| | - John J Rasweiler
- Department of Obstetrics and Gynecology, State University Downstate Medical Center, 450 Clarkson, Avenue, Brooklyn, NY, 11203, USA
| | - Sheng Zhong
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, 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.
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Kaczmarek P, Hermyt M, Rupik W. Embryology of the VNO and associated structures in the grass snake Natrix natrix (Squamata: Naticinae): a 3D perspective. Front Zool 2017; 14:1. [PMID: 28101121 PMCID: PMC5237294 DOI: 10.1186/s12983-017-0188-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/02/2017] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Snakes are considered to be vomerolfaction specialists. They are members of one of the most diverse groups of vertebrates, Squamata. The vomeronasal organ and the associated structures (such as the lacrimal duct, choanal groove, lamina transversalis anterior and cupola Jacobsoni) of adult lizards and snakes have received much anatomical, histological, physiological and behavioural attention. However, only limited embryological investigation into these structures, constrained to some anatomical or cellular studies and brief surveys, has been carried out thus far. The purpose of this study was, first, to examine the embryonic development of the vomeronasal organ and the associated structures in the grass snake (Natrix natrix), using three-dimensional reconstructions based on histological studies, and, second, to compare the obtained results with those presented in known publications on other snakes and lizards. RESULTS Five major developmental processes were taken into consideration in this study: separation of the vomeronasal organ from the nasal cavity and its specialization, development of the mushroom body, formation of the lacrimal duct, development of the cupola Jacobsoni and its relation to the vomeronasal nerve, and specialization of the sensory epithelium. Our visualizations showed the VNO in relation to the nasal cavity, choanal groove, lacrimal duct and cupola Jacobsoni at different embryonic stages. We confirmed that the choanal groove disappears gradually, which indicates that this structure is absent in adult grass snakes. On our histological sections, we observed a gradual growth in the height of the columns of the vomeronasal sensory epithelium and widening of the spaces between them. CONCLUSIONS The main ophidian taxa (Scolecophidia, Henophidia and Caenophidia), just like other squamate clades, seem to be evolutionarily conservative at some levels with respect to the VNO and associated structures morphology. Thus, it was possible to homologize certain embryonic levels of the anatomical and histological complexity, observed in the grass snake, with adult conditions of certain groups of Squamata. This may reflect evolutionary shift in Squamata from visually oriented predators to vomerolfaction specialists. Our descriptions offer material useful for future comparative studies of Squamata, both at their anatomical and histological levels.
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Affiliation(s)
- Paweł Kaczmarek
- Department of Animal Histology and Embryology, University of Silesia, 9 Bankowa Str, 40-007 Katowice, Poland
| | - Mateusz Hermyt
- Department of Animal Histology and Embryology, University of Silesia, 9 Bankowa Str, 40-007 Katowice, Poland
| | - Weronika Rupik
- Department of Animal Histology and Embryology, University of Silesia, 9 Bankowa Str, 40-007 Katowice, Poland
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Onichtchouk DV, Voronina AS. Regulation of Zygotic Genome and Cellular Pluripotency. BIOCHEMISTRY (MOSCOW) 2016; 80:1723-33. [PMID: 26878577 DOI: 10.1134/s0006297915130088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Events, manifesting transition from maternal to zygotic period of development are studied for more than 100 years, but underlying mechanisms are not yet clear. We provide a brief historical overview of development of concepts and explain the specific terminology used in the field. We further discuss differences and similarities between the zygotic genome activation and in vitro reprogramming process. Finally, we envision the future research directions within the field, where biochemical methods will play increasingly important role.
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Affiliation(s)
- D V Onichtchouk
- University of Freiburg, Developmental Biology Unit, Biologie 1, Freiburg, 79194, Germany.
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Urbansky S, González Avalos P, Wosch M, Lemke S. Folded gastrulation and T48 drive the evolution of coordinated mesoderm internalization in flies. eLife 2016; 5. [PMID: 27685537 PMCID: PMC5042651 DOI: 10.7554/elife.18318] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/30/2016] [Indexed: 12/17/2022] Open
Abstract
Gastrulation constitutes a fundamental yet diverse morphogenetic process of metazoan development. Modes of gastrulation range from stochastic translocation of individual cells to coordinated infolding of an epithelial sheet. How such morphogenetic differences are genetically encoded and whether they have provided specific developmental advantages is unclear. Here we identify two genes, folded gastrulation and t48, which in the evolution of fly gastrulation acted as a likely switch from an ingression of individual cells to the invagination of the blastoderm epithelium. Both genes are expressed and required for mesoderm invagination in the fruit fly Drosophila melanogaster but do not appear during mesoderm ingression of the midge Chironomus riparius. We demonstrate that early expression of either or both of these genes in C.riparius is sufficient to invoke mesoderm invagination similar to D.melanogaster. The possible genetic simplicity and a measurable increase in developmental robustness might explain repeated evolution of similar transitions in animal gastrulation. DOI:http://dx.doi.org/10.7554/eLife.18318.001 In animals, gastrulation is a period of time in early development during which a sphere of cells is reorganized into an embryo with cells arranged into three distinct layers (called germ layers). The process has changed substantially during the course of evolution and thus provides a great experimental system to investigate the genetic basis for differences in animal form and shape. As an example, true flies use at least two different mechanisms to make the middle germ layer (the mesoderm). In both cases, the mesoderm is made up of cells that move inwards from the boundary of the outer germ layer. In midges and some other flies, these cells migrate individually, while in others including fruit flies, the cells move together as a sheet. Fruit flies and midges shared their last common ancestor 250 million years ago and although the genes that make the mesoderm in fruit flies are well understood, little is known about how the mesoderm forms in midges. Urbansky, González Avalos et al. investigated which genes were responsible for the evolutionary transition between the different types of cell migration seen in flies. The experiments identified two genes – called folded gastrulation and t48 – that seem to operate as a simple switch between the two ways that mesoderm cells migrate. Both of these genes are active in fruit fly embryos and are required for the group migration of mesoderm cells. However, the genes do not appear to play a major role in the movement of individual mesoderm cells in midges. Further experiments demonstrate that switching on these genes in midge embryos is sufficient to invoke group mesoderm cell migrations similar to those seen in fruit flies. These findings show that it is possible to identify genetic changes that underlie substantial differences in animal form and shape over hundred million of years. The ease by which Urbansky, González Avalos et al. were able to switch between the two types of mesoderm migration might explain why similar transitions in gastrulation have evolved repeatedly in animals. The next step is to test this hypothesis in other animals. DOI:http://dx.doi.org/10.7554/eLife.18318.002
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Affiliation(s)
- Silvia Urbansky
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Paula González Avalos
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Maike Wosch
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Steffen Lemke
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
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Furness AI, Reznick DN, Springer MS, Meredith RW. Convergent evolution of alternative developmental trajectories associated with diapause in African and South American killifish. Proc Biol Sci 2016; 282:rspb.2014.2189. [PMID: 25631993 DOI: 10.1098/rspb.2014.2189] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Annual killifish adapted to life in seasonally ephemeral water-bodies exhibit desiccation resistant eggs that can undergo diapause, a period of developmental arrest, enabling them to traverse the otherwise inhospitable dry season. Environmental cues that potentially indicate the season can govern whether eggs enter a stage of diapause mid-way through development or skip this diapause and instead undergo direct development. We report, based on construction of a supermatrix phylogenetic tree of the order Cyprinodontiformes and a battery of comparative analyses, that the ability to produce diapause eggs evolved independently at least six times within African and South American killifish. We then show in species representative of these lineages that embryos entering diapause display significant reduction in development of the cranial region and circulatory system relative to direct-developing embryos. This divergence along alternative developmental pathways begins mid-way through development, well before diapause is entered, during a period of purported maximum developmental constraint (the phylotypic period). Finally, we show that entering diapause is accompanied by a dramatic reduction in metabolic rate and concomitant increase in long-term embryo survival. Morphological divergence during the phylotypic period thus allows embryos undergoing diapause to conserve energy by shunting resources away from energetically costly organs thereby increasing survival chances in an environment that necessitates remaining dormant, buried in the soil and surrounded by an eggshell for much of the year. Our results indicate that adaptation to seasonal aquatic environments in annual killifish imposes strong selection during the embryo stage leading to marked diversification during this otherwise conserved period of vertebrate development.
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Affiliation(s)
- Andrew I Furness
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - David N Reznick
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Mark S Springer
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Robert W Meredith
- Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043, USA
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