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Gunter HM, Youlten SE, Reis ALM, McCubbin T, Madala BS, Wong T, Stevanovski I, Cipponi A, Deveson IW, Santini NS, Kummerfeld S, Croucher PI, Marcellin E, Mercer TR. A universal molecular control for DNA, mRNA and protein expression. Nat Commun 2024; 15:2480. [PMID: 38509097 PMCID: PMC10954659 DOI: 10.1038/s41467-024-46456-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
The expression of genes encompasses their transcription into mRNA followed by translation into protein. In recent years, next-generation sequencing and mass spectrometry methods have profiled DNA, RNA and protein abundance in cells. However, there are currently no reference standards that are compatible across these genomic, transcriptomic and proteomic methods, and provide an integrated measure of gene expression. Here, we use synthetic biology principles to engineer a multi-omics control, termed pREF, that can act as a universal molecular standard for next-generation sequencing and mass spectrometry methods. The pREF sequence encodes 21 synthetic genes that can be in vitro transcribed into spike-in mRNA controls, and in vitro translated to generate matched protein controls. The synthetic genes provide qualitative controls that can measure sensitivity and quantitative accuracy of DNA, RNA and peptide detection. We demonstrate the use of pREF in metagenome DNA sequencing and RNA sequencing experiments and evaluate the quantification of proteins using mass spectrometry. Unlike previous spike-in controls, pREF can be independently propagated and the synthetic mRNA and protein controls can be sustainably prepared by recipient laboratories using common molecular biology techniques. Together, this provides a universal synthetic standard able to integrate genomic, transcriptomic and proteomic methods.
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Affiliation(s)
- Helen M Gunter
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- BASE mRNA Facility, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia
| | - Scott E Youlten
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Andre L M Reis
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
- School of Electrical and Information Engineering, University of Sydney, Sydney, New South Wales, Australia
| | - Tim McCubbin
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia
| | - Bindu Swapna Madala
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
| | - Ted Wong
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Igor Stevanovski
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
| | - Arcadi Cipponi
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Ira W Deveson
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
- School of Electrical and Information Engineering, University of Sydney, Sydney, New South Wales, Australia
| | - Nadia S Santini
- Centro Nacional de Investigación Disciplinaria en Conservación y Mejoramiento de Ecosistemas Forestales, INIFAP, Ciudad de México, 04010, Mexico
| | - Sarah Kummerfeld
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Peter I Croucher
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Esteban Marcellin
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia
| | - Tim R Mercer
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia.
- BASE mRNA Facility, The University of Queensland, Brisbane, Queensland, Australia.
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia.
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
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2
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Schneider RF, Gunter HM, Salewski I, Woltering JM, Meyer A. Growth dynamics and molecular bases of evolutionary novel jaw extensions in halfbeaks and needlefishes (Beloniformes). Mol Ecol 2023; 32:5798-5811. [PMID: 37750351 DOI: 10.1111/mec.17143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 08/17/2023] [Accepted: 09/05/2023] [Indexed: 09/27/2023]
Abstract
Evolutionary novelties-derived traits without clear homology found in the ancestors of a lineage-may promote ecological specialization and facilitate adaptive radiations. Examples for such novelties include the wings of bats, pharyngeal jaws of cichlids and flowers of angiosperms. Belonoid fishes (flying fishes, halfbeaks and needlefishes) feature an astonishing diversity of extremely elongated jaw phenotypes with undetermined evolutionary origins. We investigate the development of elongated jaws in a halfbeak (Dermogenys pusilla) and a needlefish (Xenentodon cancila) using morphometrics, transcriptomics and in situ hybridization. We confirm that these fishes' elongated jaws are composed of distinct base and novel 'extension' portions. These extensions are morphologically unique to belonoids, and we describe the growth dynamics of both bases and extensions throughout early development in both studied species. From transcriptomic profiling, we deduce that jaw extension outgrowth is guided by populations of multipotent cells originating from the anterior tip of the dentary. These cells are shielded from differentiation, but proliferate and migrate anteriorly during the extension's allometric growth phase. Cells left behind at the tip leave the shielded zone and undergo differentiation into osteoblast-like cells, which deposit extracellular matrix with both bone and cartilage characteristics that mineralizes and thereby provides rigidity. Such bone has characteristics akin to histological observations on the elongated 'kype' process on lower jaws of male salmon, which may hint at common conserved regulatory underpinnings. Future studies will evaluate the molecular pathways that govern the anterior migration and proliferation of these multipotent cells underlying the belonoids' evolutionary novel jaw extensions.
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Affiliation(s)
- Ralf F Schneider
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Marine Ecology, GEOMAR, Kiel, Germany
| | - Helen M Gunter
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Inken Salewski
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Joost M Woltering
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
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3
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Gunter HM, Idrisoglu S, Singh S, Han DJ, Ariens E, Peters JR, Wong T, Cheetham SW, Xu J, Rai SK, Feldman R, Herbert A, Marcellin E, Tropee R, Munro T, Mercer TR. mRNA vaccine quality analysis using RNA sequencing. Nat Commun 2023; 14:5663. [PMID: 37735471 PMCID: PMC10514319 DOI: 10.1038/s41467-023-41354-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 08/24/2023] [Indexed: 09/23/2023] Open
Abstract
The success of mRNA vaccines has been realised, in part, by advances in manufacturing that enabled billions of doses to be produced at sufficient quality and safety. However, mRNA vaccines must be rigorously analysed to measure their integrity and detect contaminants that reduce their effectiveness and induce side-effects. Currently, mRNA vaccines and therapies are analysed using a range of time-consuming and costly methods. Here we describe a streamlined method to analyse mRNA vaccines and therapies using long-read nanopore sequencing. Compared to other industry-standard techniques, VAX-seq can comprehensively measure key mRNA vaccine quality attributes, including sequence, length, integrity, and purity. We also show how direct RNA sequencing can analyse mRNA chemistry, including the detection of nucleoside modifications. To support this approach, we provide supporting software to automatically report on mRNA and plasmid template quality and integrity. Given these advantages, we anticipate that RNA sequencing methods, such as VAX-seq, will become central to the development and manufacture of mRNA drugs.
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Affiliation(s)
- Helen M Gunter
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
- BASE facility, University of Queensland, Brisbane, QLD, Australia
| | - Senel Idrisoglu
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
- BASE facility, University of Queensland, Brisbane, QLD, Australia
| | - Swati Singh
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
- BASE facility, University of Queensland, Brisbane, QLD, Australia
| | - Dae Jong Han
- BASE facility, University of Queensland, Brisbane, QLD, Australia
| | - Emily Ariens
- BASE facility, University of Queensland, Brisbane, QLD, Australia
| | | | - Ted Wong
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Seth W Cheetham
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
- BASE facility, University of Queensland, Brisbane, QLD, Australia
| | - Jun Xu
- Genome Innovation Hub, University of Queensland, Brisbane, QLD, Australia
| | - Subash Kumar Rai
- Genome Innovation Hub, University of Queensland, Brisbane, QLD, Australia
| | - Robert Feldman
- COVID19 Vaccine Corporation Limited (CVC), Auckland, New Zealand
| | - Andy Herbert
- COVID19 Vaccine Corporation Limited (CVC), Auckland, New Zealand
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Romain Tropee
- BASE facility, University of Queensland, Brisbane, QLD, Australia
| | - Trent Munro
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
- BASE facility, University of Queensland, Brisbane, QLD, Australia
| | - Tim R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia.
- BASE facility, University of Queensland, Brisbane, QLD, Australia.
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Burgon JD, Vieites DR, Jacobs A, Weidt SK, Gunter HM, Steinfartz S, Burgess K, Mable BK, Elmer KR. Functional colour genes and signals of selection in colour-polymorphic salamanders. Mol Ecol 2020; 29:1284-1299. [PMID: 32159878 DOI: 10.1111/mec.15411] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022]
Abstract
Coloration has been associated with multiple biologically relevant traits that drive adaptation and diversification in many taxa. However, despite the great diversity of colour patterns present in amphibians the underlying molecular basis is largely unknown. Here, we use insight from a highly colour-variable lineage of the European fire salamander (Salamandra salamandra bernardezi) to identify functional associations with striking variation in colour morph and pattern. The three focal colour morphs-ancestral black-yellow striped, fully yellow and fully brown-differed in pattern, visible coloration and cellular composition. From population genomic analyses of up to 4,702 loci, we found no correlations of neutral population genetic structure with colour morph. However, we identified 21 loci with genotype-phenotype associations, several of which relate to known colour genes. Furthermore, we inferred response to selection at up to 142 loci between the colour morphs, again including several that relate to coloration genes. By transcriptomic analysis across all different combinations, we found 196 differentially expressed genes between yellow, brown and black skin, 63 of which are candidate genes involved in animal coloration. The concordance across different statistical approaches and 'omic data sets provide several lines of evidence for loci linked to functional differences between colour morphs, including TYR, CAMK1 and PMEL. We found little association between colour morph and the metabolomic profile of its toxic compounds from the skin secretions. Our research suggests that current ecological and evolutionary hypotheses for the origins and maintenance of these striking colour morphs may need to be revisited.
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Affiliation(s)
- James D Burgon
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - David R Vieites
- Museo Nacional de Ciencias Naturales (MNCN), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Arne Jacobs
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Stefan K Weidt
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Helen M Gunter
- Edinburgh Genomics, King's Buildings, University of Edinburgh, Edinburgh, UK
| | - Sebastian Steinfartz
- Department of Evolutionary Biology, Unit Molecular Ecology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Karl Burgess
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Barbara K Mable
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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5
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Gunter HM, Schneider RF, Karner I, Sturmbauer C, Meyer A. Molecular investigation of genetic assimilation during the rapid adaptive radiations of East African cichlid fishes. Mol Ecol 2017; 26:6634-6653. [PMID: 29098748 DOI: 10.1111/mec.14405] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 08/06/2017] [Accepted: 08/24/2017] [Indexed: 12/19/2022]
Abstract
Adaptive radiations are characterized by adaptive diversification intertwined with rapid speciation within a lineage resulting in many ecologically specialized, phenotypically diverse species. It has been proposed that adaptive radiations can originate from ancestral lineages with pronounced phenotypic plasticity in adaptive traits, facilitating ecologically driven phenotypic diversification that is ultimately fixed through genetic assimilation of gene regulatory regions. This study aimed to investigate how phenotypic plasticity is reflected in gene expression patterns in the trophic apparatus of several lineages of East African cichlid fishes, and whether the observed patterns support genetic assimilation. This investigation used a split brood experimental design to compare adaptive plasticity in species from within and outside of adaptive radiations. The plastic response was induced in the crushing pharyngeal jaws through feeding individuals either a hard or soft diet. We find that nonradiating, basal lineages show higher levels of adaptive morphological plasticity than the derived, radiated lineages, suggesting that these differences have become partially genetically fixed during the formation of the adaptive radiations. Two candidate genes that may have undergone genetic assimilation, gif and alas1, were identified, in addition to alterations in the wiring of LPJ patterning networks. Taken together, our results suggest that genetic assimilation may have dampened the inducibility of plasticity related genes during the adaptive radiations of East African cichlids, flattening the reaction norms and canalizing their feeding phenotypes, driving adaptation to progressively more narrow ecological niches.
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Affiliation(s)
- Helen M Gunter
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.,Zukunftskolleg, University of Konstanz, Konstanz, Germany
| | - Ralf F Schneider
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.,International Max Planck Research School for Organismal Biology, University of Konstanz, Konstanz, Germany
| | | | | | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.,International Max Planck Research School for Organismal Biology, University of Konstanz, Konstanz, Germany.,Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA, USA
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6
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Schneider RF, Li Y, Meyer A, Gunter HM. Regulatory gene networks that shape the development of adaptive phenotypic plasticity in a cichlid fish. Mol Ecol 2014; 23:4511-26. [PMID: 25041245 DOI: 10.1111/mec.12851] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 06/14/2014] [Accepted: 06/25/2014] [Indexed: 01/07/2023]
Abstract
Phenotypic plasticity is the ability of organisms with a given genotype to develop different phenotypes according to environmental stimuli, resulting in individuals that are better adapted to local conditions. In spite of their ecological importance, the developmental regulatory networks underlying plastic phenotypes often remain uncharacterized. We examined the regulatory basis of diet-induced plasticity in the lower pharyngeal jaw (LPJ) of the cichlid fish Astatoreochromis alluaudi, a model species in the study of adaptive plasticity. Through raising juvenile A. alluaudi on either a hard or soft diet (hard-shelled or pulverized snails) for between 1 and 8 months, we gained insight into the temporal regulation of 19 previously identified candidate genes during the early stages of plasticity development. Plasticity in LPJ morphology was first detected between 3 and 5 months of diet treatment. The candidate genes, belonging to various functional categories, displayed dynamic expression patterns that consistently preceded the onset of morphological divergence and putatively contribute to the initiation of the plastic phenotypes. Within functional categories, we observed striking co-expression, and transcription factor binding site analysis was used to examine the prospective basis of their coregulation. We propose a regulatory network of LPJ plasticity in cichlids, presenting evidence for regulatory crosstalk between bone and muscle tissues, which putatively facilitates the development of this highly integrated trait. Through incorporating a developmental time-course into a phenotypic plasticity study, we have identified an interconnected, environmentally responsive regulatory network that shapes the development of plasticity in a key innovation of East African cichlids.
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Affiliation(s)
- Ralf F Schneider
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457, Konstanz, Germany; International Max Planck Research School for Organismal Biology, University of Konstanz, Universitätsstr 10, 78457, Konstanz, Germany
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Philibert R, Gunter HM, Kolassa IT. The search for peripheral biomarkers for major depression: benefiting from successes in the biology of smoking. Am J Med Genet B Neuropsychiatr Genet 2014; 165B:230-4. [PMID: 24591099 DOI: 10.1002/ajmg.b.32227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 01/29/2014] [Indexed: 12/17/2022]
Abstract
The search for robust, clinically useful markers for major depression (MD) has been relatively unproductive. This is unfortunate because MD is one of the largest socio-economic challenges for much of the world and the development of reliable biomarkers for MD could aid in the prevention or treatment of this common syndrome. In this editorial, we compare the approaches taken in the search for biomarkers for MD to that of the more successful searches for biomarkers for tobacco use, and identify several substantive barriers. We suggest that many of the existing clinical repositories used in these biomarkers searches for MD may be of limited value. We conclude that in the future greater attention should be given to the clinical definitions, characterization of confounding environmental factors and age of subjects included in studies. © 2014 Wiley Periodicals, Inc.
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Affiliation(s)
- Robert Philibert
- Department of Psychiatry, University of Iowa, Iowa City, Iowa; Zukunftskolleg, University of Konstanz, Konstanz, Germany
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Gunter HM, Koppermann C, Meyer A. Revisiting de Beer's textbook example of heterochrony and jaw elongation in fish: calmodulin expression reflects heterochronic growth, and underlies morphological innovation in the jaws of belonoid fishes. EvoDevo 2014; 5:8. [PMID: 24499543 PMCID: PMC3927394 DOI: 10.1186/2041-9139-5-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 12/12/2013] [Indexed: 01/08/2023] Open
Abstract
Background Heterochronic shifts during ontogeny can result in adaptively important innovations and might be initiated by simple developmental switches. Understanding the nature of these developmental events can provide insights into fundamental molecular mechanisms of evolutionary change. Fishes from the Suborder Belonoidei display a vast array of extreme craniofacial morphologies that appear to have arisen through a series of heterochronic shifts. We performed a molecular heterochrony study, comparing postembryonic jaw development in representatives of the Suborder Belonoidei, the halfbeak Dermogenys pusilla (where the lower jaw is considerably elongated compared to the upper jaw) and the needlefish Belone belone (where both jaws are elongated), to a representative of their sister group the Suborder Adrianichthyoidei, the medaka Oryzias latipes, which has retained the ancestral morphology. Results Early in development, the lower jaw displays accelerated growth both in needlefish and halfbeak compared to medaka, and secondary acceleration of the upper jaw is seen in needlefish later in their development, representing a case of mosaic heterochrony. We identified toothless extensions of the dentaries as innovations of Belonoid fishes and the source of heterochronic growth. The molecular basis of growth heterochronies in the Belonoidei was examined through comparing expression of skeletogenic genes during development of halfbeak and medaka. The calmodulin paralogue calm1 was identified as a potential regulator of jaw length in halfbeak as its expression gradually increases in the lower jaw, but not the upper jaw, in a pattern that matches its outgrowth. Moreover, medaka displays equal expression of calm1 in the upper and lower jaws, consistent with the lack of jaw outgrowth in this species. Conclusions Heterochronic shifts in jaw growth have occurred repeatedly during the evolution of Belonoid fishes and we identify toothless extensions of the dentaries as an important innovation of this group. Our results suggest that calm1 contributes to jaw heterochrony in halfbeak, potentially driving further heterochronic shifts in jaw growth across the Suborder Belonoidei, such as the upper jaw acceleration observed in needlefish.
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Affiliation(s)
| | | | - Axel Meyer
- Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University of Konstanz, Universitätstrasse 10, 78457 Constance, Germany.
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9
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Gunter HM, Fan S, Xiong F, Franchini P, Fruciano C, Meyer A. Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish. Mol Ecol 2013; 22:4516-31. [PMID: 23952004 DOI: 10.1111/mec.12417] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/25/2013] [Accepted: 05/28/2013] [Indexed: 11/29/2022]
Abstract
Adaptive phenotypic plasticity, the ability of an organism to change its phenotype to match local environments, is increasingly recognized for its contribution to evolution. However, few empirical studies have explored the molecular basis of plastic traits. The East African cichlid fish Astatoreochromis alluaudi displays adaptive phenotypic plasticity in its pharyngeal jaw apparatus, a structure that is widely seen as an evolutionary key innovation that has contributed to the remarkable diversity of cichlid fishes. It has previously been shown that in response to different diets, the pharyngeal jaws change their size, shape and dentition: hard diets induce an adaptive robust molariform tooth phenotype with short jaws and strong internal bone structures, while soft diets induce a gracile papilliform tooth phenotype with elongated jaws and slender internal bone structures. To gain insight into the molecular underpinnings of these adaptations and enable future investigations of the role that phenotypic plasticity plays during the formation of adaptive radiations, the transcriptomes of the two divergent jaw phenotypes were examined. Our study identified a total of 187 genes whose expression differs in response to hard and soft diets, including immediate early genes, extracellular matrix genes and inflammatory factors. Transcriptome results are interpreted in light of expression of candidate genes-markers for tooth size and shape, bone cells and mechanically sensitive pathways. This study opens up new avenues of research at new levels of biological organization into the roles of phenotypic plasticity during speciation and radiation of cichlid fishes.
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Affiliation(s)
- Helen M Gunter
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457, Konstanz, Germany
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Radtke KM, Ruf M, Gunter HM, Dohrmann K, Schauer M, Meyer A, Elbert T. Transgenerational impact of intimate partner violence on methylation in the promoter of the glucocorticoid receptor. Transl Psychiatry 2011; 1:e21. [PMID: 22832523 PMCID: PMC3309516 DOI: 10.1038/tp.2011.21] [Citation(s) in RCA: 382] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Prenatal exposure to maternal stress can have lifelong implications for psychological function, such as behavioral problems and even the development of mental illness. Previous research suggests that this is due to transgenerational epigenetic programming of genes operating in the hypothalamic-pituitary-adrenal axis, such as the glucocorticoid receptor (GR). However, it is not known whether intrauterine exposure to maternal stress affects the epigenetic state of these genes beyond infancy. Here, we analyze the methylation status of the GR gene in mothers and their children, at 10-19 years after birth. We combine these data with a retrospective evaluation of maternal exposure to intimate partner violence (IPV). Methylation of the mother's GR gene was not affected by IPV. For the first time, we show that methylation status of the GR gene of adolescent children is influenced by their mother's experience of IPV during pregnancy. As these sustained epigenetic modifications are established in utero, we consider this to be a plausible mechanism by which prenatal stress may program adult psychosocial function.
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Affiliation(s)
- K M Radtke
- Department of Psychology, University of Konstanz and Center for Psychiatry Reichenau, Konstanz, Germany,Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - M Ruf
- Department of Psychology, University of Konstanz and Center for Psychiatry Reichenau, Konstanz, Germany
| | - H M Gunter
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany,Zukunftskolleg, University of Konstanz, Konstanz, Germany
| | - K Dohrmann
- Department of Psychology, University of Konstanz and Center for Psychiatry Reichenau, Konstanz, Germany
| | - M Schauer
- Department of Psychology, University of Konstanz and Center for Psychiatry Reichenau, Konstanz, Germany
| | - A Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany,Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, 78457 Konstanz, Germany. E-mail:
| | - T Elbert
- Department of Psychology, University of Konstanz and Center for Psychiatry Reichenau, Konstanz, Germany,Department of Psychology, University of Konstanz and Center for Psychiatry Reichenau, 78457 Konstanz, Germany. E-mail:
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11
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Gunter HM, Clabaut C, Salzburger W, Meyer A. Identification and characterization of gene expression involved in the coloration of cichlid fish using microarray and qRT-PCR approaches. J Mol Evol 2011; 72:127-37. [PMID: 21267555 DOI: 10.1007/s00239-011-9431-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 01/03/2011] [Indexed: 01/09/2023]
Abstract
It has been suggested that speciation on the basis of sexual selection is an important mechanism for the generation of new species for East African cichlids, where male body coloration is one of the major discriminatory factors used by females in mate choice. To gain insight into the molecular basis of cichlid coloration, we studied the Lake Malawi cichlid Pseudotropheus saulosi, comparing transcription in the bright blue skin of males to the yellow skin of females. Our cDNA microarray experiments identified 46 clones that exhibited expression differences between the two sexes, of which five were confirmed to be differentially expressed by relative quantitative real-time PCR (qRT-PCR). This gene list includes a representative from the endosomal-to-Golgi vesicle trafficking pathway, Coatomer protein complex, subunit zeta-1 (Copz-1), which is known to be a critical determinant of pigmentation in humans and zebrafish. With the support of microscopic images of the skin of these specimens, we interpret the transcriptional differences between the blue males and yellow females. Here, we provide insight into the putative functional diversification of genes involved in the coloration of cichlids and by extension, on the evolution of coloration in teleost fish.
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Affiliation(s)
- Helen M Gunter
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstr 10, 78457 Constance, Germany
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Elmer KR, Fan S, Gunter HM, Jones JC, Boekhoff S, Kuraku S, Meyer A. Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes. Mol Ecol 2010; 19 Suppl 1:197-211. [PMID: 20331780 DOI: 10.1111/j.1365-294x.2009.04488.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Crater lakes provide a natural laboratory to study speciation of cichlid fishes by ecological divergence. Up to now, there has been a dearth of transcriptomic and genomic information that would aid in understanding the molecular basis of the phenotypic differentiation between young species. We used next-generation sequencing (Roche 454 massively parallel pyrosequencing) to characterize the diversity of expressed sequence tags between ecologically divergent, endemic and sympatric species of cichlid fishes from crater lake Apoyo, Nicaragua: benthic Amphilophus astorquii and limnetic Amphilophus zaliosus. We obtained 24 174 A. astorquii and 21 382 A. zaliosus high-quality expressed sequence tag contigs, of which 13 106 pairs are orthologous between species. Based on the ratio of nonsynonymous to synonymous substitutions, we identified six sequences exhibiting signals of strong diversifying selection (K(a)/K(s) > 1). These included genes involved in biosynthesis, metabolic processes and development. This transcriptome sequence variation may be reflective of natural selection acting on the genomes of these young, sympatric sister species. Based on Ks ratios and p-distances between 3'-untranslated regions (UTRs) calibrated to previously published species divergence times, we estimated a neutral transcriptome-wide substitutional mutation rate of approximately 1.25 x 10(-6) per site per year. We conclude that next-generation sequencing technologies allow us to infer natural selection acting to diversify the genomes of young species, such as crater lake cichlids, with much greater scope than previously possible.
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Affiliation(s)
- K R Elmer
- Department of Biology, University of Konstanz, Germany
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Gunter HM, Degnan BM. Impact of ecologically relevant heat shocks on Hsp developmental function in the vetigastropodHaliotis asinina. J Exp Zool 2008; 310:450-64. [DOI: 10.1002/jez.b.21217] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Jones JC, Gunter HM, Meyer A. Will he still look good with the lights on? Spectral tuning of visual pigments in fish. J Biol 2008; 7:26. [PMID: 18828890 PMCID: PMC2776405 DOI: 10.1186/jbiol86] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Koop D, Richards GS, Wanninger A, Gunter HM, Degnan BM. The role of MAPK signaling in patterning and establishing axial symmetry in the gastropod Haliotis asinina. Dev Biol 2007; 311:200-12. [PMID: 17916345 DOI: 10.1016/j.ydbio.2007.08.035] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Revised: 08/14/2007] [Accepted: 08/20/2007] [Indexed: 10/22/2022]
Abstract
Gastropods are members of the Spiralia, a diverse group of invertebrates that share a common early developmental program, which includes spiral cleavage and a larval trochophore stage. The spiral cleavage program results in the division of the embryo into four quadrants. Specification of the dorsal (D) quadrant is intimately linked with body plan organization and in equally cleaving gastropods occurs when one of the vegetal macromeres makes contact with overlying micromeres and receives an inductive signal that activates a MAPK signaling cascade. Following the induction of the 3D macromere, the embryo begins to gastrulate and assumes a bilateral cleavage pattern. Here we inhibit MAPK activation in 3D with U0126 and examine its effect on the formation and patterning of the trochophore, using a suite of territory-specific markers. The head (pretrochal) region appears to maintain quadri-radial symmetry in U0126-treated embryos, supporting a role for MAPK signaling in 3D in establishing dorsoventral polarity in this region. Posterior (posttrochal) structures - larval musculature, shell and foot--fail to develop in MAPK inhibited trochophores. Inhibition of 3D specification by an alternative method--monensin treatment--yields similar abnormal trochophores. However, genes that are normally expressed in the ectodermal structures (shell and foot) are detected in U0126- and monensin-perturbed larvae in patterns that suggest that this region has latent dorsoventral polarity that is manifested even in the absence of D quadrant specification.
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Affiliation(s)
- Demian Koop
- School of Integrative Biology, University of Queensland, Brisbane QLD 4072, Australia
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Gunter HM, Degnan BM. Developmental expression of Hsp90, Hsp70 and HSF during morphogenesis in the vetigastropod Haliotis asinina. Dev Genes Evol 2007; 217:603-12. [PMID: 17647016 DOI: 10.1007/s00427-007-0171-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 06/18/2007] [Indexed: 01/13/2023]
Abstract
Heat shock proteins (Hsps) have dual functions, participating in both the stress response and a broad range of developmental processes. At physiological temperatures, it has been demonstrated in deuterostomes (vertebrates) and ecdysozoans (insects) that Hsps are expressed in tissues that are undergoing differentiation and morphogenesis. Here we investigate the developmental expression of Hsp70, Hsp90 and their regulatory transcription factor heat shock transcription factor (HSF) in the marine gastropod Haliotis asinina, a representative of the 3rd major lineage of bilaterian animals, the Lophotrochozoa. HasHsp70, HasHsp90 and HasHSF are maternally expressed in H. asinina and are progressively restricted to the micromere lineage during cleavage. During larval morphogenesis, they are expressed in unique and overlapping patterns in the prototroch, foot, and mantle. Hsp expression peaked in these tissues during periods of cell differentiation and morphogenesis, returning to lower levels after morphogenesis was complete. These patterns of Hsp and HSF expression in H. asinina are akin to those observed in ecdysozoans and deuterostomes, with Hsps being activated in cells and tissues undergoing morphogenesis.
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Affiliation(s)
- Helen M Gunter
- School of Integrative Biology, University of Queensland, Brisbane, Queensland 4072, Australia
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