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Usai G, Fambrini M, Pugliesi C, Simoni S. Exploring the patterns of evolution: Core thoughts and focus on the saltational model. Biosystems 2024; 238:105181. [PMID: 38479653 DOI: 10.1016/j.biosystems.2024.105181] [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: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.
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Affiliation(s)
- Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Samuel Simoni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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2
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Cannizzaro AG, Balding D, Lazo-Wasem EA, Sawicki TR. Morphological and molecular analyses reveal a new species of stygobitic amphipod in the genus Crangonyx(Crustacea: Crangonyctidae) from Jackson County, Florida, with a redescription of Crangonyx floridanusand notes on its taxonomy and biogeography. J NAT HIST 2019. [DOI: 10.1080/00222933.2019.1584341] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Andrew G. Cannizzaro
- Department of Biological Sciences, Florida Agricultural and Mechanical University, Tallahassee, FL, USA
| | - Donna Balding
- Department of Natural Sciences, Middle Georgia State University, Macon, GA, USA
| | - Eric A. Lazo-Wasem
- Division of Invertebrate Zoology, Yale Peabody Museum of Natural History, Yale University, New Haven, CT, USA
| | - Thomas R. Sawicki
- Department of Biological Sciences, Florida Agricultural and Mechanical University, Tallahassee, FL, USA
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3
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Nonsrirach T, Lauprasert K. Preliminary report on the genetic structure of Glyphoglossus molossus(Anura: Microhylidae) from the Khorat Plateau, north-eastern Thailand. J NAT HIST 2019. [DOI: 10.1080/00222933.2019.1618940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Thanade Nonsrirach
- Department of Biology, Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand
| | - Komsorn Lauprasert
- Department of Biology, Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand
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4
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Crowner A, Khatri S, Blichmann D, Voss SR. Rediscovering the Axolotl as a Model for Thyroid Hormone Dependent Development. Front Endocrinol (Lausanne) 2019; 10:237. [PMID: 31031711 PMCID: PMC6473073 DOI: 10.3389/fendo.2019.00237] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 03/25/2019] [Indexed: 12/30/2022] Open
Abstract
The Mexican axolotl (Ambystoma mexicanum) is an important model organism in biomedical research. Much current attention is focused on the axolotl's amazing ability to regenerate tissues and whole organs after injury. However, not forgotten is the axolotl's equally amazing ability to thwart aspects of tissue maturation and retain juvenile morphology into the adult phase of life. Unlike close tiger salamander relatives that undergo a thyroid hormone regulated metamorphosis, the axolotl does not typically undergo a metamorphosis. Instead, the axolotl exhibits a paedomorphic mode of development that enables a completely aquatic life cycle. The evolution of paedomorphosis allowed axolotls to exploit relatively permanent habitats in Mexico, and preadapted axolotls for domestication and laboratory study. In this perspective, we first introduce the axolotl and the various meanings of paedomorphosis, and then stress the need to move beyond endocrinology-guided approaches to understand the axolotl's hypothyroid state. With the recent completion of the axolotl genome assembly and established methods to manipulate gene functions, the axolotl is poised to provide new insights about paedomorphosis and the role of thyroid hormone in development and evolution.
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5
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Oromi N, Valbuena‐Ureña E, Soler‐Membrives A, Amat F, Camarasa S, Carranza S, Sanuy D, Denoël M. Genetic structure of lake and stream populations in a Pyrenean amphibian (
Calotriton asper
) reveals evolutionary significant units associated with paedomorphosis. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12250] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Neus Oromi
- Departament de Ciència Animal (Fauna Silvestre) Universitat de Lleida Lleida Catalonia Spain
- Laboratory of Fish and Amphibian Ethology Behavioural Biology Group Freshwater and OCeanic science Unit of reSearch (FOCUS) University of Liège Liège Belgium
| | - Emilio Valbuena‐Ureña
- Unitat de Zoologia Facultat de Biociències Universitat Autònoma de Barcelona Barcelona Catalonia Spain
- Centre de Fauna Salvatge de Torreferrussa (Catalan Wildlife Service – Forestal Catalana) Finca de Torreferrusa Barcelona Catalonia Spain
| | - Anna Soler‐Membrives
- Unitat de Zoologia Facultat de Biociències Universitat Autònoma de Barcelona Barcelona Catalonia Spain
| | - Felix Amat
- Àrea d'Herpetologia Museu de Granollers Ciències Naturals Granollers Catalonia Spain
| | - Sebastià Camarasa
- Departament de Ciència Animal (Fauna Silvestre) Universitat de Lleida Lleida Catalonia Spain
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
| | - Delfi Sanuy
- Departament de Ciència Animal (Fauna Silvestre) Universitat de Lleida Lleida Catalonia Spain
| | - Mathieu Denoël
- Laboratory of Fish and Amphibian Ethology Behavioural Biology Group Freshwater and OCeanic science Unit of reSearch (FOCUS) University of Liège Liège Belgium
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6
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Sanchez E, Küpfer E, Goedbloed DJ, Nolte AW, Lüddecke T, Schulz S, Vences M, Steinfartz S. Morphological and transcriptomic analyses reveal three discrete primary stages of postembryonic development in the common fire salamander,Salamandra salamandra. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:96-108. [DOI: 10.1002/jez.b.22792] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 12/14/2017] [Accepted: 01/25/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Eugenia Sanchez
- Zoological Institute; Technische Universität Braunschweig; Braunschweig Germany
| | - Eliane Küpfer
- Zoological Institute; Technische Universität Braunschweig; Braunschweig Germany
| | - Daniel J. Goedbloed
- Zoological Institute; Technische Universität Braunschweig; Braunschweig Germany
| | - Arne W. Nolte
- Department of Evolutionary Genetics; Max Planck Institute for Evolutionary Biology; Plön Germany
- Ecological Genomics; Institute for Biology and Environmental Sciences; Carl von Ossietzky Universität Oldenburg; Oldenburg Germany
| | - Tim Lüddecke
- Zoological Institute; Technische Universität Braunschweig; Braunschweig Germany
| | - Stefan Schulz
- Institute of Organic Chemistry; Technische Universität Braunschweig; Braunschweig Germany
| | - Miguel Vences
- Zoological Institute; Technische Universität Braunschweig; Braunschweig Germany
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Percino-Daniel R, Recuero E, Vázquez-Domínguez E, Zamudio KR, Parra-Olea G. All grown-up and nowhere to go: paedomorphosis and local adaptation inAmbystomasalamanders in the Cuenca Oriental of Mexico. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12750] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Ruth Percino-Daniel
- Instituto de Biología; Universidad Nacional Autónoma de México; AP 70-153 Circuito Exterior Ciudad Universitaria México DF CP 04510 México
| | - Ernesto Recuero
- Departamento de Ecología de la Biodiversidad; Instituto de Ecología; Universidad Nacional Autónoma de México; Ap. Postal 70-275 Ciudad Universitaria México DF 04510 México
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad; Instituto de Ecología; Universidad Nacional Autónoma de México; Ap. Postal 70-275 Ciudad Universitaria México DF 04510 México
| | - Kelly R. Zamudio
- Department of Ecology and Evolutionary Biology; Cornell University; Ithaca NY 14853 USA
| | - Gabriela Parra-Olea
- Instituto de Biología; Universidad Nacional Autónoma de México; AP 70-153 Circuito Exterior Ciudad Universitaria México DF CP 04510 México
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8
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Voss SR, Palumbo A, Nagarajan R, Gardiner DM, Muneoka K, Stromberg AJ, Athippozhy AT. Gene expression during the first 28 days of axolotl limb regeneration I: Experimental design and global analysis of gene expression. ACTA ACUST UNITED AC 2015; 2:120-136. [PMID: 27168937 PMCID: PMC4860271 DOI: 10.1002/reg2.37] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
While it is appreciated that global gene expression analyses can provide novel insights about complex biological processes, experiments are generally insufficiently powered to achieve this goal. Here we report the results of a robust microarray experiment of axolotl forelimb regeneration. At each of 20 post‐amputation time points, we estimated gene expression for 10 replicate RNA samples that were isolated from 1 mm of heterogeneous tissue collected from the distal limb tip. We show that the limb transcription program diverges progressively with time from the non‐injured state, and divergence among time adjacent samples is mostly gradual. However, punctuated episodes of transcription were identified for five intervals of time, with four of these coinciding with well‐described stages of limb regeneration—amputation, early bud, late bud, and pallet. The results suggest that regeneration is highly temporally structured and regulated by mechanisms that function within narrow windows of time to coordinate transcription within and across cell types of the regenerating limb. Our results provide an integrative framework for hypothesis generation using this complex and highly informative data set.
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Affiliation(s)
- S Randal Voss
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA; Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky 40506, USA
| | - Alex Palumbo
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA
| | - Radha Nagarajan
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky 40506, USA
| | - David M Gardiner
- Department of Developmental and Cell Biology, UC-Irvine, Irvine, California 92697, USA
| | - Ken Muneoka
- Department of Molecular and Cellular Biology, Tulane University, New Orleans, Louisiana 70118, USA
| | - Arnold J Stromberg
- Department of Statistics, University of Kentucky, Lexington, Kentucky 40506, USA
| | - Antony T Athippozhy
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA; Department of Statistics, University of Kentucky, Lexington, Kentucky 40506, USA
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9
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Pardo-Diaz C, Salazar C, Jiggins CD. Towards the identification of the loci of adaptive evolution. Methods Ecol Evol 2015; 6:445-464. [PMID: 25937885 PMCID: PMC4409029 DOI: 10.1111/2041-210x.12324] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/28/2014] [Indexed: 12/17/2022]
Abstract
1. Establishing the genetic and molecular basis underlying adaptive traits is one of the major goals of evolutionary geneticists in order to understand the connection between genotype and phenotype and elucidate the mechanisms of evolutionary change. Despite considerable effort to address this question, there remain relatively few systems in which the genes shaping adaptations have been identified. 2. Here, we review the experimental tools that have been applied to document the molecular basis underlying evolution in several natural systems, in order to highlight their benefits, limitations and suitability. In most cases, a combination of DNA, RNA and functional methodologies with field experiments will be needed to uncover the genes and mechanisms shaping adaptation in nature.
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Affiliation(s)
- Carolina Pardo-Diaz
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del RosarioCarrera 24 No 63C-69, Bogotá 111221, Colombia
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del RosarioCarrera 24 No 63C-69, Bogotá 111221, Colombia
| | - Chris D Jiggins
- Department of Zoology, University of CambridgeDowning Street, Cambridge, CB2 3EJ, UK
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10
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Sousounis K, Athippozhy AT, Voss SR, Tsonis PA. Plasticity for axolotl lens regeneration is associated with age-related changes in gene expression. ACTA ACUST UNITED AC 2014; 1:47-57. [PMID: 27499863 PMCID: PMC4895297 DOI: 10.1002/reg2.25] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/10/2014] [Accepted: 09/03/2014] [Indexed: 12/11/2022]
Abstract
Mexican axolotls lose potential for lens regeneration 2 weeks after hatching. We used microarrays to identify differently expressed genes before and after this critical time, using RNA isolated from iris. Over 3700 genes were identified as differentially expressed in response to lentectomy between young (7 days post‐hatching) and old (3 months post‐hatching) axolotl larvae. Strikingly, many of the genes were only expressed in the early or late iris. Genes that were highly expressed in young iris significantly enriched electron transport chain, transcription, metabolism, and cell cycle gene ontologies, all of which are associated with lens regeneration. In contrast, genes associated with cellular differentiation and tissue maturation were uniquely expressed in old iris. Many of these expression differences strongly suggest that young and old iris samples were collected before and after the spleen became developmentally competent to produce and secrete cells with humoral and innate immunity functions. Our study establishes the axolotl as a powerful model to investigate age‐related cellular differentiation and immune system ontogeny within the context of tissue regeneration.
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Affiliation(s)
- Konstantinos Sousounis
- Department of Biology and Center for Tissue Regeneration and Engineering University of Dayton Dayton OH USA
| | - Antony T Athippozhy
- Department of Biology and Spinal Cord and Brain Injury Research Center University of Kentucky Lexington KY 40503 USA
| | - S Randal Voss
- Department of Biology and Spinal Cord and Brain Injury Research Center University of Kentucky Lexington KY 40503 USA
| | - Panagiotis A Tsonis
- Department of Biology and Center for Tissue Regeneration and Engineering University of Dayton Dayton OH USA
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11
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Aran RP, Steffen MA, Martin SD, Lopez OI, Bonett RM. Reduced effects of thyroid hormone on gene expression and metamorphosis in a paedomorphic plethodontid salamander. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 322:294-303. [DOI: 10.1002/jez.b.22580] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 05/08/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Robert P. Aran
- Department of Biological Science; University of Tulsa; Tulsa Oklahoma
| | | | - Samuel D. Martin
- Department of Biological Science; University of Tulsa; Tulsa Oklahoma
| | - Olivia I. Lopez
- Department of Biological Science; University of Tulsa; Tulsa Oklahoma
| | - Ronald M. Bonett
- Department of Biological Science; University of Tulsa; Tulsa Oklahoma
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12
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Page RB, Boley MA, Kump DK, Voss SR. Genomics of a metamorphic timing QTL: met1 maps to a unique genomic position and regulates morph and species-specific patterns of brain transcription. Genome Biol Evol 2014; 5:1716-30. [PMID: 23946331 PMCID: PMC3787675 DOI: 10.1093/gbe/evt123] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Very little is known about genetic factors that regulate life history transitions during ontogeny. Closely related tiger salamanders (Ambystoma species complex) show extreme variation in metamorphic timing, with some species foregoing metamorphosis altogether, an adaptive trait called paedomorphosis. Previous studies identified a major effect quantitative trait locus (met1) for metamorphic timing and expression of paedomorphosis in hybrid crosses between the biphasic Eastern tiger salamander (Ambystoma tigrinum tigrinum) and the paedomorphic Mexican axolotl (Ambystoma mexicanum). We used existing hybrid mapping panels and a newly created hybrid cross to map the met1 genomic region and determine the effect of met1 on larval growth, metamorphic timing, and gene expression in the brain. We show that met1 maps to the position of a urodele-specific chromosome rearrangement on linkage group 2 that uniquely brought functionally associated genes into linkage. Furthermore, we found that more than 200 genes were differentially expressed during larval development as a function of met1 genotype. This list of differentially expressed genes is enriched for proteins that function in the mitochondria, providing evidence of a link between met1, thyroid hormone signaling, and mitochondrial energetics associated with metamorphosis. Finally, we found that met1 significantly affected metamorphic timing in hybrids, but not early larval growth rate. Collectively, our results show that met1 regulates species and morph-specific patterns of brain transcription and life history variation.
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13
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Denoël M, Ficetola GF. Heterochrony in a complex world: disentangling environmental processes of facultative paedomorphosis in an amphibian. J Anim Ecol 2014; 83:606-15. [PMID: 24180255 DOI: 10.1111/1365-2656.12173] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 10/23/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Mathieu Denoël
- Laboratory of Fish and Amphibian Ethology; Behavioural Biology Unit; Department of Biology, Ecology and Evolution; University of Liege; 22 Quai van Beneden 4020 Liege Belgium
| | - Gentile F. Ficetola
- Department of Environmental and Earth Sciences; University of Milano-Bicocca; 1 Piazza della Scienza 20126 Milano Italy
- Laboratory of Alpine Ecology (LECA); CNRS UMR 5553; Joseph Fourier University; 38041 Grenoble France
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14
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Reyes-Ruiz JM, Limon A, Korn MJ, Nakamura PA, Shirkey NJ, Wong JK, Miledi R. Profiling neurotransmitter receptor expression in the Ambystoma mexicanum brain. Neurosci Lett 2013; 538:32-7. [PMID: 23353105 DOI: 10.1016/j.neulet.2013.01.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 12/18/2012] [Accepted: 01/11/2013] [Indexed: 11/25/2022]
Abstract
Ability to regenerate limbs and central nervous system (CNS) is unique to few vertebrates, most notably the axolotl (Ambystoma sp.). However, despite the fact the neurotransmitter receptors are involved in axonal regeneration, little is known regarding its expression profile. In this project, RT-PCR and qPCR were performed to gain insight into the neurotransmitter receptors present in Ambystoma. Its functional ability was studied by expressing axolotl receptors in Xenopus laevis oocytes by either injection of mRNA or by direct microtransplantation of brain membranes. Oocytes injected with axolotl mRNA expressed ionotropic receptors activated by GABA, aspartate+glycine and kainate, as well as metabotropic receptors activated by acetylcholine and glutamate. Interestingly, we did not see responses following the application of serotonin. Membranes from the axolotl brain were efficiently microtransplanted into Xenopus oocytes and two types of native GABA receptors that differed in the temporal course of their responses and affinities to GABA were observed. Results of this study are necessary for further characterization of axolotl neurotransmitter receptors and may be useful for guiding experiments aimed at understanding activity-dependant limb and CNS regeneration.
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16
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Elinson RP, del Pino EM. Developmental diversity of amphibians. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2012; 1:345-69. [PMID: 22662314 PMCID: PMC3364608 DOI: 10.1002/wdev.23] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The current model amphibian, Xenopus laevis, develops rapidly in water to a tadpole which metamorphoses into a frog. Many amphibians deviate from the X. laevis developmental pattern. Among other adaptations, their embryos develop in foam nests on land or in pouches on their mother's back or on a leaf guarded by a parent. The diversity of developmental patterns includes multinucleated oogenesis, lack of RNA localization, huge non-pigmented eggs, and asynchronous, irregular early cleavages. Variations in patterns of gastrulation highlight the modularity of this critical developmental period. Many species have eliminated the larva or tadpole and directly develop to the adult. The wealth of developmental diversity among amphibians coupled with the wealth of mechanistic information from X. laevis permit comparisons that provide deeper insights into developmental processes.
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Affiliation(s)
- Richard P Elinson
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA, USA.
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17
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Huggins P, Johnson CK, Schoergendorfer A, Putta S, Bathke AC, Stromberg AJ, Voss SR. Identification of differentially expressed thyroid hormone responsive genes from the brain of the Mexican Axolotl (Ambystoma mexicanum). Comp Biochem Physiol C Toxicol Pharmacol 2012; 155:128-35. [PMID: 21457787 PMCID: PMC3166550 DOI: 10.1016/j.cbpc.2011.03.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 03/23/2011] [Accepted: 03/23/2011] [Indexed: 01/20/2023]
Abstract
The Mexican axolotl (Ambystoma mexicanum) presents an excellent model to investigate mechanisms of brain development that are conserved among vertebrates. In particular, metamorphic changes of the brain can be induced in free-living aquatic juveniles and adults by simply adding thyroid hormone (T4) to rearing water. Whole brains were sampled from juvenile A. mexicanum that were exposed to 0, 8, and 18 days of 50 nM T4, and these were used to isolate RNA and make normalized cDNA libraries for 454 DNA sequencing. A total of 1,875,732 high quality cDNA reads were assembled with existing ESTs to obtain 5884 new contigs for human RefSeq protein models, and to develop a custom Affymetrix gene expression array (Amby_002) with approximately 20,000 probe sets. The Amby_002 array was used to identify 303 transcripts that differed statistically (p<0.05, fold change >1.5) as a function of days of T4 treatment. Further statistical analyses showed that Amby_002 performed concordantly in comparison to an existing, small format expression array. This study introduces a new A. mexicanum microarray resource for the community and the first lists of T4-responsive genes from the brain of a salamander amphibian.
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Affiliation(s)
- P Huggins
- Department of Statistics, University of Kentucky, Lexington, KY 40506, USA
| | - CK Johnson
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - A Schoergendorfer
- Department of Statistics, University of Kentucky, Lexington, KY 40506, USA
| | - S Putta
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - AC Bathke
- Department of Statistics, University of Kentucky, Lexington, KY 40506, USA
| | - AJ Stromberg
- Department of Statistics, University of Kentucky, Lexington, KY 40506, USA
| | - SR Voss
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
- Communicating author: Randal Voss: , Tel: 859-257-9888; Fax: 859-257-1717
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18
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Comparative transcriptomics and gene expression in larval tiger salamander (Ambystoma tigrinum) gill and lung tissues as revealed by pyrosequencing. Gene 2011; 492:329-38. [PMID: 22138480 DOI: 10.1016/j.gene.2011.11.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 10/21/2011] [Accepted: 11/10/2011] [Indexed: 01/15/2023]
Abstract
Biologists are beginning to unravel the complexities of gene expression in model organisms by studying the transcriptome, the complement of genes that are transcribed in a given tissue. It is unclear, however, if findings from model systems apply to non-model organisms because of environmental effects on gene expression. Furthermore, there have been few efforts to quantify how transcriptome or gene expression varies across individuals and across tissues in natural environments. Herein, we describe transcriptomic profiling of gene expression in lung and gill tissue of three larval tiger salamanders. We do so with a hierarchical experimental design that captures variation in expression among genes, among tissues, and among individuals. Using 454 pyrosequencing, we produced high-quality sequence data of 59 megabases and assembled ~200,000 reads into 19,501 contigs. These contigs BLASTed to 3,599 transcripts, of which 721 were expressed in both tissues, 1,668 were unique to gill, and 1,210 unique to lung. Our data showed tissue-specific patterns in gene expression level with variation among transcripts and individuals. We identified genes and gene ontology terms related to respiration and compared their relative expression levels between gill and lung tissues. We also found evidence of exogenous genes associated with larval salamanders, and we identified ~1400 potential molecular markers (microsatellites and single nucleotide polymorphisms) that are associated with expressed genes. Given the tissue-specific differences we observed in transcriptomes, these data reinforce the idea that changes in gene expression serve as a primary mechanism underlying phenotypic plasticity.
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