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Falcon F, Tanaka EM, Rodriguez-Terrones D. Transposon waves at the water-to-land transition. Curr Opin Genet Dev 2023; 81:102059. [PMID: 37343338 DOI: 10.1016/j.gde.2023.102059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/02/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023]
Abstract
The major transitions in vertebrate evolution are associated with significant genomic reorganizations. In contrast to the evolutionary processes that occurred at the origin of vertebrates or prior to the radiation of teleost fishes, no whole-genome duplication events occurred during the water-to-land transition, and it remains an open question how did genome dynamics contribute to this prominent evolutionary event. Indeed, the recent sequencing of sarcopterygian and amphibian genomes has revealed that the extant lineages immediately preceding and succeeding this transition harbor an exceptional number of transposable elements and it is tempting to speculate that these sequences might have catalyzed the adaptations that enabled vertebrates to venture into land. Here, we review the genome dynamics associated with the major transitions in vertebrate evolution and discuss how the highly repetitive genomic landscapes revealed by recent efforts to characterize the genomes of amphibians and sarcopterygians argue for turbulent genome dynamics occurring before the water-to-land transition and possibly enabling it.
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Affiliation(s)
- Francisco Falcon
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter, 1030, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria. https://twitter.com/@FcoJFalcon
| | - Elly M Tanaka
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter, 1030, Vienna, Austria.
| | - Diego Rodriguez-Terrones
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter, 1030, Vienna, Austria.
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Nowoshilow S, Schloissnig S, Fei JF, Dahl A, Pang AWC, Pippel M, Winkler S, Hastie AR, Young G, Roscito JG, Falcon F, Knapp D, Powell S, Cruz A, Cao H, Habermann B, Hiller M, Tanaka EM, Myers EW. Author Correction: The axolotl genome and the evolution of key tissue formation regulators. Nature 2018; 559:E2. [PMID: 29795340 DOI: 10.1038/s41586-018-0141-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the originally published version of this Article, the sequenced axolotl strain (the homozygous white mutant) was denoted as 'D/D' rather than 'd/d' in Fig. 1a and the accompanying legend, the main text and the Methods section. The original Article has been corrected online.
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Affiliation(s)
- Sergej Nowoshilow
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.,DFG Research Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany.,Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, 1030, Vienna, Austria
| | | | - Ji-Feng Fei
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China
| | - Andreas Dahl
- DFG Research Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany.,Deep Sequencing Group, Biotechnology Center (Biotec) Technische Universität Dresden, Dresden, Germany
| | | | - Martin Pippel
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | | | - Juliana G Roscito
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology, Dresden, Germany
| | - Francisco Falcon
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Langebio-Cinvestav, Irapuato, Mexico
| | - Dunja Knapp
- DFG Research Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany
| | - Sean Powell
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Alfredo Cruz
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Langebio-Cinvestav, Irapuato, Mexico
| | - Han Cao
- Bionano Genomics, San Diego, California, USA
| | - Bianca Habermann
- IBDM-Institut de Biologie du Développement de Marseille, CNRS & Aix-Marseille Université, Marseille, France
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology, Dresden, Germany
| | - Elly M Tanaka
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany. .,Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria. .,DFG Research Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany. .,Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, 1030, Vienna, Austria.
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology, Dresden, Germany
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Cervantes-Pérez SA, Espinal-Centeno A, Oropeza-Aburto A, Caballero-Pérez J, Falcon F, Aragón-Raygoza A, Sánchez-Segura L, Herrera-Estrella L, Cruz-Hernández A, Cruz-Ramírez A. Transcriptional profiling of the CAM plant Agave salmiana reveals conservation of a genetic program for regeneration. Dev Biol 2018; 442:28-39. [PMID: 29705332 DOI: 10.1016/j.ydbio.2018.04.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 12/21/2017] [Revised: 03/06/2018] [Accepted: 04/24/2018] [Indexed: 10/17/2022]
Abstract
In plants, the best characterized plant regeneration process is de novo organogenesis. This type of regeneration is characterized by the formation of a multicellular structure called callus. Calli are induced via phytohormone treatment of plant sections. The callus formation in plants like Agave species with Crassulacean Acid Metabolism (CAM) is poorly studied. In this study, we induced callus formation from Agave salmiana leaves and describe cell arrangement in this tissue. Moreover, we determined and analyzed the transcriptional program of calli, as well as those of differentiated root and leaf tissues, by using RNA-seq. We were able to reconstruct 170,844 transcripts of which 40,644 have a full Open Reading Frame (ORF). The global profile obtained by Next Generation Sequencing (NGS) reveals that several callus-enriched protein coding transcripts are orthologs of previously reported factors highly expressed in Arabidopsis calli. At least 62 genes were differentially expressed in Agave calli, 50 of which were up-regulated. Several of these are actively involved in the perception of, and response to, auxin and cytokinin. Not only are these the first results for the A. salmiana callus, but they provide novel data from roots and leaves of this Agave species, one of the largest non-tree plants in nature.
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Affiliation(s)
| | - Annie Espinal-Centeno
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada-LANGEBIO, CINVESTAV-Irapuato, Gto, Mexico.
| | - Araceli Oropeza-Aburto
- Metabolic Engineering Group, Unidad de Genómica Avanzada-LANGEBIO, CINVESTAV-Irapuato, Gto, Mexico.
| | - Juan Caballero-Pérez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada-LANGEBIO, CINVESTAV-Irapuato, Gto, Mexico.
| | - Francisco Falcon
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada-LANGEBIO, CINVESTAV-Irapuato, Gto, Mexico.
| | - Alejandro Aragón-Raygoza
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada-LANGEBIO, CINVESTAV-Irapuato, Gto, Mexico.
| | - Lino Sánchez-Segura
- Departamento de Ingeniería Genética, Unidad Irapuato, CINVESTAV-Irapuato, Gto, Mexico.
| | - Luis Herrera-Estrella
- Metabolic Engineering Group, Unidad de Genómica Avanzada-LANGEBIO, CINVESTAV-Irapuato, Gto, Mexico.
| | | | - Alfredo Cruz-Ramírez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada-LANGEBIO, CINVESTAV-Irapuato, Gto, Mexico; Escuela de Agronomía, Universidad de La Salle Bajío, León, Gto, Mexico.
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Caballero-Pérez J, Espinal-Centeno A, Falcon F, García-Ortega LF, Curiel-Quesada E, Cruz-Hernández A, Bako L, Chen X, Martínez O, Alberto Arteaga-Vázquez M, Herrera-Estrella L, Cruz-Ramírez A. Transcriptional landscapes of Axolotl (Ambystoma mexicanum). Dev Biol 2018; 433:227-239. [DOI: 10.1016/j.ydbio.2017.08.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/12/2017] [Accepted: 08/17/2017] [Indexed: 12/22/2022]
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