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Olivares-Costa M, Oyarzún GM, Verbel-Vergara D, González MP, Arancibia D, Andrés ME, Opazo JC. Evolution of lysine-specific demethylase 1 and REST corepressor gene families and their molecular interaction. Commun Biol 2023; 6:1267. [PMID: 38097664 PMCID: PMC10721905 DOI: 10.1038/s42003-023-05652-x] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Lysine-specific demethylase 1A (LSD1) binds to the REST corepressor (RCOR) protein family of corepressors to erase transcriptionally active marks on histones. Functional diversity in these complexes depends on the type of RCOR included, which modulates the catalytic activity of the complex. Here, we studied the duplicative history of the RCOR and LSD gene families and analyzed the evolution of their interaction. We found that RCOR genes are the product of the two rounds of whole-genome duplications that occurred early in vertebrate evolution. In contrast, the origin of the LSD genes traces back before to the divergence of animals and plants. Using bioinformatics tools, we show that the RCOR and LSD1 interaction precedes the RCOR repertoire expansion that occurred in the last common ancestor of jawed vertebrates. Overall, we trace LSD1-RCOR complex evolution and propose that animal non-model species offer advantages in addressing questions about the molecular biology of this epigenetic complex.
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Affiliation(s)
- Montserrat Olivares-Costa
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Ciencias Biomédica, Facultad de Medicina, Universidad Católica del Norte, Coquimbo, Chile
| | - Gianluca Merello Oyarzún
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA
| | - Daniel Verbel-Vergara
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcela P González
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Duxan Arancibia
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta, Chile
| | - María E Andrés
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Juan C Opazo
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile.
- Integrative Biology Group, Valdivia, Chile.
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile.
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2
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Martínez D, Nualart D, Loncoman C, Opazo JC, Zabala K, Morera FJ, Mardones GA, Vargas-Chacoff L. Discovery of BbX transcription factor in the patagonian blennie: Exploring expression changes following combined bacterial and thermal stress exposure. Dev Comp Immunol 2023; 149:105056. [PMID: 37730191 DOI: 10.1016/j.dci.2023.105056] [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] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 09/10/2023] [Accepted: 09/10/2023] [Indexed: 09/22/2023]
Abstract
High-Mobility Group (HMG) proteins are involved in different processes such as transcription, replication, DNA repair, and immune response. The role of HMG proteins in the immune response of fish has been studied mainly for HMGB1, where its expression can be induced by the stimulation of viral/bacterial PAMPs and can act as a proinflammatory mediator and as a global regulator of transcription in response to temperature. However, for BbX this role remains to be discovered. In this work, we identified the BbX of E. maclovinus and evaluated the temporal expression levels after simultaneous challenge with P. salmonis and thermal stress. Phylogenetic analysis does not significantly deviate from the expected organismal relationships suggesting orthologous relationships and that BbX was present in the common ancestor of the group. BbX mRNA expression levels were very high in the intestinal tissue of E. maclovinus (foregut, midgut, and hindgut). Nevertheless, the protein levels analyzed by WB showed the highest levels of BbX protein in the liver (constitutive expression). On the other hand, the mRNA expression levels of BbX in the liver of E. maclovinus injected with P. salmonis and subjected to thermal stress showed an increase at days 16 and 20 in all treatments applied at 12 °C and 18 °C. Meanwhile, the protein levels quantified by WB showed a statistically significant increase in the HMG-Bbx at all experimental times (4, 8, 12, 16, and 20 dpi). However, at 4 dpi the HMG-Bbx protein levels were much higher than the other days evaluated. The results suggest that BbX protein may be implicated in the response mechanism to temperature and bacterial stimulation in the foregut, midgut, hindgut, and liver, according to our findings at the level of mRNA and protein. Furthermore, our WB analysis suggests an effect of P. salmonis on the expression of this protein that can be observed in condition C+ 12 °C compared to C- 12 °C. Then, there is an effect of temperature that can be evidenced in the condition AM 18 °C and SM 18 °C, compared to AB 18 °C and SB 18 °C at 4, 8, and 12 dpi. We found not differences in the levels of this protein if the thermal stress is achieved through acclimatization or shock. More research is necessary to clarify the importance of this type of HMG in the immune response and thermal tolerance in fish.
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Affiliation(s)
- Danixa Martínez
- Laboratorio Institucional de Investigación, Facultad de Ciencias de La Naturaleza, Universidad San Sebastián, Puerto Montt, Chile.
| | - Daniela Nualart
- Escuela de Graduados, Programa de Doctorado en Ciencias de La Acuicultura, Universidad Austral de Chile, Puerto Montt, Chile; Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems, BASE, University Austral of Chile, Valdivia, Chile; Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - Carlos Loncoman
- Instituto de Bioquímica y Microbiología, Laboratorio de Bioquímica Farmacológica, Virología y Biotecnología, Universidad Austral de Chile, Valdivia, Chile
| | - Juan C Opazo
- Integrative Biology Group, Valdivia, Chile; Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile; Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile
| | - Kattina Zabala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile
| | - Francisco J Morera
- Integrative Biology Group, Valdivia, Chile; Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gonzalo A Mardones
- Integrative Biology Group, Valdivia, Chile; Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile
| | - Luis Vargas-Chacoff
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems, BASE, University Austral of Chile, Valdivia, Chile; Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Casilla 567, Valdivia, Chile; Integrative Biology Group, Valdivia, Chile.
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3
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Storz JF, Liphardt S, Quiroga-Carmona M, Bautista NM, Opazo JC, Wheeler TB, D'Elía G, Good JM. Genomic insights into the mystery of mouse mummies on the summits of Atacama volcanoes. Curr Biol 2023; 33:R1040-R1042. [PMID: 37875074 PMCID: PMC10652914 DOI: 10.1016/j.cub.2023.08.081] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 10/26/2023]
Abstract
Our understanding of the limits of animal life is continually revised by scientific exploration of extreme environments. Here we report the discovery of mummified cadavers of leaf-eared mice, Phyllotis vaccarum, from the summits of three different Andean volcanoes at elevations 6,029-6,233 m above sea level in the Puna de Atacama in Chile and Argentina. Such extreme elevations were previously assumed to be completely uninhabitable by mammals. In combination with a live-captured specimen of the same species from the nearby summit of Volcán Llullaillaco (6,739 m)1, the summit mummies represent the highest altitude physical records of mammals in the world. We also report a chromosome-level genome assembly for P. vaccarum that, in combination with a whole-genome re-sequencing analysis and radiocarbon dating analysis, provides insights into the provenance and antiquity of the summit mice. Radiocarbon data indicate that the most ancient of the mummies are, at most, a few centuries old. Genomic polymorphism data revealed a high degree of continuity between the summit mice and conspecifics from lower elevations in the surrounding Altiplano. Genomic data also revealed equal numbers of males and females among the summit mice and evidence of close kinship between some individuals from the same summits. These findings bolster evidence for resident populations of Phyllotis at elevations >6,000 m and challenge assumptions about the environmental limits of vertebrate life and the physiological tolerances of small mammals.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA.
| | - Schuyler Liphardt
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Marcial Quiroga-Carmona
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA; Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile
| | - Naim M Bautista
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile; Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Valdivia, Chile; Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, 5090000, Chile
| | - Timothy B Wheeler
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Guillermo D'Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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4
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Storz JF, Quiroga-Carmona M, Liphardt S, Bautista NM, Opazo JC, Rico Cernohorska A, Salazar-Bravo J, Good JM, D'Elía G. Extreme high-elevation mammal surveys reveal unexpectedly high upper range limits of Andean mice. bioRxiv 2023:2023.08.22.554215. [PMID: 37662254 PMCID: PMC10473662 DOI: 10.1101/2023.08.22.554215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
In the world's highest mountain ranges, uncertainty about the upper elevational range limits of alpine animals represents a critical knowledge gap regarding the environmental limits of life and presents a problem for detecting range shifts in response to climate change. Here we report results of mountaineering mammal surveys in the Central Andes, which led to the discovery of multiple species of mice living at extreme elevations that far surpass previously assumed range limits for mammals. We live-trapped small mammals from ecologically diverse sites spanning >6700 m of vertical relief, from the desert coast of northern Chile to the summits of the highest volcanoes in the Andes. We used molecular sequence data and whole-genome sequence data to confirm the identities of species that represent new elevational records and to test hypotheses regarding species limits. These discoveries contribute to a new appreciation of the environmental limits of vertebrate life.
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5
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Opazo JC, Vandewege MW, Hoffmann FG, Zavala K, Meléndez C, Luchsinger C, Cavieres VA, Vargas-Chacoff L, Morera FJ, Burgos PV, Tapia-Rojas C, Mardones GA. How Many Sirtuin Genes Are Out There? Evolution of Sirtuin Genes in Vertebrates With a Description of a New Family Member. Mol Biol Evol 2023; 40:6993039. [PMID: 36656997 PMCID: PMC9897032 DOI: 10.1093/molbev/msad014] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/21/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
Studying the evolutionary history of gene families is a challenging and exciting task with a wide range of implications. In addition to exploring fundamental questions about the origin and evolution of genes, disentangling their evolution is also critical to those who do functional/structural studies to allow a deeper and more precise interpretation of their results in an evolutionary context. The sirtuin gene family is a group of genes that are involved in a variety of biological functions mostly related to aging. Their duplicative history is an open question, as well as the definition of the repertoire of sirtuin genes among vertebrates. Our results show a well-resolved phylogeny that represents an improvement in our understanding of the duplicative history of the sirtuin gene family. We identified a new sirtuin gene family member (SIRT3.2) that was apparently lost in the last common ancestor of amniotes but retained in all other groups of jawed vertebrates. According to our experimental analyses, elephant shark SIRT3.2 protein is located in mitochondria, the overexpression of which leads to an increase in cellular levels of ATP. Moreover, in vitro analysis demonstrated that it has deacetylase activity being modulated in a similar way to mammalian SIRT3. Our results indicate that there are at least eight sirtuin paralogs among vertebrates and that all of them can be traced back to the last common ancestor of the group that existed between 676 and 615 millions of years ago.
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Affiliation(s)
| | - Michael W Vandewege
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Catalina Meléndez
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Charlotte Luchsinger
- Department of Physiology, School of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Viviana A Cavieres
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Luis Vargas-Chacoff
- Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile,Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile,Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile,Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems, BASE, Universidad Austral de Chile, Valdivia, Chile
| | - Francisco J Morera
- Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile,Applied Biochemistry Laboratory, Facultad de Ciencias Veterinarias, Instituto de Farmacología y Morfofisiología, Universidad Austral de Chile, Valdivia, Chile
| | - Patricia V Burgos
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile,Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile,Centro de Envejecimiento y Regeneración (CARE-UC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica, Santiago, Chile
| | - Cheril Tapia-Rojas
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile,Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
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6
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Cabezas-Bratesco D, Mcgee FA, Colenso CK, Zavala K, Granata D, Carnevale V, Opazo JC, Brauchi SE. Sequence and structural conservation reveal fingerprint residues in TRP channels. eLife 2022; 11:73645. [PMID: 35686986 PMCID: PMC9242649 DOI: 10.7554/elife.73645] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Transient receptor potential (TRP) proteins are a large family of cation-selective channels, surpassed in variety only by voltage-gated potassium channels. Detailed molecular mechanisms governing how membrane voltage, ligand binding, or temperature can induce conformational changes promoting the open state in TRP channels are still a matter of debate. Aiming to unveil distinctive structural features common to the transmembrane domains within the TRP family, we performed phylogenetic reconstruction, sequence statistics, and structural analysis over a large set of TRP channel genes. Here, we report an exceptionally conserved set of residues. This fingerprint is composed of twelve residues localized at equivalent three-dimensional positions in TRP channels from the different subtypes. Moreover, these amino acids are arranged in three groups, connected by a set of aromatics located at the core of the transmembrane structure. We hypothesize that differences in the connectivity between these different groups of residues harbor the apparent differences in coupling strategies used by TRP subgroups.
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Affiliation(s)
| | - Francisco A Mcgee
- Department of Biology, Temple University, Philadelphia, United States
| | - Charlotte K Colenso
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Daniele Granata
- Department of Biology, Temple University, Philadelphia, United States
| | | | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
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7
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Opazo JC, Hoffmann FG, Zavala K, Edwards SV. Evolution of the DAN gene family in vertebrates. Dev Biol 2021; 482:34-43. [PMID: 34902310 DOI: 10.1016/j.ydbio.2021.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 06/25/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022]
Abstract
The DAN gene family (DAN, Differential screening-selected gene Aberrant in Neuroblastoma) is a group of genes that is expressed during development and plays fundamental roles in limb bud formation and digitation, kidney formation and morphogenesis and left-right axis specification. During adulthood the expression of these genes are associated with diseases, including cancer. Although most of the attention to this group of genes has been dedicated to understanding its role in physiology and development, its evolutionary history remains poorly understood. Thus, the goal of this study is to investigate the evolutionary history of the DAN gene family in vertebrates, with the objective of complementing the already abundant physiological information with an evolutionary context. Our results recovered the monophyly of all DAN gene family members and divide them into five main groups. In addition to the well-known DAN genes, our phylogenetic results revealed the presence of two new DAN gene lineages; one is only retained in cephalochordates, whereas the other one (GREM3) was only identified in cartilaginous fish, holostean fish, and coelacanth. According to the phyletic distribution of the genes, the ancestor of gnathostomes possessed a repertoire of eight DAN genes, and during the radiation of the group GREM1, GREM2, SOST, SOSTDC1, and NBL1 were retained in all major groups, whereas, GREM3, CER1, and DAND5 were differentially lost.
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Affiliation(s)
- Juan C Opazo
- Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile; Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; David Rockefeller Center for Latin American Studies, Harvard University, Cambridge, MA, 02138, USA; Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Chile.
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, 39762, USA; Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, 39762, USA
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
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8
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Gutierrez J, Platt R, Opazo JC, Ray DA, Hoffmann F, Vandewege M. Evolutionary history of the vertebrate Piwi gene family. PeerJ 2021; 9:e12451. [PMID: 34760405 PMCID: PMC8574217 DOI: 10.7717/peerj.12451] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/18/2021] [Indexed: 11/28/2022] Open
Abstract
PIWIs are regulatory proteins that belong to the Argonaute family. Piwis are primarily expressed in gonads and protect the germline against the mobilization and propagation of transposable elements (TEs) through transcriptional gene silencing. Vertebrate genomes encode up to four Piwi genes: Piwil1, Piwil2, Piwil3 and Piwil4, but their duplication history is unresolved. We leveraged phylogenetics, synteny and expression analyses to address this void. Our phylogenetic analysis suggests Piwil1 and Piwil2 were retained in all vertebrate members. Piwil4 was the result of Piwil1 duplication in the ancestor of gnathostomes, but was independently lost in ray-finned fishes and birds. Further, Piwil3 was derived from a tandem Piwil1 duplication in the common ancestor of marsupial and placental mammals, but was secondarily lost in Atlantogenata (Xenarthra and Afrotheria) and some rodents. The evolutionary rate of Piwil3 is considerably faster than any Piwi among all lineages, but an explanation is lacking. Our expression analyses suggest Piwi expression has mostly been constrained to gonads throughout vertebrate evolution. Vertebrate evolution is marked by two early rounds of whole genome duplication and many multigene families are linked to these events. However, our analyses suggest Piwi expansion was independent of whole genome duplications.
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Affiliation(s)
- Javier Gutierrez
- Department of Biology, Eastern New Mexico University, Portales, NM, United States of America
| | - Roy Platt
- Host Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile.,Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States of America
| | - Federico Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, United States of America.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, United States of America
| | - Michael Vandewege
- Department of Biology, Eastern New Mexico University, Portales, NM, United States of America
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9
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Hoffmann FG, Storz JF, Kuraku S, Vandewege MW, Opazo JC. Whole-Genome Duplications and the Diversification of the Globin-X Genes of Vertebrates. Genome Biol Evol 2021; 13:evab205. [PMID: 34480557 PMCID: PMC8525914 DOI: 10.1093/gbe/evab205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 12/28/2022] Open
Abstract
Globin-X (GbX) is an enigmatic member of the vertebrate globin gene family with a wide phyletic distribution that spans protostomes and deuterostomes. Unlike canonical globins such as hemoglobins and myoglobins, functional data suggest that GbX does not have a primary respiratory function. Instead, evidence suggests that the monomeric, membrane-bound GbX may play a role in cellular signaling or protection against the oxidation of membrane lipids. Recently released genomes from key vertebrates provide an excellent opportunity to address questions about the early stages of the evolution of GbX in vertebrates. We integrate bioinformatics, synteny, and phylogenetic analyses to characterize the diversity of GbX genes in nonteleost ray-finned fishes, resolve relationships between the GbX genes of cartilaginous fish and bony vertebrates, and demonstrate that the GbX genes of cyclostomes and gnathostomes derive from independent duplications. Our study highlights the role that whole-genome duplications (WGDs) have played in expanding the repertoire of genes in vertebrate genomes. Our results indicate that GbX paralogs have a remarkably high rate of retention following WGDs relative to other globin genes and provide an evolutionary framework for interpreting results of experiments that examine functional properties of GbX and patterns of tissue-specific expression. By identifying GbX paralogs that are products of different WGDs, our results can guide the design of experimental work to explore whether gene duplicates that originate via WGDs have evolved novel functional properties or expression profiles relative to singleton or tandemly duplicated copies of GbX.
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Affiliation(s)
- Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, USA
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, USA
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Shigehiro Kuraku
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | | | - Juan C Opazo
- Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile
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10
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Tejada-Martinez D, de Magalhães JP, Opazo JC. Positive selection and gene duplications in tumour suppressor genes reveal clues about how cetaceans resist cancer. Proc Biol Sci 2021; 288:20202592. [PMID: 33622125 DOI: 10.1098/rspb.2020.2592] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cetaceans are the longest-living species of mammals and the largest in the history of the planet. They have developed mechanisms against diseases such cancer, although the underlying molecular bases of these remain unknown. The goal of this study was to investigate the role of natural selection in the evolution of 1077 tumour suppressor genes (TSGs) in cetaceans. We used a comparative genomic approach to analyse two sources of molecular variation in the form of dN/dS rates and gene copy number variation. We found a signal of positive selection in the ancestor of cetaceans within the CXCR2 gene, an important regulator of DNA damage, tumour dissemination and immune system. Further, in the ancestor of baleen whales, we found six genes exhibiting positive selection relating to diseases such as breast carcinoma, lung neoplasm (ADAMTS8) and leukaemia (ANXA1). The TSGs turnover rate (gene gain and loss) was almost 2.4-fold higher in cetaceans when compared with other mammals, and notably even faster in baleen whales. The molecular variants in TSGs found in baleen whales, combined with the faster gene turnover rate, could have favoured the evolution of their particular traits of anti-cancer resistance, gigantism and longevity. Additionally, we report 71 genes with duplications, of which 11 genes are linked to longevity (e.g. NOTCH3 and SIK1) and are important regulators of senescence, cell proliferation and metabolism. Overall, these results provide evolutionary evidence that natural selection in TSGs could act on species with large body sizes and extended lifespan, providing novel insights into the genetic basis of disease resistance.
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Affiliation(s)
- Daniela Tejada-Martinez
- Programa de Doctorado en Ciencias mención Ecología y Evolución, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK.,Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Valdivia, Chile.,Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile
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11
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Prothmann A, Hoffmann FG, Opazo JC, Herbener P, Storz JF, Burmester T, Hankeln T. The Globin Gene Family in Arthropods: Evolution and Functional Diversity. Front Genet 2020; 11:858. [PMID: 32922435 PMCID: PMC7457136 DOI: 10.3389/fgene.2020.00858] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/14/2020] [Indexed: 01/23/2023] Open
Abstract
Globins are small heme-proteins that reversibly bind oxygen. Their most prominent roles in vertebrates are the transport and storage of O2 for oxidative energy metabolism, but recent research has suggested alternative, non-respiratory globin functions. In the species-rich and ecologically highly diverse taxon of arthropods, the copper-containing hemocyanin is considered the main respiratory protein. However, recent studies have suggested the presence of globin genes and their proteins in arthropod taxa, including model species like Drosophila. To systematically assess the taxonomic distribution, evolution and diversity of globins in arthropods, we systematically searched transcriptome and genome sequence data and found a conserved, widespread occurrence of three globin classes in arthropods: hemoglobin-like (HbL), globin X (GbX), and globin X-like (GbXL) protein lineages. These globin types were previously identified in protostome and deuterostome animals including vertebrates, suggesting their early ancestry in Metazoa. The HbL genes show multiple, lineage-specific gene duplications in all major arthropod clades. Some HbL genes (e.g., Glob2 and 3 of Drosophila) display particularly fast substitution rates, possibly indicating the evolution of novel functions, e.g., in spermatogenesis. In contrast, arthropod GbX and GbXL globin genes show high evolutionary stability: GbXL is represented by a single-copy gene in all arthropod groups except Brachycera, and representatives of the GbX clade are present in all examined taxa except holometabolan insects. GbX and GbXL both show a brain-specific expression. Most arthropod GbX and GbXL proteins, but also some HbL variants, include sequence motifs indicative of potential N-terminal acylation (i.e., N-myristoylation, 3C-palmitoylation). All arthropods except for the brachyceran Diptera harbor at least one such potentially acylated globin copy, confirming the hypothesis of an essential, conserved globin function associated with the cell membrane. In contrast to other animals, the fourth ancient globin lineage, represented by neuroglobin, appears to be absent in arthropods, and the putative arthropod orthologs of the fifth metazoan globin lineage, androglobin, lack a recognizable globin domain. Thus, the remarkable evolutionary stability of some globin variants is contrasted by occasional dynamic gene multiplication or even loss of otherwise strongly conserved globin lineages in arthropod phylogeny.
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Affiliation(s)
- Andreas Prothmann
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, University of Mainz, Mainz, Germany
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi, MS, United States.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS, United States
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Valdivia, Chile
| | - Peter Herbener
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, University of Mainz, Mainz, Germany
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
| | | | - Thomas Hankeln
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, University of Mainz, Mainz, Germany
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12
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Abstract
Environmental limits of animal life are invariably revised when the animals themselves are investigated in their natural habitats. Here we report results of a scientific mountaineering expedition to survey the high-altitude rodent fauna of Volcán Llullaillaco in the Puna de Atacama of northern Chile, an effort motivated by video documentation of mice (genus Phyllotis) at a record altitude of 6,205 m. Among numerous trapping records at altitudes of >5,000 m, we captured a specimen of the yellow-rumped leaf-eared mouse (Phyllotis xanthopygus rupestris) on the very summit of Llullaillaco at 6,739 m. This summit specimen represents an altitudinal world record for mammals, far surpassing all specimen-based records from the Himalayas and other mountain ranges. This discovery suggests that we may have generally underestimated the altitudinal range limits and physiological tolerances of small mammals simply because the world's high summits remain relatively unexplored by biologists.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588;
| | - Marcial Quiroga-Carmona
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile, 5090000
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile, 5090000
- Millennium Nucleus of Ion Channels-Associated Diseases, Santiago, Chile, 8380453
| | - Thomas Bowen
- Department of Anthropology, California State University, Fresno, CA 93740
| | | | - Scott J Steppan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Guillermo D'Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile, 5090000;
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13
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Teta P, D’Elía G, Opazo JC. Integrative taxonomy of the southernmost tucu-tucus in the world: differentiation of the nominal forms associated with Ctenomys magellanicus Bennett, 1836 (Rodentia, Hystricomorpha, Ctenomyidae). Mamm Biol 2020. [DOI: 10.1007/s42991-020-00015-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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14
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Opazo JC, Kuraku S, Zavala K, Toloza-Villalobos J, Hoffmann FG. Evolution of nodal and nodal-related genes and the putative composition of the heterodimers that trigger the nodal pathway in vertebrates. Evol Dev 2019; 21:205-217. [PMID: 31210006 DOI: 10.1111/ede.12292] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 11/30/2018] [Revised: 04/03/2019] [Accepted: 05/13/2019] [Indexed: 02/06/2023]
Abstract
Nodal is a signaling molecule that belongs to the transforming growth factor-β superfamily that plays key roles during the early stages of development of animals. In vertebrates Nodal forms an heterodimer with a GDF1/3 protein to activate the Nodal pathway. Vertebrates have a paralog of nodal in their genomes labeled Nodal-related, but the evolutionary history of these genes is a matter of debate, mainly because of the presence of a variable numbers of genes in the vertebrate genomes sequenced so far. Thus, the goal of this study was to investigate the evolutionary history of the Nodal and Nodal-related genes with an emphasis in tracking changes in the number of genes among vertebrates. Our results show the presence of two gene lineages (Nodal and Nodal-related) that can be traced back to the ancestor of jawed vertebrates. These lineages have undergone processes of differential retention and lineage-specific expansions. Our results imply that Nodal and Nodal-related duplicated at the latest in the ancestor of gnathostomes, and they still retain a significant level of functional redundancy. By comparing the evolution of the Nodal/Nodal-related with GDF1/3 gene family, it is possible to infer that there are several types of heterodimers that can trigger the Nodal pathway among vertebrates.
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Affiliation(s)
- Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Jessica Toloza-Villalobos
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, Mississippi.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, Mississippi
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15
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D'elía G, Jaksic F, Bacigalupe LD, Bozinovic F, Canto JL, Correa C, Fontúrbel FE, Lisón F, Méndez MA, Nespolo R, Opazo JC, Palma RE, Rau JR, Rodríguez SM, Rodríguez-Serrano E, Sabat P, Vásquez RA, Victoriano P. Sugerencias para mejorar la regulación chilena de manipulación de vertebrados terrestres en poblaciones naturales en el contexto de investigaciones científicas. Gayana (Concepc ) 2019. [DOI: 10.4067/s0717-65382019000100063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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16
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Stanic K, Reig G, Figueroa RJ, Retamal PA, Wichmann IA, Opazo JC, Owen GI, Corvalán AH, Concha ML, Amigo JD. The Reprimo gene family member, reprimo-like (rprml), is required for blood development in embryonic zebrafish. Sci Rep 2019; 9:7131. [PMID: 31073223 PMCID: PMC6509255 DOI: 10.1038/s41598-019-43436-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/24/2019] [Indexed: 11/09/2022] Open
Abstract
The Reprimo gene family comprises a group of single-exon genes for which their physiological function remains poorly understood. Heretofore, mammalian Reprimo (RPRM) has been described as a putative p53-dependent tumor suppressor gene that functions at the G2/M cell cycle checkpoint. Another family member, Reprimo-like (RPRML), has not yet an established role in physiology or pathology. Importantly, RPRML expression pattern is conserved between zebrafish and human species. Here, using CRISPR-Cas9 and antisense morpholino oligonucleotides, we disrupt the expression of rprml in zebrafish and demonstrate that its loss leads to impaired definitive hematopoiesis. The formation of hemangioblasts and the primitive wave of hematopoiesis occur normally in absence of rprml. Later in development there is a significant reduction in erythroid-myeloid precursors (EMP) at the posterior blood island (PBI) and a significant decline of definitive hematopoietic stem/progenitor cells (HSPCs). Furthermore, loss of rprml also increases the activity of caspase-3 in endothelial cells within the caudal hematopoietic tissue (CHT), the first perivascular niche where HSPCs reside during zebrafish embryonic development. Herein, we report an essential role for rprml during hematovascular development in zebrafish embryos, specifically during the definitive waves of hematopoiesis, indicating for the first time a physiological role for the rprml gene.
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Affiliation(s)
- Karen Stanic
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - German Reig
- Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Universidad Bernardo O´Higgins, Escuela de Tecnología Médica and Centro Integrativo de Biología y Química Aplicada (CIBQA), Santiago, Chile
| | - Ricardo J Figueroa
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pedro A Retamal
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ignacio A Wichmann
- Advanced Center for Chronic Diseases (ACCDiS), Santiago, Chile.,Laboratorio de Oncología, Departamento de Hematología y Oncología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Gareth I Owen
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,Advanced Center for Chronic Diseases (ACCDiS), Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Alejandro H Corvalán
- Advanced Center for Chronic Diseases (ACCDiS), Santiago, Chile.,Laboratorio de Oncología, Departamento de Hematología y Oncología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Miguel L Concha
- Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Biomedical Neuroscience Institute, Santiago, Chile, Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
| | - Julio D Amigo
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
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17
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Hoffmann FG, Vandewege MW, Storz JF, Opazo JC. Gene Turnover and Diversification of the α- and β-Globin Gene Families in Sauropsid Vertebrates. Genome Biol Evol 2018; 10:344-358. [PMID: 29340581 PMCID: PMC5786229 DOI: 10.1093/gbe/evy001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2018] [Indexed: 11/24/2022] Open
Abstract
The genes that encode the α- and β-chain subunits of vertebrate hemoglobin have served as a model system for elucidating general principles of gene family evolution, but little is known about patterns of evolution in amniotes other than mammals and birds. Here, we report a comparative genomic analysis of the α- and β-globin gene clusters in sauropsids (archosaurs and nonavian reptiles). The objectives were to characterize changes in the size and membership composition of the α- and β-globin gene families within and among the major sauropsid lineages, to reconstruct the evolutionary history of the sauropsid α- and β-globin genes, to resolve orthologous relationships, and to reconstruct evolutionary changes in the developmental regulation of gene expression. Our comparisons revealed contrasting patterns of evolution in the unlinked α- and β-globin gene clusters. In the α-globin gene cluster, which has remained in the ancestral chromosomal location, evolutionary changes in gene content are attributable to the differential retention of paralogous gene copies that were present in the common ancestor of tetrapods. In the β-globin gene cluster, which was translocated to a new chromosomal location, evolutionary changes in gene content are attributable to differential gene gains (via lineage-specific duplication events) and gene losses (via lineage-specific deletions and inactivations). Consequently, all major groups of amniotes possess unique repertoires of embryonic and postnatally expressed β-type globin genes that diversified independently in each lineage. These independently derived β-type globins descend from a pair of tandemly linked paralogs in the most recent common ancestor of sauropsids.
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Affiliation(s)
- Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University
| | | | - Jay F Storz
- School of Biological Sciences, University of Nebraska
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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18
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Abstract
Growth differentiation factors 1 (GDF1) and 3 (GDF3) are members of the transforming growth factor superfamily (TGF-β) that is involved in fundamental early-developmental processes that are conserved across vertebrates. The evolutionary history of these genes is still under debate due to ambiguous definitions of homologous relationships among vertebrates. Thus, the goal of this study was to unravel the evolution of the GDF1 and GDF3 genes of vertebrates, emphasizing the understanding of homologous relationships and their evolutionary origin. Our results revealed that the GDF1 and GDF3 genes found in anurans and mammals are the products of independent duplication events of an ancestral gene in the ancestor of each of these lineages. The main implication of this result is that the GDF1 and GDF3 genes of anurans and mammals are not 1:1 orthologs. In other words, genes that participate in fundamental processes during early development have been reinvented two independent times during the evolutionary history of tetrapods.
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Affiliation(s)
- Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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19
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Giorello FM, Feijoo M, D'Elía G, Naya DE, Valdez L, Opazo JC, Lessa EP. An association between differential expression and genetic divergence in the Patagonian olive mouse (Abrothrix olivacea). Mol Ecol 2018; 27:3274-3286. [PMID: 29940092 DOI: 10.1111/mec.14778] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 06/13/2017] [Revised: 05/30/2018] [Accepted: 05/31/2018] [Indexed: 12/19/2022]
Abstract
Recent molecular studies have found striking differences between desert-adapted species and model mammals regarding water conservation. In particular, aquaporin 4, a classical gene involved in water regulation of model species, is absent or not expressed in the kidneys of desert-adapted species. To further understand the molecular response to water availability, we studied the Patagonian olive mouse Abrothrix olivacea, a species with an unusually broad ecological tolerance that exhibits a great urine concentration capability. The species is able to occupy both the arid Patagonian steppe and the Valdivian and Magellanic forests. We sampled 95 olive mouse specimens from four localities (two in the steppe and two in the forests) and analysed both phenotypic variables and transcriptomic data to investigate the response of this species to the contrasting environmental conditions. The relative size of the kidney and the ratio of urine to plasma concentrations were, as expected, negatively correlated with annual rainfall. Expression analyses uncovered nearly 3,000 genes that were differentially expressed between steppe and forest samples and indicated that this species resorts to the "classical" gene pathways for water regulation. Differential expression across biomes also involves genes that involved in immune and detoxification functions. Overall, genes that were differentially expressed showed a slight tendency to be more divergent and to display an excess of intermediate allele frequencies, relative to the remaining loci. Our results indicate that both differential expression in pathways involved in water conservation and geographical allelic variation are important in the occupation of contrasting habitats by the Patagonian olive mouse.
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Affiliation(s)
- Facundo M Giorello
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Espacio de Biología Vegetal del Noreste, Centro Universitario de Tacuarembó, Universidad de la República, Tacuarembó, Uruguay
| | - Matias Feijoo
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Guillermo D'Elía
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Daniel E Naya
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Lourdes Valdez
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Enrique P Lessa
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Amigo JD, Opazo JC, Jorquera R, Wichmann IA, Garcia-Bloj BA, Alarcon MA, Owen GI, Corvalán AH. The Reprimo Gene Family: A Novel Gene Lineage in Gastric Cancer with Tumor Suppressive Properties. Int J Mol Sci 2018; 19:E1862. [PMID: 29941787 PMCID: PMC6073456 DOI: 10.3390/ijms19071862] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/20/2018] [Accepted: 04/21/2018] [Indexed: 12/18/2022] Open
Abstract
The reprimo (RPRM) gene family is a group of single exon genes present exclusively within the vertebrate lineage. Two out of three members of this family are present in humans: RPRM and RPRM-Like (RPRML). RPRM induces cell cycle arrest at G2/M in response to p53 expression. Loss-of-expression of RPRM is related to increased cell proliferation and growth in gastric cancer. This evidence suggests that RPRM has tumor suppressive properties. However, the molecular mechanisms and signaling partners by which RPRM exerts its functions remain unknown. Moreover, scarce studies have attempted to characterize RPRML, and its functionality is unclear. Herein, we highlight the role of the RPRM gene family in gastric carcinogenesis, as well as its potential applications in clinical settings. In addition, we summarize the current knowledge on the phylogeny and expression patterns of this family of genes in embryonic zebrafish and adult humans. Strikingly, in both species, RPRM is expressed primarily in the digestive tract, blood vessels and central nervous system, supporting the use of zebrafish for further functional characterization of RPRM. Finally, drawing on embryonic and adult expression patterns, we address the potential relevance of RPRM and RPRML in cancer. Active investigation or analytical research in the coming years should contribute to novel translational applications of this poorly understood gene family as potential biomarkers and development of novel cancer therapies.
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Affiliation(s)
- Julio D Amigo
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8330025 Santiago, Chile.
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, 5090000 Valdivia, Chile.
| | - Roddy Jorquera
- CORE Biodata, Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, 8330024 Santiago, Chile.
| | - Ignacio A Wichmann
- Laboratory of Oncology, Facultad de Medicina, Pontificia Universidad Católica de Chile, 8330034 Santiago, Chile.
- Departamento de Oncología y Hematología, Facultad de Medicina, Pontificia Universidad Católica de Chile, 8330034 Santiago, Chile.
- CORE Biodata, Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, 8330024 Santiago, Chile.
| | - Benjamin A Garcia-Bloj
- Laboratory of Oncology, Facultad de Medicina, Pontificia Universidad Católica de Chile, 8330034 Santiago, Chile.
| | - Maria Alejandra Alarcon
- Laboratory of Oncology, Facultad de Medicina, Pontificia Universidad Católica de Chile, 8330034 Santiago, Chile.
- Departamento de Oncología y Hematología, Facultad de Medicina, Pontificia Universidad Católica de Chile, 8330034 Santiago, Chile.
| | - Gareth I Owen
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8330025 Santiago, Chile.
- Laboratory of Oncology, Facultad de Medicina, Pontificia Universidad Católica de Chile, 8330034 Santiago, Chile.
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile.
| | - Alejandro H Corvalán
- Laboratory of Oncology, Facultad de Medicina, Pontificia Universidad Católica de Chile, 8330034 Santiago, Chile.
- Departamento de Oncología y Hematología, Facultad de Medicina, Pontificia Universidad Católica de Chile, 8330034 Santiago, Chile.
- CORE Biodata, Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, 8330024 Santiago, Chile.
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21
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Opazo JC, Zavala K, Miranda-Rottmann S, Araya R. Evolution of dopamine receptors: phylogenetic evidence suggests a later origin of the DRD 2l and DRD 4rs dopamine receptor gene lineages. PeerJ 2018; 6:e4593. [PMID: 29666757 PMCID: PMC5900934 DOI: 10.7717/peerj.4593] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/17/2018] [Indexed: 01/11/2023] Open
Abstract
Dopamine receptors are integral membrane proteins whose endogenous ligand is dopamine. They play a fundamental role in the central nervous system and dysfunction of dopaminergic neurotransmission is responsible for the generation of a variety of neuropsychiatric disorders. From an evolutionary standpoint, phylogenetic relationships among the DRD1 class of dopamine receptors are still a matter of debate as in the literature different tree topologies have been proposed. In contrast, phylogenetic relationships among the DRD2 group of receptors are well understood. Understanding the time of origin of the different dopamine receptors is also an issue that needs further study, especially for the genes that have restricted phyletic distributions (e.g., DRD2l and DRD4rs). Thus, the goal of this study was to investigate the evolution of dopamine receptors, with emphasis on shedding light on the phylogenetic relationships among the D1 class of dopamine receptors and the time of origin of the DRD2l and DRD4rs gene lineages. Our results recovered the monophyly of the two groups of dopamine receptors. Within the DRD1 group the monophyly of each paralog was recovered with strong support, and phylogenetic relationships among them were well resolved. Within the DRD1 class of dopamine receptors we recovered the sister group relationship between the DRD1C and DRD1E, and this clade was recovered sister to a cyclostome sequence. The DRD1 clade was recovered sister to the aforementioned clade, and the group containing DRD5 receptors was sister to all other DRD1 paralogs. In agreement with the literature, among the DRD2 class of receptors, DRD2 was recovered sister to DRD3, whereas DRD4 was sister to the DRD2/DRD3 clade. According to our phylogenetic tree, the DRD2l and DRD4rs gene lineages would have originated in the ancestor of gnathostomes between 615 and 473 mya. Conservation of sequences required for dopaminergic neurotransmission and small changes in regulatory regions suggest a functional refinement of the dopaminergic pathways along evolution.
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Affiliation(s)
- Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | | | - Roberto Araya
- Department of Neurosciences, Faculty of Medicine, University of Montreal, Montreal, Canada
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22
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Stanic K, Quiroz A, Lemus CG, Wichmann IA, Corvalán AH, Owen GI, Opazo JC, Concha ML, Amigo JD. Expression of RPRM/rprm in the Olfactory System of Embryonic Zebrafish ( Danio rerio). Front Neuroanat 2018; 12:23. [PMID: 29636669 PMCID: PMC5881088 DOI: 10.3389/fnana.2018.00023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/12/2018] [Indexed: 01/22/2023] Open
Abstract
The Reprimo (RPRM) family is composed of highly conserved single-exon genes. The expression pattern of this gene family has been recently described during zebrafish (Danio rerio) embryogenesis, and primarily locates in the nervous system. Its most characterized member, RPRM, which duplicated to give rise rprma and rprmb in the fish lineage, is known to act as a tumor-suppressor gene in mammalian models. Here, we describe in detail the spatiotemporal expression of three rprm genes (rprma, rprmb, and rprml) within distinct anatomical structures in the developing peripheral and central nervous system. In the zebrafish, rprma mRNA is expressed in the olfactory placodes (OP) and olfactory epithelium (OE), rprmb is observed in the tectum opticum (TeO) and trigeminal ganglion (Tg), whereas rprml is found primarily in the telencephalon (Tel). At protein level, RPRM is present in a subset of cells in the OP, and neurons in the OE, TeO, hindbrain and sensory peripheral structures. Most importantly, the expression of RPRM has been conserved between teleosts and mammals. Thus, we provide a reference dataset describing the expression patterns of RPRM gene products during zebrafish and mouse development as a first step to approach the physiological role of the RPRM gene family.
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Affiliation(s)
- Karen Stanic
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alonso Quiroz
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carmen G Lemus
- Anatomy and Developmental Biology Program, Faculty of Medicine, Institute of Biomedical Sciences, Universidad de Chile, Santiago, Chile
| | - Ignacio A Wichmann
- Advanced Center for Chronic Diseases, Santiago, Chile.,UC Center for Investigation in Oncology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandro H Corvalán
- Advanced Center for Chronic Diseases, Santiago, Chile.,UC Center for Investigation in Oncology, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Oncología y Hematología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gareth I Owen
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,Advanced Center for Chronic Diseases, Santiago, Chile.,UC Center for Investigation in Oncology, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Oncología y Hematología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Miguel L Concha
- Anatomy and Developmental Biology Program, Faculty of Medicine, Institute of Biomedical Sciences, Universidad de Chile, Santiago, Chile.,Biomedical Neuroscience Institute, Universidad de Chile, Santiago, Chile
| | - Julio D Amigo
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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23
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Abstract
The relaxin/insulin-like (RLN/INSL) gene family is a group of genes that encode peptide hormones involved in a variety of physiological functions related to reproduction. Previous studies have shown that relaxin plays a key role in widening of the pubic bone during labor and in gamete maturation. Because of these functions, studying the evolution of RLN1, the gene encoding for relaxin, is relevant in livestock species, most of which belong in the group Laurasiatheria, which includes cow, pig, horse, goat, and sheep in addition to bats, cetaceans and carnivores. Experimental evidence suggests that cows do not synthesize relaxin, but respond to it, and sheep apparently have a truncated RLN1 gene. Thus, we made use of genome sequence data to characterize the genomic locus of the RLN1 gene in Laurasiatherian mammals to better understand how cows lost the ability to synthesize this peptide. We found that all ruminants in our study (cow, giraffe, goat, sheep and Tibetan antelope) lack a functional RLN1 gene, and document the progressive loss of RLN1 in the lineage leading to cows. Our analyses indicate that 1 - all ruminants have lost all key regulatory elements upstream of the first exon, 2 - giraffe, goat, sheep and Tibetan antelope have multiple inactivating mutations in the RLN1 pseudogene, and 3 - the cow genome has lost all traces of RLN1. The 5' regulatory sequence plays a key role in activating expression, and the loss of this sequence would impair synthesis of mRNA. Our results suggest that changes in regulatory sequence preceded mutations in coding sequence and highlight the importance of these regions in maintaining proper gene function. In addition, we found that all bovids examined posses copies of the relaxin receptors, which explains why they are able to respond to relaxin despite their inability to produce it.
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Affiliation(s)
- Loggan Malone
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS 39762, USA
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Peter L Ryan
- Department of Animal and Dairy Sciences, Facility for Organismal and Cellular Imaging (FOCI), Mississippi State University, MS 39762, USA; Department of Pathobiology & Population Medicine, Mississippi State University, MS 39762, USA
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS 39762, USA; Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, MS 39762, USA.
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Abstract
Evolutionary studies of genes that have been functionally characterized and whose variation has been associated with pathological conditions represent an opportunity to understand the genetic basis of pathologies. α2-Adrenoreceptors (ADRA2) are a class of G protein-coupled receptors that regulate several physiological processes including blood pressure, platelet aggregation, insulin secretion, lipolysis, and neurotransmitter release. This gene family has been extensively studied from a molecular/physiological perspective, yet much less is known about its evolutionary history. Accordingly, the goal of this study was to investigate the evolutionary history of α2-adrenoreceptors (ADRA2) in vertebrates. Our results show that in addition to the three well-recognized α2-adrenoreceptor genes (ADRA2A, ADRA2B and ADRA2C), we recovered a clade that corresponds to the fourth member of the α2-adrenoreceptor gene family (ADRA2D). We also recovered a clade that possesses two ADRA2 sequences found in two lamprey species. Furthermore, our results show that mammals and crocodiles are characterized by possessing three α2-adrenoreceptor genes, whereas all other vertebrate groups possess the full repertoire of α2-adrenoreceptor genes. Among vertebrates ADRA2D seems to be a dispensable gene, as it was lost two independent times during the evolutionary history of the group. Additionally, we found that most examined species possess the most common alleles described for humans; however, there are cases in which non-human mammals possess the alternative variant. Finally, transcript abundance profiles revealed that during the early evolutionary history of gnathostomes, the expression of ADRA2D in different taxonomic groups became specialized to different tissues, but in the ancestor of sarcopterygians this specialization would have been lost.
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Affiliation(s)
- Héctor A Céspedes
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Michael W Vandewege
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; David Rockefeller Center For Latin American Studies, Harvard University, Cambridge, MA 02138, USA.
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25
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Figueroa RJ, Carrasco-Avino G, Wichmann IA, Lange M, Owen GI, Siekmann AF, Corvalán AH, Opazo JC, Amigo JD. Reprimo tissue-specific expression pattern is conserved between zebrafish and human. PLoS One 2017; 12:e0178274. [PMID: 28562620 PMCID: PMC5451059 DOI: 10.1371/journal.pone.0178274] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/10/2017] [Indexed: 01/28/2023] Open
Abstract
Reprimo (RPRM), a member of the RPRM gene family, is a tumor-suppressor gene involved in the regulation of the p53-mediated cell cycle arrest at G2/M. RPRM has been associated with malignant tumor progression and proposed as a potential biomarker for early cancer detection. However, the expression and role of RPRM, as well as its family, are poorly understood and their physiology is as yet unstudied. In this scenario, a model system like the zebrafish could serve to dissect the role of the RPRM family members in vivo. Phylogenetic analysis reveals that RPRM and RPRML have been differentially retained by most species throughout vertebrate evolution, yet RPRM3 has been retained only in a small group of distantly related species, including zebrafish. Herein, we characterized the spatiotemporal expression of RPRM (present in zebrafish as an infraclass duplication rprma/rprmb), RPRML and RPRM3 in the zebrafish. By whole-mount in situ hybridization (WISH) and fluorescent in situ hybridization (FISH), we demonstrate that rprm (rprma/rprmb) and rprml show a similar spatiotemporal expression profile during zebrafish development. At early developmental stages rprmb is expressed in somites. After one day post-fertilization, rprm (rprma/rprmb) and rprml are expressed in the notochord, brain, blood vessels and digestive tube. On the other hand, rprm3 shows the most unique expression profile, being expressed only in the central nervous system (CNS). We assessed the expression patterns of RPRM gene transcripts in adult zebrafish and human RPRM protein product in tissue samples by RT-qPCR and immunohistochemistry (IHC) staining, respectively. Strikingly, tissue-specific expression patterns of the RPRM transcripts and protein are conserved between zebrafish and humans. We propose the zebrafish as a powerful tool to elucidate the both physiological and pathological roles of the RPRM gene family.
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Affiliation(s)
- Ricardo J. Figueroa
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gonzalo Carrasco-Avino
- Advanced Center for Chronic Diseases (ACCDiS), Santiago, Chile
- Pathology Department, Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Ignacio A. Wichmann
- Advanced Center for Chronic Diseases (ACCDiS), Santiago, Chile
- Departamento de Oncología y Hematología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Martin Lange
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - Gareth I. Owen
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Santiago, Chile
- Departamento de Oncología y Hematología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Center UC for Investigation in Oncology (CITO), Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Alejandro H. Corvalán
- Advanced Center for Chronic Diseases (ACCDiS), Santiago, Chile
- Departamento de Oncología y Hematología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center UC for Investigation in Oncology (CITO), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan C. Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Julio D. Amigo
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- * E-mail:
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26
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Opazo JC, Zavala K, Krall P, Arias RA. Evolution of gremlin 2 in cetartiodactyl mammals: gene loss coincides with lack of upper jaw incisors in ruminants. PeerJ 2017; 5:e2901. [PMID: 28149683 PMCID: PMC5274524 DOI: 10.7717/peerj.2901] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 12/12/2016] [Indexed: 11/20/2022] Open
Abstract
Understanding the processes that give rise to genomic variability in extant species is an active area of research within evolutionary biology. With the availability of whole genome sequences, it is possible to quantify different forms of variability such as variation in gene copy number, which has been described as an important source of genetic variability and in consequence of phenotypic variability. Most of the research on this topic has been focused on understanding the biological significance of gene duplication, and less attention has been given to the evolutionary role of gene loss. Gremlin 2 is a member of the DAN gene family and plays a significant role in tooth development by blocking the ligand-signaling pathway of BMP2 and BMP4. The goal of this study was to investigate the evolutionary history of gremlin 2 in cetartiodactyl mammals, a group that possesses highly divergent teeth morphology. Results from our analyses indicate that gremlin 2 has experienced a mixture of gene loss, gene duplication, and rate acceleration. Although the last common ancestor of cetartiodactyls possessed a single gene copy, pigs and camels are the only cetartiodactyl groups that have retained gremlin 2. According to the phyletic distribution of this gene and synteny analyses, we propose that gremlin 2 was lost in the common ancestor of ruminants and cetaceans between 56.3 and 63.5 million years ago as a product of a chromosomal rearrangement. Our analyses also indicate that the rate of evolution of gremlin 2 has been accelerated in the two groups that have retained this gene. Additionally, the lack of this gene could explain the high diversity of teeth among cetartiodactyl mammals; specifically, the presence of this gene could act as a biological constraint. Thus, our results support the notions that gene loss is a way to increase phenotypic diversity and that gremlin 2 is a dispensable gene, at least in cetartiodactyl mammals.
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Affiliation(s)
- Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile , Valdivia , Chile
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile , Valdivia , Chile
| | - Paola Krall
- Unidad de Nefrología, Universidad Austral de Chile , Valdivia , Chile
| | - Rodrigo A Arias
- Instituto de Producción Animal, Universidad Austral de Chile , Valdivia , Chile
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Zavala K, Vandewege MW, Hoffmann FG, Opazo JC. Evolution of the β-adrenoreceptors in vertebrates. Gen Comp Endocrinol 2017; 240:129-137. [PMID: 27769631 DOI: 10.1016/j.ygcen.2016.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 10/13/2016] [Accepted: 10/17/2016] [Indexed: 11/19/2022]
Abstract
The study of the evolutionary history of genes related to human disease lies at the interface of evolution and medicine. These studies provide the evolutionary context on which medical researchers should work, and are also useful in providing information to suggest further genetic experiments, especially in model species where genetic manipulations can be made. Here we studied the evolution of the β-adrenoreceptor gene family in vertebrates with the aim of adding an evolutionary framework to the already abundant physiological information. Our results show that in addition to the three already described vertebrate β-adrenoreceptor genes there is an additional group containing cyclostome sequences. We suggest that β-adrenoreceptors diversified as a product of the two whole genome duplications that occurred in the ancestor of vertebrates. Gene expression patterns are in general consistent across species, suggesting that expression dynamics were established early in the evolutionary history of vertebrates, and have been maintained since then. Finally, amino acid polymorphisms that are associated to pathological conditions in humans appear to be common in non-human mammals, suggesting that the phenotypic effects of these mutations depend on epistatic interaction with other positions. The evolutionary analysis of the β-adrenoreceptors delivers new insights about the diversity of these receptors in vertebrates, the evolution of the expression patterns and a comparative perspective regarding the polymorphisms that in humans are linked to pathological conditions.
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Affiliation(s)
- Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Michael W Vandewege
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS, USA
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS, USA; Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, MS, USA
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.
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28
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Wichmann IA, Zavala K, Hoffmann FG, Vandewege MW, Corvalán AH, Amigo JD, Owen GI, Opazo JC. Evolutionary history of the reprimo tumor suppressor gene family in vertebrates with a description of a new reprimo gene lineage. Gene 2016; 591:245-254. [PMID: 27432065 DOI: 10.1016/j.gene.2016.07.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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: 03/28/2016] [Revised: 07/12/2016] [Accepted: 07/14/2016] [Indexed: 11/19/2022]
Abstract
Genes related to human diseases should be natural targets for evolutionary studies, since they could provide clues regarding the genetic bases of pathologies and potential treatments. Here we studied the evolution of the reprimo gene family, a group of tumor-suppressor genes that are implicated in p53-mediated cell cycle arrest. These genes, especially the reprimo duplicate located on human chromosome 2, have been associated with epigenetic modifications correlated with transcriptional silencing and cancer progression. We demonstrate the presence of a third reprimo lineage that, together with the reprimo and reprimo-like genes, appears to have been differentially retained during the evolutionary history of vertebrates. We present evidence that these reprimo lineages originated early in vertebrate evolution and expanded as a result of the two rounds of whole genome duplications that occurred in the last common ancestor of vertebrates. The reprimo gene has been lost in birds, and the third reprimo gene lineage has been retained in only a few distantly related species, such as coelacanth and gar. Expression analyses revealed that the reprimo paralogs are mainly expressed in the nervous system. Different vertebrate lineages have retained different reprimo paralogs, and even in species that have retained multiple copies, only one of them is heavily expressed.
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Affiliation(s)
- Ignacio A Wichmann
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, Santiago, Chile; Departamento de Oncología y Hematología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS, USA; Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, MS, USA
| | - Michael W Vandewege
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS, USA
| | - Alejandro H Corvalán
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, Santiago, Chile; Departamento de Oncología y Hematología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile; Center UC for Investigation in Oncology (CITO), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Julio D Amigo
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gareth I Owen
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, Santiago, Chile; Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile; Center UC for Investigation in Oncology (CITO), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.
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Abstract
Rosids are a monophyletic group that includes approximately 70,000 species in 140 families, and they are found in a variety of habitats and life forms. Many important crops such as fruit trees and legumes are rosids. The evolutionary success of this group may have been influenced by their ability to produce flavonoids, secondary metabolites that are synthetized through a branch of the phenylpropanoid pathway where chalcone synthase is a key enzyme. In this work, we studied the evolution of the chalcone synthase gene family in 12 species belonging to the rosid clade. Our results show that the last common ancestor of the rosid clade possessed six chalcone synthase gene lineages that were differentially retained during the evolutionary history of the group. In fact, of the six gene lineages that were present in the last common ancestor, 7 species retained 2 of them, whereas the other 5 only retained one gene lineage. We also show that one of the gene lineages was disproportionately expanded in species that belonged to the order Fabales (soybean, barrel medic and Lotus japonicas). Based on the available literature, we suggest that this gene lineage possesses stress-related biological functions (e.g., response to UV light, pathogen defense). We propose that the observed expansion of this clade was a result of a selective pressure to increase the amount of enzymes involved in the production of phenylpropanoid pathway-derived secondary metabolites, which is consistent with the hypothesis that suggested that lineage-specific expansions fuel plant adaptation.
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Affiliation(s)
- Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Juan C. Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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30
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Opazo JC, Hoffmann FG, Natarajan C, Witt CC, Berenbrink M, Storz JF. Gene turnover in the avian globin gene families and evolutionary changes in hemoglobin isoform expression. Mol Biol Evol 2015; 32:871-87. [PMID: 25502940 PMCID: PMC4379397 DOI: 10.1093/molbev/msu341] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The apparent stasis in the evolution of avian chromosomes suggests that birds may have experienced relatively low rates of gene gain and loss in multigene families. To investigate this possibility and to explore the phenotypic consequences of variation in gene copy number, we examined evolutionary changes in the families of genes that encode the α- and β-type subunits of hemoglobin (Hb), the tetrameric α2β2 protein responsible for blood-O2 transport. A comparative genomic analysis of 52 bird species revealed that the size and membership composition of the α- and β-globin gene families have remained remarkably constant during approximately 100 My of avian evolution. Most interspecific variation in gene content is attributable to multiple independent inactivations of the α(D)-globin gene, which encodes the α-chain subunit of a functionally distinct Hb isoform (HbD) that is expressed in both embryonic and definitive erythrocytes. Due to consistent differences in O2-binding properties between HbD and the major adult-expressed Hb isoform, HbA (which incorporates products of the α(A)-globin gene), recurrent losses of α(D)-globin contribute to among-species variation in blood-O2 affinity. Analysis of HbA/HbD expression levels in the red blood cells of 122 bird species revealed high variability among lineages and strong phylogenetic signal. In comparison with the homologous gene clusters in mammals, the low retention rate for lineage-specific gene duplicates in the avian globin gene clusters suggests that the developmental regulation of Hb synthesis in birds may be more highly conserved, with orthologous genes having similar stage-specific expression profiles and similar functional properties in disparate taxa.
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Affiliation(s)
- Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University
| | | | - Christopher C Witt
- Department of Biology, University of New Mexico Museum of Southwestern Biology, University of New Mexico
| | - Michael Berenbrink
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln
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31
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Opazo JC, Lee AP, Hoffmann FG, Toloza-Villalobos J, Burmester T, Venkatesh B, Storz JF. Ancient Duplications and Expression Divergence in the Globin Gene Superfamily of Vertebrates: Insights from the Elephant Shark Genome and Transcriptome. Mol Biol Evol 2015; 32:1684-94. [PMID: 25743544 DOI: 10.1093/molbev/msv054] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Comparative analyses of vertebrate genomes continue to uncover a surprising diversity of genes in the globin gene superfamily, some of which have very restricted phyletic distributions despite their antiquity. Genomic analysis of the globin gene repertoire of cartilaginous fish (Chondrichthyes) should be especially informative about the duplicative origins and ancestral functions of vertebrate globins, as divergence between Chondrichthyes and bony vertebrates represents the most basal split within the jawed vertebrates. Here, we report a comparative genomic analysis of the vertebrate globin gene family that includes the complete globin gene repertoire of the elephant shark (Callorhinchus milii). Using genomic sequence data from representatives of all major vertebrate classes, integrated analyses of conserved synteny and phylogenetic relationships revealed that the last common ancestor of vertebrates possessed a repertoire of at least seven globin genes: single copies of androglobin and neuroglobin, four paralogous copies of globin X, and the single-copy progenitor of the entire set of vertebrate-specific globins. Combined with expression data, the genomic inventory of elephant shark globins yielded four especially surprising findings: 1) there is no trace of the neuroglobin gene (a highly conserved gene that is present in all other jawed vertebrates that have been examined to date), 2) myoglobin is highly expressed in heart, but not in skeletal muscle (reflecting a possible ancestral condition in vertebrates with single-circuit circulatory systems), 3) elephant shark possesses two highly divergent globin X paralogs, one of which is preferentially expressed in gonads, and 4) elephant shark possesses two structurally distinct α-globin paralogs, one of which is preferentially expressed in the brain. Expression profiles of elephant shark globin genes reveal distinct specializations of function relative to orthologs in bony vertebrates and suggest hypotheses about ancestral functions of vertebrate globins.
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Affiliation(s)
- Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Alison P Lee
- Institute of Molecular and Cell Biology, Comparative and Medical Genomics Laboratory, Agency for Science, Technology, and Research Biopolis, Singapore
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University
| | - Jessica Toloza-Villalobos
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | | | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, Comparative and Medical Genomics Laboratory, Agency for Science, Technology, and Research Biopolis, Singapore Departments of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln
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32
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Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutiérrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, Caballero J, Hubley RM, Smit AF, Platt RN, Lavoie CA, Ramakodi MP, Finger JW, Suh A, Isberg SR, Miles L, Chong AY, Jaratlerdsiri W, Gongora J, Moran C, Iriarte A, McCormack J, Burgess SC, Edwards SV, Lyons E, Williams C, Breen M, Howard JT, Gresham CR, Peterson DG, Schmitz J, Pollock DD, Haussler D, Triplett EW, Zhang G, Irie N, Jarvis ED, Brochu CA, Schmidt CJ, McCarthy FM, Faircloth BC, Hoffmann FG, Glenn TC, Gabaldón T, Paten B, Ray DA. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 2014; 346:1254449. [PMID: 25504731 PMCID: PMC4386873 DOI: 10.1126/science.1254449] [Citation(s) in RCA: 230] [Impact Index Per Article: 23.0] [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] [Indexed: 12/28/2022]
Abstract
To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.
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Affiliation(s)
- Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.
| | - Edward L Braun
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Joel Armstrong
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Dent Earl
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Ngan Nguyen
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Glenn Hickey
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Michael W Vandewege
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - John A St John
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Salvador Capella-Gutiérrez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Todd A Castoe
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA. Department of Biology, University of Texas, Arlington, TX 76019, USA
| | - Colin Kern
- Department of Computer and Information Sciences, University of Delaware, Newark, DE 19717, USA
| | - Matthew K Fujita
- Department of Biology, University of Texas, Arlington, TX 76019, USA
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Jerzy Jurka
- Genetic Information Research Institute, Mountain View, CA 94043, USA
| | - Kenji K Kojima
- Genetic Information Research Institute, Mountain View, CA 94043, USA
| | | | | | - Arian F Smit
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Roy N Platt
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Christine A Lavoie
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Meganathan P Ramakodi
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - John W Finger
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Alexander Suh
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany. Department of Evolutionary Biology (EBC), Uppsala University, SE-752 36 Uppsala, Sweden
| | - Sally R Isberg
- Porosus Pty. Ltd., Palmerston, NT 0831, Australia. Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia. Centre for Crocodile Research, Noonamah, NT 0837, Australia
| | - Lee Miles
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Amanda Y Chong
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | | | - Jaime Gongora
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Christopher Moran
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Andrés Iriarte
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - John McCormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, CA 90041, USA
| | - Shane C Burgess
- College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Eric Lyons
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Christina Williams
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA
| | - Jason T Howard
- Howard Hughes Medical Institute, Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Cathy R Gresham
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Jürgen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
| | - David D Pollock
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - David Haussler
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA. Howard Hughes Medical Institute, Bethesda, MD 20814, USA
| | - Eric W Triplett
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China. Center for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Naoki Irie
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Erich D Jarvis
- Howard Hughes Medical Institute, Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Christopher A Brochu
- Department of Earth and Environmental Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Carl J Schmidt
- Department of Animal and Food Sciences, University of Delaware, Newark, DE 19717, USA
| | - Fiona M McCarthy
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Brant C Faircloth
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90019, USA. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain. Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Benedict Paten
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA
| | - David A Ray
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.
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33
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Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Núñez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farré M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Håstad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alström P, Fjeldså J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J, Jarvis ED, Gilbert MTP, Wang J. Comparative genomics reveals insights into avian genome evolution and adaptation. Science 2014; 346:1311-20. [PMID: 25504712 DOI: 10.1126/science.1251385] [Citation(s) in RCA: 647] [Impact Index Per Article: 64.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
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Affiliation(s)
- Guojie Zhang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.
| | - Cai Li
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Qiye Li
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Bo Li
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Denis M Larkin
- Royal Veterinary College, University of London, London, UK
| | - Chul Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea. Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Agostinho Antunes
- Centro de Investigación en Ciencias del Mar y Limnología (CIMAR)/Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal. Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Matthew J Greenwold
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Robert W Meredith
- Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043, USA
| | - Anders Ödeen
- Department of Animal Ecology, Uppsala University, Norbyvägen 18D, S-752 36 Uppsala, Sweden
| | - Jie Cui
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia. Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore 169857, Singapore
| | - Qi Zhou
- Department of Integrative Biology University of California, Berkeley, CA 94720, USA
| | - Luohao Xu
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hailin Pan
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Zongji Wang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Lijun Jin
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Pei Zhang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Haofu Hu
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Wei Yang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Jiang Hu
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Jin Xiao
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Zhikai Yang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Yang Liu
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Qiaolin Xie
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Hao Yu
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Jinmin Lian
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Ping Wen
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Fang Zhang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Hui Li
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Yongli Zeng
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Zijun Xiong
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Shiping Liu
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Long Zhou
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Zhiyong Huang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Na An
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Jie Wang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. BGI Education Center,University of Chinese Academy of Sciences,Shenzhen, 518083, China
| | - Qiumei Zheng
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Yingqi Xiong
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Guangbiao Wang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Bo Wang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Jingjing Wang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Yu Fan
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Rute R da Fonseca
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Alonzo Alfaro-Núñez
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Jason T Howard
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Ganeshkumar Ganapathy
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Andreas Pfenning
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Osceola Whitney
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Miriam V Rivas
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Erina Hara
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Julia Smith
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Marta Farré
- Royal Veterinary College, University of London, London, UK
| | - Jitendra Narayan
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Gancho Slavov
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | | | - Rui Borges
- Centro de Investigación en Ciencias del Mar y Limnología (CIMAR)/Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal. Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - João Paulo Machado
- Centro de Investigación en Ciencias del Mar y Limnología (CIMAR)/Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal. Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Imran Khan
- Centro de Investigación en Ciencias del Mar y Limnología (CIMAR)/Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal. Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Mark S Springer
- Department of Biology, University of California Riverside, Riverside, CA 92521, USA
| | - John Gatesy
- Department of Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Olle Håstad
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Post Office Box 7011, S-750 07, Uppsala, Sweden
| | - Roger H Sawyer
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea. Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea. Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Kyu-Won Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hyeon Jeong Kim
- Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea
| | - Seoae Cho
- Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea
| | - Ning Li
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China
| | - Yinhua Huang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China. College of Animal Science and Technology, China Agricultural University, Beijing 100094, China
| | - Michael W Bruford
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK
| | - Xiangjiang Zhan
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK. Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 China
| | - Andrew Dixon
- International Wildlife Consultants, Carmarthen SA33 5YL, Wales, UK
| | - Mads F Bertelsen
- Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, DK-2000 Frederiksberg, Denmark
| | - Elizabeth Derryberry
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA. Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Wesley Warren
- The Genome Institute at Washington University, St. Louis, MO 63108, USA
| | - Richard K Wilson
- The Genome Institute at Washington University, St. Louis, MO 63108, USA
| | - Shengbin Li
- College of Medicine and Forensics, Xi'an Jiaotong University, Xi'an, 710061, China
| | - David A Ray
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia. Nova Southeastern University Oceanographic Center 8000 N Ocean Drive, Dania, FL 33004, USA
| | - Darren Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630, USA
| | - David Haussler
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Oliver A Ryder
- Genetics Division, San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, CA 92027, USA
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Gary R Graves
- Department of Vertebrate Zoology, MRC-116, National Museum of Natural History, Smithsonian Institution, Post Office Box 37012, Washington, DC 20013-7012, USA. Center for Macroecology, Evolution and Climate, the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China. Swedish Species Information Centre, Swedish University of Agricultural Sciences, Box 7007, SE-750 07 Uppsala, Sweden
| | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate, the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark
| | - David P Mindell
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Edward L Braun
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. Imperial College London, Grand Challenges in Ecosystems and the Environment Initiative, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - David W Burt
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The Roslin Institute Building, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Peter Houde
- Department of Biology, New Mexico State University, Box 30001 MSC 3AF, Las Cruces, NM 88003, USA
| | - Yong Zhang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Huanming Yang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China
| | - Jian Wang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | | | - Erich D Jarvis
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, 6102, Australia.
| | - Jun Wang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Department of Medicine, University of Hong Kong, Hong Kong.
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Abstract
The relaxin/insulin-like gene family includes signaling molecules that perform a variety of physiological roles mostly related to reproduction and neuroendocrine regulation. Several previous studies have focused on the evolutionary history of relaxin genes in anthropoid primates, with particular attention on resolving the duplication history of RLN1 and RLN2 genes, which are found as duplicates only in apes. These studies have revealed that the RLN1 and RLN2 paralogs in apes have a more complex history than their phyletic distribution would suggest. In this regard, alternative scenarios have been proposed to explain the timing of duplication, and the history of gene gain and loss along the organismal tree. In this article, we revisit the question and specifically reconstruct phylogenies based on coding and noncoding sequence in anthropoid primates to readdress the timing of the duplication event giving rise to RLN1 and RLN2 in apes. Results from our phylogenetic analyses based on noncoding sequence revealed that the duplication event that gave rise to the RLN1 and RLN2 occurred in the last common ancestor of catarrhine primates, between ∼44.2 and 29.6 Ma, and not in the last common ancestor of apes or anthropoids, as previously suggested. Comparative analyses based on coding and noncoding sequence suggests an event of convergent evolution at the sequence level between co-ortholog genes, the single-copy RLN gene found in New World monkeys and the RLN1 gene of apes, where changes in a fraction of the convergent sites appear to be driven by positive selection.
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Affiliation(s)
- José Ignacio Arroyo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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Abstract
BACKGROUND Hair represents an evolutionary innovation that appeared early on mammalian evolutionary history, and presumably contributed significantly to the rapid radiation of the group. An interesting event in hair evolution has been its secondary loss in some mammalian groups, such as cetaceans, whose hairless phenotype appears to be an adaptive response to better meet the environmental conditions. To determine whether different repertoire of keratin genes among mammals can potentially explain the phenotypic hair features of different lineages, we characterized the type I and II clusters of alpha keratins from eight mammalian species, including the hairless dolphin and minke whale representing the order Cetacea. RESULTS We combined the available genomic information with phylogenetic analysis to conduct a comprehensive analysis of the evolutionary patterns of keratin gene clusters. We found that both type I and II gene clusters are fairly conserved among the terrestrial mammals included in this study, with lineage specific gene duplication and gene loss. Nevertheless, there is also evidence for an increased rate of pseudogenization in the cetacean lineage when compared to their terrestrial relatives, especially among the hair type keratins. CONCLUSIONS Here we present a comprehensive characterization of alpha-keratin genes among mammals and elucidate the mechanisms involved in the evolution of this gene family. We identified lineage-specific gene duplications and gene loss among the Laurasiatherian and Euarchontoglires species included in the study. Interestingly, cetaceans present an increased loss of hair-type keratin genes when compared to other terrestrial mammals. As suggested by the 'less-is-more' hypothesis, we do not rule out the possibility that the gene loss of hair-type keratin genes in these species might be associated to the hairless phenotype and could have been adaptive in response to new selective pressures imposed by the colonization of a new habitat. Our study provides support for the idea that pseudogenes are not simply 'genomic fossils' but instead have adaptive roles during the evolutionary process.
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Affiliation(s)
- Mariana F Nery
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.
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Nery MF, Arroyo JI, Opazo JC. Genomic organization and differential signature of positive selection in the alpha and beta globin gene clusters in two cetacean species. Genome Biol Evol 2014; 5:2359-67. [PMID: 24259315 PMCID: PMC3879965 DOI: 10.1093/gbe/evt176] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The hemoglobin of jawed vertebrates is a heterotetramer protein that contains two α- and two β-chains, which are encoded by members of α- and β-globin gene families. Given the hemoglobin role in mediating an adaptive response to chronic hypoxia, it is likely that this molecule may have experienced a selective pressure during the evolution of cetaceans, which have to deal with hypoxia tolerance during prolonged diving. This selective pressure could have generated a complex history of gene turnover in these clusters and/or changes in protein structure themselves. Accordingly, we aimed to characterize the genomic organization of α- and β-globin gene clusters in two cetacean species and to detect a possible role of positive selection on them using a phylogenetic framework. Maximum likelihood and Bayesian phylogeny reconstructions revealed that both cetacean species had retained a similar complement of putatively functional genes. For the α-globin gene cluster, the killer whale presents a complement of genes composed of HBZ, HBK, and two functional copies of HBA and HBQ genes, whereas the dolphin possesses HBZ, HBK, HBA and HBQ genes, and one HBA pseudogene. For the β-globin gene cluster, both species retained a complement of four genes, two early expressed genes—HBE and HBH—and two adult expressed genes—HBD and HBB. Our natural selection analysis detected two positively selected sites in the HBB gene (56 and 62) and four in HBA (15, 21, 49, 120). Interestingly, only the genes that are expressed during the adulthood showed the signature of positive selection.
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Affiliation(s)
- Mariana F Nery
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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Giorello FM, Feijoo M, D’Elía G, Valdez L, Opazo JC, Varas V, Naya DE, Lessa EP. Characterization of the kidney transcriptome of the South American olive mouse Abrothrix olivacea. BMC Genomics 2014; 15:446. [PMID: 24909751 PMCID: PMC4189146 DOI: 10.1186/1471-2164-15-446] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 05/27/2014] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The olive mouse Abrothrix olivacea is a cricetid rodent of the subfamily Sigmodontinae that inhabits a wide range of contrasting environments in southern South America, from aridlands to temperate rainforests. Along its distribution, it presents different geographic forms that make the olive mouse a good focal case for the study of geographical variation in response to environmental variation. We chose to characterize the kidney transcriptome because this organ has been shown to be associated with multiple physiological processes, including water reabsorption. RESULTS Transcriptomes of thirteen kidneys from individuals from Argentina and Chile were sequenced using Illumina technology in order to obtain a kidney reference transcriptome. After combining the reads produced for each sample, we explored three assembly strategies to obtain the best reconstruction of transcripts, TrinityNorm and DigiNorm, which include its own normalization algorithms for redundant reads removal, and Multireads, which simply consist on the assembly of the joined reads. We found that Multireads strategy produces a less fragmented assembly than normalization algorithms but recovers fewer number of genes. In general, about 15000 genes were annotated, of which almost half had at least one coding sequence reconstructed at 99% of its length. We also built a list of highly expressed genes, of which several are involved in water conservation under laboratory conditions using mouse models. CONCLUSION Based on our assembly results, Trinity's in silico normalization is the best algorithm in terms of cost-benefit returns; however, our results also indicate that normalization should be avoided if complete or nearly complete coding sequences of genes are desired. Given that this work is the first to characterize the transcriptome of any member of Sigmodontinae, a subfamily of cricetid rodents with about 400 living species, it will provide valuable resources for future ecological and evolutionary genomic analyses.
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Affiliation(s)
- Facundo M Giorello
- />Departamento de Ecología y Evolución, Facultad de
Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Matias Feijoo
- />Departamento de Ecología y Evolución, Facultad de
Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Guillermo D’Elía
- />Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Lourdes Valdez
- />Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Juan C Opazo
- />Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Valeria Varas
- />Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Daniel E Naya
- />Departamento de Ecología y Evolución, Facultad de
Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Enrique P Lessa
- />Departamento de Ecología y Evolución, Facultad de
Ciencias, Universidad de la República, Montevideo, Uruguay
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Nery MF, Arroyo JI, Opazo JC. Accelerated Evolutionary Rate of the Myoglobin Gene in Long-Diving Whales. J Mol Evol 2013; 76:380-7. [DOI: 10.1007/s00239-013-9572-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 06/29/2013] [Indexed: 10/26/2022]
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Gaitán-Espitia JD, Nespolo RF, Opazo JC. The complete mitochondrial genome of the land snail Cornu aspersum (Helicidae: Mollusca): intra-specific divergence of protein-coding genes and phylogenetic considerations within Euthyneura. PLoS One 2013; 8:e67299. [PMID: 23826260 PMCID: PMC3691120 DOI: 10.1371/journal.pone.0067299] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 05/16/2013] [Indexed: 11/19/2022] Open
Abstract
The complete sequences of three mitochondrial genomes from the land snail Cornu aspersum were determined. The mitogenome has a length of 14050 bp, and it encodes 13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes. It also includes nine small intergene spacers, and a large AT-rich intergenic spacer. The intra-specific divergence analysis revealed that COX1 has the lower genetic differentiation, while the most divergent genes were NADH1, NADH3 and NADH4. With the exception of Euhadra herklotsi, the structural comparisons showed the same gene order within the family Helicidae, and nearly identical gene organization to that found in order Pulmonata. Phylogenetic reconstruction recovered Basommatophora as polyphyletic group, whereas Eupulmonata and Pulmonata as paraphyletic groups. Bayesian and Maximum Likelihood analyses showed that C. aspersum is a close relative of Cepaea nemoralis, and with the other Helicidae species form a sister group of Albinaria caerulea, supporting the monophyly of the Stylommatophora clade.
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Affiliation(s)
- Juan Diego Gaitán-Espitia
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
- Programa de Doctorado en Ciencias mención Ecología y Evolución, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Roberto F. Nespolo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Juan C. Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
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41
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Abstract
Cetaceans are unique in being the only mammals completely adapted to an aquatic environment. This adaptation has required complex changes and sometimes a complete restructuring of physiology, behavior and morphology. Identifying genes that have been subjected to selection pressure during cetacean evolution would greatly enhance our knowledge of the ways in which genetic variation in this mammalian order has been shaped by natural selection. Here, we performed a genome-wide scan for positive selection in the dolphin lineage. We employed models of codon substitution that account for variation of selective pressure over branches on the tree and across sites in a sequence. We analyzed 7,859 nuclear-coding ortholog genes and using a series of likelihood ratio tests (LRTs), we identified 376 genes (4.8%) with molecular signatures of positive selection in the dolphin lineage. We used the cow as the sister group and compared estimates of selection in the cetacean genome to this using the same methods. This allowed us to define which genes have been exclusively under positive selection in the dolphin lineage. The enrichment analysis found that the identified positively selected genes are significantly over-represented for three exclusive functional categories only in the dolphin lineage: segment specification, mesoderm development and system development. Of particular interest for cetacean adaptation to an aquatic life are the following GeneOntology targets under positive selection: genes related to kidney, heart, lung, eye, ear and nervous system development.
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Affiliation(s)
- Mariana F. Nery
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Programa de Doctorado en Ciencias mención Ecología y Evolución, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Dimar J. González
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Juan C. Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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Abstract
Subsequent to the two rounds of whole-genome duplication that occurred in the common
ancestor of vertebrates, a third genome duplication occurred in the stem lineage of
teleost fishes. This teleost-specific genome duplication (TGD) is thought to have provided
genetic raw materials for the physiological, morphological, and behavioral diversification
of this highly speciose group. The extreme physiological versatility of teleost fish is
manifest in their diversity of blood–gas transport traits, which reflects the myriad
solutions that have evolved to maintain tissue O2 delivery in the face of
changing metabolic demands and environmental O2 availability during different
ontogenetic stages. During the course of development, regulatory changes in
blood–O2 transport are mediated by the expression of multiple,
functionally distinct hemoglobin (Hb) isoforms that meet the particular
O2-transport challenges encountered by the developing embryo or fetus (in
viviparous or oviparous species) and in free-swimming larvae and adults. The main
objective of the present study was to assess the relative contributions of whole-genome
duplication, large-scale segmental duplication, and small-scale gene duplication in
producing the extraordinary functional diversity of teleost Hbs. To accomplish this, we
integrated phylogenetic reconstructions with analyses of conserved synteny to characterize
the genomic organization and evolutionary history of the globin gene clusters of teleosts.
These results were then integrated with available experimental data on functional
properties and developmental patterns of stage-specific gene expression. Our results
indicate that multiple α- and β-globin genes
were present in the common ancestor of gars (order Lepisoteiformes) and teleosts. The
comparative genomic analysis revealed that teleosts possess a dual set of TGD-derived
globin gene clusters, each of which has undergone lineage-specific changes in gene content
via repeated duplication and deletion events. Phylogenetic reconstructions revealed that
paralogous genes convergently evolved similar functional properties in different teleost
lineages. Consistent with other recent studies of globin gene family evolution in
vertebrates, our results revealed evidence for repeated evolutionary transitions in the
developmental regulation of Hb synthesis.
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Affiliation(s)
- Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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Storz JF, Opazo JC, Hoffmann FG. Gene duplication, genome duplication, and the functional diversification of vertebrate globins. Mol Phylogenet Evol 2012; 66:469-78. [PMID: 22846683 DOI: 10.1016/j.ympev.2012.07.013] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Revised: 06/21/2012] [Accepted: 07/16/2012] [Indexed: 11/28/2022]
Abstract
The functional diversification of the vertebrate globin gene superfamily provides an especially vivid illustration of the role of gene duplication and whole-genome duplication in promoting evolutionary innovation. For example, key globin proteins that evolved specialized functions in various aspects of oxidative metabolism and oxygen signaling pathways (hemoglobin [Hb], myoglobin [Mb], and cytoglobin [Cygb]) trace their origins to two whole-genome duplication events in the stem lineage of vertebrates. The retention of the proto-Hb and Mb genes in the ancestor of jawed vertebrates permitted a physiological division of labor between the oxygen-carrier function of Hb and the oxygen-storage function of Mb. In the Hb gene lineage, a subsequent tandem gene duplication gave rise to the proto α- and β-globin genes, which permitted the formation of multimeric Hbs composed of unlike subunits (α(2)β(2)). The evolution of this heteromeric quaternary structure was central to the emergence of Hb as a specialized oxygen-transport protein because it provided a mechanism for cooperative oxygen-binding and allosteric regulatory control. Subsequent rounds of duplication and divergence have produced diverse repertoires of α- and β-like globin genes that are ontogenetically regulated such that functionally distinct Hb isoforms are expressed during different stages of prenatal development and postnatal life. In the ancestor of jawless fishes, the proto Mb and Hb genes appear to have been secondarily lost, and the Cygb homolog evolved a specialized respiratory function in blood-oxygen transport. Phylogenetic and comparative genomic analyses of the vertebrate globin gene superfamily have revealed numerous instances in which paralogous globins have convergently evolved similar expression patterns and/or similar functional specializations in different organismal lineages.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA.
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Hoffmann FG, Opazo JC, Hoogewijs D, Hankeln T, Ebner B, Vinogradov SN, Bailly X, Storz JF. Evolution of the globin gene family in deuterostomes: lineage-specific patterns of diversification and attrition. Mol Biol Evol 2012; 29:1735-45. [PMID: 22319164 PMCID: PMC3375472 DOI: 10.1093/molbev/mss018] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In the Metazoa, globin proteins display an underlying unity in tertiary structure that belies an extraordinary diversity in primary structures, biochemical properties, and physiological functions. Phylogenetic reconstructions can reveal which of these functions represent novel, lineage-specific innovations, and which represent ancestral functions that are shared with homologous globin proteins in other eukaryotes and even prokaryotes. To date, our understanding of globin diversity in deuterostomes has been hindered by a dearth of genomic sequence data from the Ambulacraria (echinoderms + hemichordates), the sister group of chordates, and the phylum Xenacoelomorpha, which includes xenoturbellids, acoelomorphs, and nemertodermatids. Here, we report the results of a phylogenetic and comparative genomic analysis of the globin gene repertoire of deuterostomes. We first characterized the globin genes of the acorn worm, Saccoglossus kowalevskii, a representative of the phylum Hemichordata. We then integrated genomic sequence data from the acorn worm into a comprehensive analysis of conserved synteny and phylogenetic relationships among globin genes from representatives of the eight lineages that comprise the superphylum Deuterostomia. The primary aims were 1) to unravel the evolutionary history of the globin gene superfamily in deuterostomes and 2) to use the estimated phylogeny to gain insights into the functional evolution of deuterostome globins. Results of our analyses indicate that the deuterostome common ancestor possessed a repertoire of at least four distinct globin paralogs and that different subsets of these ancestral genes have been retained in each of the descendant organismal lineages. In each major deuterostome group, a different subset of ancestral precursor genes underwent lineage-specific expansions of functional diversity through repeated rounds of gene duplication and divergence. By integrating results of the phylogenetic analysis with available functional data, we discovered that circulating oxygen-transport hemoglobins evolved independently in several deuterostome lineages and that intracellular nerve globins evolved independently in chordates and acoelomorph worms.
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Affiliation(s)
- Federico G Hoffmann
- Department of Biochemistry and Molecular Biology, Mississippi State University, USA.
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Arroyo JI, Hoffmann FG, Opazo JC. Gene turnover and differential retention in the relaxin/insulin-like gene family in primates. Mol Phylogenet Evol 2012; 63:768-76. [PMID: 22405815 DOI: 10.1016/j.ympev.2012.02.011] [Citation(s) in RCA: 14] [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: 03/29/2011] [Revised: 02/15/2012] [Accepted: 02/17/2012] [Indexed: 11/28/2022]
Abstract
The relaxin/insulin-like gene family is related to the insulin gene family, and includes two separate types of peptides: relaxins (RLNs) and insulin-like peptides (INSLs) that perform a variety of physiological roles including testicular descent, growth and differentiation of the mammary glands, trophoblast development, and cell differentiation. In vertebrates, these genes are found on three separate genomic loci, and in mammals, variation in the number and nature of genes in this family is mostly restricted to the Relaxin Family Locus B. For example, this locus contains a single copy of RLN in platypus and opossum, whereas it contains copies of the INSL6, INSL4, RLN2 and RLN1 genes in human and chimp. The main objective of this research is to characterize changes in the size and membership composition of the RLN/INSL gene family in primates, reconstruct the history of the RLN/INSL genes of primates, and test competing evolutionary scenarios regarding the origin of INSL4 and of the duplicated copies of the RLN gene of apes. Our results show that the relaxin/INSL-like gene family of primates has had a more dynamic evolutionary history than previously thought, including several examples of gene duplications and losses which are consistent with the predictions of the birth-and-death model of gene family evolution. In particular, we found that the differential retention of relatively old paralogs played a key role in shaping the gene complement of this family in primates. Two examples of this phenomenon are the origin of the INSL4 gene of catarrhines (the group that includes Old World monkeys and apes), and of the duplicate RLN1 and RLN2 paralogs of apes. In the case of INSL4, comparative genomics and phylogenetic analyses indicate that the origin of this gene, which was thought to represent a catarrhine-specific evolutionary innovation, is as old as the split between carnivores and primates, which took place approximately 97 million years ago. In addition, in the case of the RLN1 and RLN2 genes of apes our phylogenetic trees and topology tests indicate that the duplication that gave rise to these two genes maps to the last common ancestor of anthropoid primates. All these genomic changes in gene complement, which are particularly prevalent among anthropoid primates, might be linked to the many physiological and anatomical changes found in this group. Given the various roles of members of the RLN/INSL-like gene family in reproductive biology, it might be that changes in this gene family are associated to changes in reproductive traits.
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Affiliation(s)
- José Ignacio Arroyo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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Arroyo JI, Hoffmann FG, Opazo JC. Gene Duplication and Positive Selection Explains Unusual Physiological Roles of the Relaxin Gene in the European Rabbit. J Mol Evol 2012; 74:52-60. [DOI: 10.1007/s00239-012-9487-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 01/25/2012] [Indexed: 10/28/2022]
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Pierron D, Opazo JC, Heiske M, Papper Z, Uddin M, Chand G, Wildman DE, Romero R, Goodman M, Grossman LI. Silencing, positive selection and parallel evolution: busy history of primate cytochromes C. PLoS One 2011; 6:e26269. [PMID: 22028846 PMCID: PMC3196546 DOI: 10.1371/journal.pone.0026269] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 09/23/2011] [Indexed: 12/20/2022] Open
Abstract
Cytochrome c (cyt c) participates in two crucial cellular processes, energy production and apoptosis, and unsurprisingly is a highly conserved protein. However, previous studies have reported for the primate lineage (i) loss of the paralogous testis isoform, (ii) an acceleration and then a deceleration of the amino acid replacement rate of the cyt c somatic isoform, and (iii) atypical biochemical behavior of human cyt c. To gain insight into the cause of these major evolutionary events, we have retraced the history of cyt c loci among primates. For testis cyt c, all primate sequences examined carry the same nonsense mutation, which suggests that silencing occurred before the primates diversified. For somatic cyt c, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses yielded the same tree topology. The evolutionary analyses show that a fast accumulation of non-synonymous mutations (suggesting positive selection) occurred specifically on the anthropoid lineage root and then continued in parallel on the early catarrhini and platyrrhini stems. Analysis of evolutionary changes using the 3D structure suggests they are focused on the respiratory chain rather than on apoptosis or other cyt c functions. In agreement with previous biochemical studies, our results suggest that silencing of the cyt c testis isoform could be linked with the decrease of primate reproduction rate. Finally, the evolution of cyt c in the two sister anthropoid groups leads us to propose that somatic cyt c evolution may be related both to COX evolution and to the convergent brain and body mass enlargement in these two anthropoid clades.
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Affiliation(s)
- Denis Pierron
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- Perinatology Research Branch, National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland and Detroit, Michigan, United States of America
| | - Juan C. Opazo
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- Instituto de Ecologia y Evolucion, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Margit Heiske
- Laboratoire de Physiopathologie Mitochondriale, INSERM, Université Victor Segalen Bordeaux 2, Bordeaux, France
| | - Zack Papper
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
| | - Monica Uddin
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- School of Public Health, The University of Michigan, Ann Arbor, Michigan, United States of America
| | - Gopi Chand
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- Perinatology Research Branch, National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland and Detroit, Michigan, United States of America
| | - Derek E. Wildman
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- Perinatology Research Branch, National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland and Detroit, Michigan, United States of America
- Department Of Obstetrics and Gynecology, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
| | - Roberto Romero
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- Perinatology Research Branch, National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland and Detroit, Michigan, United States of America
| | - Morris Goodman
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
| | - Lawrence I. Grossman
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- * E-mail:
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Hoffmann FG, Opazo JC, Storz JF. Whole-genome duplications spurred the functional diversification of the globin gene superfamily in vertebrates. Mol Biol Evol 2011; 29:303-12. [PMID: 21965344 DOI: 10.1093/molbev/msr207] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
It has been hypothesized that two successive rounds of whole-genome duplication (WGD) in the stem lineage of vertebrates provided genetic raw materials for the evolutionary innovation of many vertebrate-specific features. However, it has seldom been possible to trace such innovations to specific functional differences between paralogous gene products that derive from a WGD event. Here, we report genomic evidence for a direct link between WGD and key physiological innovations in the vertebrate oxygen transport system. Specifically, we demonstrate that key globin proteins that evolved specialized functions in different aspects of oxidative metabolism (hemoglobin, myoglobin, and cytoglobin) represent paralogous products of two WGD events in the vertebrate common ancestor. Analysis of conserved macrosynteny between the genomes of vertebrates and amphioxus (subphylum Cephalochordata) revealed that homologous chromosomal segments defined by myoglobin + globin-E, cytoglobin, and the α-globin gene cluster each descend from the same linkage group in the reconstructed proto-karyotype of the chordate common ancestor. The physiological division of labor between the oxygen transport function of hemoglobin and the oxygen storage function of myoglobin played a pivotal role in the evolution of aerobic energy metabolism, supporting the hypothesis that WGDs helped fuel key innovations in vertebrate evolution.
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Nespolo RF, Bacigalupe LD, Figueroa CC, Koteja P, Opazo JC. Using new tools to solve an old problem: the evolution of endothermy in vertebrates. Trends Ecol Evol 2011; 26:414-23. [DOI: 10.1016/j.tree.2011.04.004] [Citation(s) in RCA: 43] [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: 10/15/2010] [Revised: 04/05/2011] [Accepted: 04/11/2011] [Indexed: 01/13/2023]
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Hoffmann FG, Opazo JC, Storz JF. Differential loss and retention of cytoglobin, myoglobin, and globin-E during the radiation of vertebrates. Genome Biol Evol 2011; 3:588-600. [PMID: 21697098 PMCID: PMC3156568 DOI: 10.1093/gbe/evr055] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [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] [Indexed: 11/12/2022] Open
Abstract
If rates of postduplication gene retention are positively correlated with levels of functional constraint, then gene duplicates that have been retained in a restricted number of taxonomic lineages would be expected to exhibit relatively low levels of sequence conservation. Paradoxical patterns are presented by gene duplicates that have been retained in a small number of taxa but which are nonetheless subject to strong purifying selection relative to paralogous members of the same multigene family. This pattern suggests that such genes may have been co-opted for novel, lineage-specific functions. One possible example involves the enigmatic globin-E gene (GbE), which appears to be exclusively restricted to birds. Available data indicate that this gene is expressed exclusively in the avian eye, but its physiological function remains a mystery. In contrast to the highly restricted phyletic distribution of GbE, the overwhelming majority of jawed vertebrates (gnathostomes) possess copies of the related cytoglobin (Cygb) and myoglobin (Mb) genes. The purpose of the present study was 1) to assess the phyletic distribution of the Cygb, Mb, and GbE genes among vertebrates, 2) to elucidate the duplicative origins and evolutionary histories of these three genes, and 3) to evaluate the relative levels of functional constraint of these genes based on comparative sequence analysis. To accomplish these objectives, we conducted a combined phylogenetic and comparative genomic analysis involving taxa that represent each of the major lineages of gnathostome vertebrates. Results of synteny comparisons and phylogenetic topology tests revealed that GbE is clearly not the product of a recent, bird-specific duplication event. Instead, GbE originated via duplication of a proto-Mb gene in the stem lineage of gnathostomes. Unlike the Mb gene, which has been retained in all major gnathostome lineages other than amphibians, the GbE gene has been retained only in the lineage leading to modern birds and has been independently lost in at least four major lineages: teleost fish, amphibians, mammals, and nonavian reptiles. Despite the restricted phyletic distribution of this gene, our results indicate that GbE is one of the most highly conserved globins in the avian genome.
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