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Rives N, Lamba V, Christina Cheng CH, Zhuang X. Diverse origins of near-identical antifreeze proteins in unrelated fish lineages provide insights into evolutionary mechanisms of new gene birth and protein sequence convergence. bioRxiv 2024:2024.03.12.584730. [PMID: 38559027 PMCID: PMC10980009 DOI: 10.1101/2024.03.12.584730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Determining the origins of novel genes and the genetic mechanisms underlying the emergence of new functions is challenging yet crucial for understanding evolutionary innovations. The novel fish antifreeze proteins, exemplifying convergent evolution, represent excellent opportunities to investigate the evolutionary origins and pathways of new genes. Particularly notable is the near-identical type I antifreeze proteins (AFPI) in four phylogenetically divergent fish taxa. This study tested the hypothesis of protein sequence convergence beyond functional convergence in three unrelated AFPI-bearing fish lineages, revealing different paths by which a similar protein arose from diverse genomic resources. Comprehensive comparative analyses of de novo sequenced genome of the winter flounder and grubby sculpin, available high-quality genome of the cunner, and those of 14 other relevant species found that the near-identical AFPI originated from a distinct genetic precursor in each lineage, and independently evolved coding regions for the novel ice-binding protein while retaining sequence identity in the regulatory regions with their respective ancestor. The deduced evolutionary processes and molecular mechanisms is consistent with the Innovation-Amplification-Divergence (IAD) model applicable to AFPI formation in all three lineages, a new Duplication-Degeneration-Divergence (DDD) model we propose for the sculpin lineage, and a DDD model with gene fission for the cunner lineage. This investigation illustrates the multiple ways by which a novel functional gene with sequence convergence at the protein level could evolve across divergent species, advancing our understanding of the mechanistic intricacies in new gene formation.
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Affiliation(s)
- Nathan Rives
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Vinita Lamba
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - C.-H. Christina Cheng
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL, USA
| | - Xuan Zhuang
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
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Zhuang X, Cheng CHC. Propagation of a De Novo Gene under Natural Selection: Antifreeze Glycoprotein Genes and Their Evolutionary History in Codfishes. Genes (Basel) 2021; 12:genes12111777. [PMID: 34828383 PMCID: PMC8622921 DOI: 10.3390/genes12111777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 09/23/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 11/16/2022] Open
Abstract
The de novo birth of functional genes from non-coding DNA as an important contributor to new gene formation is increasingly supported by evidence from diverse eukaryotic lineages. However, many uncertainties remain, including how the incipient de novo genes would continue to evolve and the molecular mechanisms underlying their evolutionary trajectory. Here we address these questions by investigating evolutionary history of the de novo antifreeze glycoprotein (AFGP) gene and gene family in gadid (codfish) lineages. We examined AFGP phenotype on a phylogenetic framework encompassing a broad sampling of gadids from freezing and non-freezing habitats. In three select species representing different AFGP-bearing clades, we analyzed all AFGP gene family members and the broader scale AFGP genomic regions in detail. Codon usage analyses suggest that motif duplication produced the intragenic AFGP tripeptide coding repeats, and rapid sequence divergence post-duplication stabilized the recombination-prone long repetitive coding region. Genomic loci analyses support AFGP originated once from a single ancestral genomic origin, and shed light on how the de novo gene proliferated into a gene family. Results also show the processes of gene duplication and gene loss are distinctive in separate clades, and both genotype and phenotype are commensurate with differential local selective pressures.
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Affiliation(s)
- Xuan Zhuang
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
- Correspondence: (X.Z.); (C.-H.C.C.)
| | - C.-H. Christina Cheng
- Department of Evolution, Ecology, and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA
- Correspondence: (X.Z.); (C.-H.C.C.)
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Blight LK, Ainley DG, Ackley SF, Ballard G, Ballerini T, Brownell RL, Cheng CHC, Chiantore M, Costa D, Coulter MC, Dayton P, Devries AL, Dunbar R, Earle S, Eastman JT, Emslie SD, Evans CW, Garrott RA, Kim S, Kooyman G, Lescroël A, Lizotte M, Massaro M, Olmastroni S, Ponganis PJ, Russell J, Siniff DB, Smith WO, Stewart BS, Stirling I, Willis J, Wilson P, Woehler EJ. Fishing for Data in the Ross Sea. Science 2010; 330:1316. [DOI: 10.1126/science.330.6009.1316] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Louise K. Blight
- Centre for Applied Conservation Research, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | | | - Stephen F. Ackley
- Geological Sciences Department, University of Texas San Antonio, San Antonio, TX 78249, USA
| | | | - Tosca Ballerini
- Center for Coastal Physical Oceanography, Old Dominion University, Norfolk, VA 23529, USA
| | - Robert L. Brownell
- NOAA Fisheries, Southwest Fisheries Science Center, Pacific Grove, CA 93950, USA
| | | | | | - Daniel Costa
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA
| | - Malcolm C. Coulter
- Specialist Group on Storks, Ibises, and Spoonbills, Chocorua, NH 03817, USA
| | - Paul Dayton
- Scripps Institution of Oceanography, University of California, La Jolla, CA 92093, USA
| | - Arthur L. Devries
- Department of Animal Biology, University of Illinois, Urbana, IL 61801, USA
| | - Robert Dunbar
- Department of Environmental Earth Systems Science, Stanford University, Stanford, CA 94305, USA
| | - Sylvia Earle
- National Geographic Society, Washington, DC 20090, USA
| | - Joseph T. Eastman
- Department of Biomedical Sciences, Ohio University, Athens, OH 45701, USA
| | - Steven D. Emslie
- Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403, USA
| | - Clive W. Evans
- School of Biological Sciences, University of Auckland, PB 92019 Auckland, New Zealand
| | - Robert A. Garrott
- Ecology Department, Montana State University, Bozeman, MT 59717, USA
| | - Stacy Kim
- Moss Landing Marine Laboratories, Moss Landing, CA 95062, USA
| | - Gerald Kooyman
- Scripps Institution of Oceanography, University of California, La Jolla, CA 92093, USA
| | - Amélie Lescroël
- Biodiversité et gestion des territoires, Université de Rennes 1, UMR 7204, Museum National d'Histoire Naturelle, 35042 Rennes Cedex, France
| | - Michael Lizotte
- Sustainability Office, University of Wisconsin, Oshkosh, 650 Witzel Avenue, Oshkosh, WI 54902, USA
| | - Melanie Massaro
- School of Biological Sciences and Gateway Antarctica, University of Canterbury, Christchurch, New Zealand
| | - Silvia Olmastroni
- Department of Environmental Sciences, Applied Ecology, University of Siena, 53100 Siena, Italy
| | - Paul J. Ponganis
- Scripps Institution of Oceanography, University of California, La Jolla, CA 92093, USA
| | - Joellen Russell
- Department of Geosciences, University of Arizona, Tucson, AZ 85721, USA
| | - Donald B. Siniff
- Department of Ecology, Evolution, and Behavioral Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Walker O. Smith
- Virginia Institute of Marine Sciences, College of William & Mary, Gloucester Point, VA 23062, USA
| | | | - Ian Stirling
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Jay Willis
- HR Wallingford, Ltd., Oxfordshire OX10 8BA, UK
| | | | - Eric J. Woehler
- School of Zoology, University of Tasmania, Sandy Bay, Tasmania 7005, Australia
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