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Article

Propagation of a De Novo Gene under Natural Selection: Antifreeze Glycoprotein Genes and Their Evolutionary History in Codfishes

1
Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
2
Department of Evolution, Ecology, and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA
*
Authors to whom correspondence should be addressed.
Academic Editors: Manyuan Long and Esther Betran
Genes 2021, 12(11), 1777; https://doi.org/10.3390/genes12111777
Received: 23 September 2021 / Revised: 8 November 2021 / Accepted: 8 November 2021 / Published: 9 November 2021
(This article belongs to the Special Issue How Do New Genes Originate and Evolve?)
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. View Full-Text
Keywords: de novo gene; new gene evolution; repetitive protein; gene family expansion; evolutionary process; molecular mechanism; gadid; antifreeze glycoprotein de novo gene; new gene evolution; repetitive protein; gene family expansion; evolutionary process; molecular mechanism; gadid; antifreeze glycoprotein
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MDPI and ACS Style

Zhuang, X.; Cheng, C.-H.C. Propagation of a De Novo Gene under Natural Selection: Antifreeze Glycoprotein Genes and Their Evolutionary History in Codfishes. Genes 2021, 12, 1777. https://doi.org/10.3390/genes12111777

AMA Style

Zhuang X, Cheng C-HC. Propagation of a De Novo Gene under Natural Selection: Antifreeze Glycoprotein Genes and Their Evolutionary History in Codfishes. Genes. 2021; 12(11):1777. https://doi.org/10.3390/genes12111777

Chicago/Turabian Style

Zhuang, Xuan, and C.-H. C. Cheng. 2021. "Propagation of a De Novo Gene under Natural Selection: Antifreeze Glycoprotein Genes and Their Evolutionary History in Codfishes" Genes 12, no. 11: 1777. https://doi.org/10.3390/genes12111777

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