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

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...

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Autores principales:	Xuan Zhuang, C.-H. Christina Cheng
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	de novo gene new gene evolution repetitive protein gene family expansion evolutionary process molecular mechanism Genetics QH426-470
Acceso en línea:	https://doaj.org/article/f2d432ad91d94eabb2707e52d8e7aa80
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spelling	oai:doaj.org-article:f2d432ad91d94eabb2707e52d8e7aa802021-11-25T17:41:50ZPropagation of a De Novo Gene under Natural Selection: Antifreeze Glycoprotein Genes and Their Evolutionary History in Codfishes10.3390/genes121117772073-4425https://doaj.org/article/f2d432ad91d94eabb2707e52d8e7aa802021-11-01T00:00:00Zhttps://www.mdpi.com/2073-4425/12/11/1777https://doaj.org/toc/2073-4425The 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 <i>AFGP</i> 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 <i>AFGP</i> 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.Xuan ZhuangC.-H. Christina ChengMDPI AGarticlede novo genenew gene evolutionrepetitive proteingene family expansionevolutionary processmolecular mechanismGeneticsQH426-470ENGenes, Vol 12, Iss 1777, p 1777 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	de novo gene new gene evolution repetitive protein gene family expansion evolutionary process molecular mechanism Genetics QH426-470
spellingShingle	de novo gene new gene evolution repetitive protein gene family expansion evolutionary process molecular mechanism Genetics QH426-470 Xuan Zhuang C.-H. Christina Cheng Propagation of a De Novo Gene under Natural Selection: Antifreeze Glycoprotein Genes and Their Evolutionary History in Codfishes
description	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 <i>AFGP</i> 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 <i>AFGP</i> 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.
format	article
author	Xuan Zhuang C.-H. Christina Cheng
author_facet	Xuan Zhuang C.-H. Christina Cheng
author_sort	Xuan Zhuang
title	Propagation of a De Novo Gene under Natural Selection: Antifreeze Glycoprotein Genes and Their Evolutionary History in Codfishes
title_short	Propagation of a De Novo Gene under Natural Selection: Antifreeze Glycoprotein Genes and Their Evolutionary History in Codfishes
title_full	Propagation of a De Novo Gene under Natural Selection: Antifreeze Glycoprotein Genes and Their Evolutionary History in Codfishes
title_fullStr	Propagation of a De Novo Gene under Natural Selection: Antifreeze Glycoprotein Genes and Their Evolutionary History in Codfishes
title_full_unstemmed	Propagation of a De Novo Gene under Natural Selection: Antifreeze Glycoprotein Genes and Their Evolutionary History in Codfishes
title_sort	propagation of a de novo gene under natural selection: antifreeze glycoprotein genes and their evolutionary history in codfishes
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/f2d432ad91d94eabb2707e52d8e7aa80
work_keys_str_mv	AT xuanzhuang propagationofadenovogeneundernaturalselectionantifreezeglycoproteingenesandtheirevolutionaryhistoryincodfishes AT chchristinacheng propagationofadenovogeneundernaturalselectionantifreezeglycoproteingenesandtheirevolutionaryhistoryincodfishes
_version_	1718412141106561024

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

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