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...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-11-01
|
| Series: | Genes |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-4425/12/11/1777 |
| _version_ | 1797510263085203456 |
|---|---|
| author | Xuan Zhuang C.-H. Christina Cheng |
| author_facet | Xuan Zhuang C.-H. Christina Cheng |
| author_sort | Xuan Zhuang |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-10T05:29:05Z |
| format | Article |
| id | doaj.art-f2d432ad91d94eabb2707e52d8e7aa80 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T05:29:05Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-f2d432ad91d94eabb2707e52d8e7aa802023-11-22T23:28:39ZengMDPI AGGenes2073-44252021-11-011211177710.3390/genes12111777Propagation of a De Novo Gene under Natural Selection: Antifreeze Glycoprotein Genes and Their Evolutionary History in CodfishesXuan Zhuang0C.-H. Christina Cheng1Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USADepartment of Evolution, Ecology, and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USAThe 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.https://www.mdpi.com/2073-4425/12/11/1777de novo genenew gene evolutionrepetitive proteingene family expansionevolutionary processmolecular mechanism |
| spellingShingle | Xuan Zhuang C.-H. Christina Cheng Propagation of a De Novo Gene under Natural Selection: Antifreeze Glycoprotein Genes and Their Evolutionary History in Codfishes Genes de novo gene new gene evolution repetitive protein gene family expansion evolutionary process molecular mechanism |
| title | 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_short | 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 |
| topic | de novo gene new gene evolution repetitive protein gene family expansion evolutionary process molecular mechanism |
| url | https://www.mdpi.com/2073-4425/12/11/1777 |
| work_keys_str_mv | AT xuanzhuang propagationofadenovogeneundernaturalselectionantifreezeglycoproteingenesandtheirevolutionaryhistoryincodfishes AT chchristinacheng propagationofadenovogeneundernaturalselectionantifreezeglycoproteingenesandtheirevolutionaryhistoryincodfishes |