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Published on: June 24, 2021
Divergence of duplicate genes in exon-intron structure
Guixia Xu1, Chunce Guo, Hongyan Shan
1State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
Summary
Gene duplication drives evolution, with structural changes in genes being common and leading to new functions. These structural divergences are more prevalent in duplicate genes than in non-duplicate genes over evolutionary time.
Area of Science:
- Evolutionary Biology
- Genomics
- Molecular Evolution
Background:
- Gene duplication is a fundamental mechanism in organismal evolution.
- Duplicate genes diverge in coding and regulatory regions, potentially altering function.
- While nucleotide substitutions are well-studied, structural divergences in genes are less understood.
Purpose of the Study:
- To investigate the occurrence and relative importance of structural divergences in duplicate and non-duplicate genes.
- To compare the roles of structural changes versus amino acid substitutions in gene evolution.
Main Methods:
- Analysis of 612 sibling paralog pairs from seven gene families.
- Analysis of 300 one-to-one ortholog pairs from different species.
- Comparison of genomic sequences to identify differences in exon-intron structure.
Main Results:
- Structural divergences are highly prevalent in duplicate genes, often generating functionally distinct paralogs.
- Three main mechanisms (exon/intron gain/loss, exonization/pseudoexonization, insertion/deletion) contribute to structural divergence.
- Orthologs accumulate significantly fewer structural changes than paralogs over similar evolutionary times.
Conclusions:
- Structural divergence plays a more significant role in the evolution of duplicate genes compared to non-duplicate genes.
- Mechanisms of structural divergence, like insertion/deletion and exonization, occur largely randomly and are proportional to evolutionary time.
- Functional divergence in duplicate genes is substantially influenced by alterations in exon-intron structure.
Related Concept Videos
Exon Recombination
The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Gene Duplication and Divergence
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
Gene Families
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Organization of Genes
Overview
Gene Conversion
Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
Gene Conversion
Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
