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08:05
Efficient and Rapid Isolation of Early-stage Embryos from Arabidopsis thaliana Seeds
Published on: June 7, 2013
Selection-driven divergence after gene duplication in Arabidopsis thaliana
Toni I Gossmann1, Karl J Schmid
1Leibniz-Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany. toni.gossmann@googlemail.com
Journal of Molecular Evolution
|October 4, 2011
Summary
Gene duplication drives evolutionary novelty in plants. Post-duplication selection, particularly positive selection, significantly contributes to functional divergence and the emergence of new gene functions.
Area of Science:
- Evolutionary biology
- Genomics
- Plant science
Background:
- Gene duplication is a primary driver of evolutionary novelty.
- Understanding the role of divergent selection after gene duplication is crucial but limited.
- Models for duplicated gene fates exist, but post-duplication selection mechanisms require further investigation.
Purpose of the Study:
- To investigate sequence divergence in response to neo- and subfunctionalization of segmentally duplicated genes in Arabidopsis thaliana.
- To identify orthologous gene pairs and inparalogs between Arabidopsis thaliana and Populus trichocarpa.
- To detect differences in evolutionary rates of protein-coding sequences in duplicated genes.
Main Methods:
- Comparative genomics analysis between Arabidopsis thaliana and Populus trichocarpa.
- Maximum-likelihood analyses of the nonsynonymous/synonymous substitution rate ratio (ω) in paralogous pairs.
- McDonald-Kreitman type analysis to detect positive selection.
- Analysis of gene expression (co-expression) and regulatory sequence enrichment.
Main Results:
- Analyzed 1,924 Arabidopsis thaliana paralogous pairs.
- Approximately 6.9% of paralogous pairs showed divergent ω values, indicating differential evolutionary rates.
- Observed enrichment of regulatory sequences, reduced co-expression, and evidence of positive selection in divergent paralogs.
- McDonald-Kreitman analysis supported positive selection acting on a fraction of sites in divergent lineages.
Conclusions:
- Selection following gene duplication plays a substantial role in generating gene novelties and functional divergence in plants.
- Divergent selection, including positive selection, is a key evolutionary force shaping the fate of duplicated genes.
- The findings provide insights into the mechanisms of evolutionary innovation in plant genomes.
Related Concept Videos
02:37Gene 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.
02:05Gene Evolution - Fast or Slow?
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
02:05Gene Evolution - Fast or Slow?
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
01:57Gene 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...
01:31Formation of Species
Speciation describes the formation of one or more new species from one or sometimes multiple original species. The resulting species are discrete from the parent species, and barriers to reproduction will typically exist. There are two primary mechanisms, speciation with and without geographic isolation—allopatric and sympatric speciation, respectively.
01:21Frequency-dependent Selection
When the fitness of a trait is influenced by how common it is (i.e., its frequency) relative to different traits within a population, this is referred to as frequency-dependent selection. Frequency-dependent selection may occur between species or within a single species. This type of selection can either be positive—with more common phenotypes having higher fitness—or negative, with rarer phenotypes conferring increased fitness.