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Differential evolution of duplicated medakafish mitf genes
Mingyou Li1, Feng Zhu, Yunhan Hong
1Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
International Journal of Biological Sciences
|June 20, 2013
Summary
Gene duplication drives evolution. In medaka fish, the mitf gene duplicated into mitf1 and mitf2. Mitf1 is conserved, while mitf2 shows degeneration, impacting melanocyte development and coloration diversity.
Area of Science:
- Evolutionary biology
- Genomics
- Developmental biology
Background:
- Gene duplication, particularly whole genome duplication (WGD), is a significant evolutionary mechanism.
- The diversity of animal coloration and patterning provides an ideal system for studying gene evolution.
- Microphthalmia-associated transcription factor (Mitf) is a master regulator of melanocyte development, making its duplicates valuable for evolutionary studies.
Purpose of the Study:
- To investigate the evolutionary trajectories of the mitf gene duplicates (mitf1 and mitf2) in medaka (Oryzias latipes).
- To understand the functional divergence of medaka Mitf1 and Mitf2 following gene duplication.
- To compare the evolutionary patterns of medaka mitf duplicates with those observed in other fish species.
Main Methods:
- Comparative sequence analysis of mitf1 and mitf2 in medaka.
- Analysis of melanocytic expression patterns of mitf duplicates during embryonic development.
- Reporter assays and RT-PCR to assess the gene-activating capacity of medaka Mitf2 compared to a Xiphophorus counterpart.
- Functional assays using medaka embryonic stem cells to evaluate Mitf2's efficiency in inducing melanocyte differentiation.
Main Results:
- Medaka mitf2 exhibits accelerated sequence divergence compared to mitf1.
- Mitf2 loses critical melanocytic expression during medaka embryonic development.
- Medaka Mitf2 demonstrates reduced activity in activating melanogenic gene expression and lower efficiency in inducing melanocyte differentiation compared to its Xiphophorus homolog.
- Mitf1 appears to be under purifying selection (conservation), while mitf2 shows signs of degeneration.
Conclusions:
- The medaka mitf duplicates have undergone differential evolution, with mitf1 being conserved and mitf2 degenerating.
- This pattern of differential evolution differs from the duplication-degeneration-complementation model observed in zebrafish.
- Species-specific variations in mitf duplicate evolution contribute to the vast diversity of fish body coloration and patterning.
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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.
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...
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02:32Exon 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...
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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...
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02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Overview