Limits...
Neutral and non-neutral evolution of duplicated genes with gene conversion.

Fawcett JA, Innan H - Genes (Basel) (2011)

Bottom Line: A typical pattern is so-called concerted evolution, in which the divergence between duplicates is maintained low for a long time because of frequent exchanges of DNA fragments.In addition, gene conversion affects the DNA evolution of duplicates in various ways especially when selection operates.We also explain how these theories contribute to interpreting real polymorphism and divergence data by using some intriguing examples.

View Article: PubMed Central - PubMed

Affiliation: Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan. fawcett@soken.ac.jp.

ABSTRACT
Gene conversion is one of the major mutational mechanisms involved in the DNA sequence evolution of duplicated genes. It contributes to create unique patters of DNA polymorphism within species and divergence between species. A typical pattern is so-called concerted evolution, in which the divergence between duplicates is maintained low for a long time because of frequent exchanges of DNA fragments. In addition, gene conversion affects the DNA evolution of duplicates in various ways especially when selection operates. Here, we review theoretical models to understand the evolution of duplicates in both neutral and non-neutral cases. We also explain how these theories contribute to interpreting real polymorphism and divergence data by using some intriguing examples.

No MeSH data available.


Sequence divergence of the red- and green-opsin genes in human and macaque. The graph shows the divergence between the human red-opsin (long-wave: LW) and green-opsin (medium-wave: MW) genes of intron 4, exon 5, and intron 6. The divergence data was taken from [46]. The gene structure of the region is shown below with the introns 4 and 6 represented by black lines and the exon 5 represented by a gray box. Regions where the similarity is higher between paralogs of the same species than between orthologs of other species (i.e., the introns) due to frequent gene conversion is in a light red background, whereas regions where the similarity is higher between the orthologs than the paralogs (i.e., the exon) are in a light blue background. The two blue arrows indicate the positions of the two fixed amino acid substitutions that are largely responsible for the difference in color sensitivity [53]. The amino acid sequences of the red-opsin (LW) and green-opsin (MW) genes of human and macaque [49] around the two functionally significant substitutions are shown below. The sites in blue are sites where the difference is fixed between either of the orthologous pair, and the sites of the two functionally significant substitutions are in bold.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3924837&req=5

f5-genes-02-00191: Sequence divergence of the red- and green-opsin genes in human and macaque. The graph shows the divergence between the human red-opsin (long-wave: LW) and green-opsin (medium-wave: MW) genes of intron 4, exon 5, and intron 6. The divergence data was taken from [46]. The gene structure of the region is shown below with the introns 4 and 6 represented by black lines and the exon 5 represented by a gray box. Regions where the similarity is higher between paralogs of the same species than between orthologs of other species (i.e., the introns) due to frequent gene conversion is in a light red background, whereas regions where the similarity is higher between the orthologs than the paralogs (i.e., the exon) are in a light blue background. The two blue arrows indicate the positions of the two fixed amino acid substitutions that are largely responsible for the difference in color sensitivity [53]. The amino acid sequences of the red-opsin (LW) and green-opsin (MW) genes of human and macaque [49] around the two functionally significant substitutions are shown below. The sites in blue are sites where the difference is fixed between either of the orthologous pair, and the sites of the two functionally significant substitutions are in bold.

Mentions: Innan [43] showed that even if the two copies are located closely and subject to frequent gene conversion, the two alleles can be maintained in the genome for a long period of time and divergence can accumulate if selection is sufficiently strong. If the target site of selection, i.e., the region where divergence is favored is small, this can result in the divergence between the duplicated genes being high in certain regions of the gene but very low in other regions [43–45]. It was recently shown that a peak of divergence can be a useful signature for detecting such target sites of selection in duplicated genes that are undergoing gene conversion [46]. This was demonstrated in human red- and green-opsin genes. There is good evidence suggesting that these genes residing ∼24 kb apart from each other were duplicated ∼30–40 mya (million years ago) and that high sequence similarity is maintained by ongoing frequent gene conversion [47–50]. Gene conversion is particularly prevalent in introns, whereas a number of differences have been fixed in some exons. As a result, when the coding sequences are compared, the sequences of different species such as human and macaque are more similar to each other than to the paralogs in the same species (Figure 5). By contrast, when the intronic sequences are compared, the duplicates in the same species are more similar to each other than to their orthologs in other old-world monkeys [49,51,52]. Of particular significance are two amino acid substitutions located close to each other on exon 5, which are largely responsible for the difference in color sensitivity [53]. Interestingly, the divergence increases in exon 5, while being maintained at low levels in the flanking introns, creating a large peak of divergence around these two sites of functionally important changes (Figure 5) [46]. This implies that strong selection restricted gene conversion in this region in order to preserve the newly arisen function. This idea was also used to determine sites where differences are maintained by selection under the pressure of gene conversion in duplicated genes in Drosophila and yeast [12,54].


Neutral and non-neutral evolution of duplicated genes with gene conversion.

Fawcett JA, Innan H - Genes (Basel) (2011)

Sequence divergence of the red- and green-opsin genes in human and macaque. The graph shows the divergence between the human red-opsin (long-wave: LW) and green-opsin (medium-wave: MW) genes of intron 4, exon 5, and intron 6. The divergence data was taken from [46]. The gene structure of the region is shown below with the introns 4 and 6 represented by black lines and the exon 5 represented by a gray box. Regions where the similarity is higher between paralogs of the same species than between orthologs of other species (i.e., the introns) due to frequent gene conversion is in a light red background, whereas regions where the similarity is higher between the orthologs than the paralogs (i.e., the exon) are in a light blue background. The two blue arrows indicate the positions of the two fixed amino acid substitutions that are largely responsible for the difference in color sensitivity [53]. The amino acid sequences of the red-opsin (LW) and green-opsin (MW) genes of human and macaque [49] around the two functionally significant substitutions are shown below. The sites in blue are sites where the difference is fixed between either of the orthologous pair, and the sites of the two functionally significant substitutions are in bold.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3924837&req=5

f5-genes-02-00191: Sequence divergence of the red- and green-opsin genes in human and macaque. The graph shows the divergence between the human red-opsin (long-wave: LW) and green-opsin (medium-wave: MW) genes of intron 4, exon 5, and intron 6. The divergence data was taken from [46]. The gene structure of the region is shown below with the introns 4 and 6 represented by black lines and the exon 5 represented by a gray box. Regions where the similarity is higher between paralogs of the same species than between orthologs of other species (i.e., the introns) due to frequent gene conversion is in a light red background, whereas regions where the similarity is higher between the orthologs than the paralogs (i.e., the exon) are in a light blue background. The two blue arrows indicate the positions of the two fixed amino acid substitutions that are largely responsible for the difference in color sensitivity [53]. The amino acid sequences of the red-opsin (LW) and green-opsin (MW) genes of human and macaque [49] around the two functionally significant substitutions are shown below. The sites in blue are sites where the difference is fixed between either of the orthologous pair, and the sites of the two functionally significant substitutions are in bold.
Mentions: Innan [43] showed that even if the two copies are located closely and subject to frequent gene conversion, the two alleles can be maintained in the genome for a long period of time and divergence can accumulate if selection is sufficiently strong. If the target site of selection, i.e., the region where divergence is favored is small, this can result in the divergence between the duplicated genes being high in certain regions of the gene but very low in other regions [43–45]. It was recently shown that a peak of divergence can be a useful signature for detecting such target sites of selection in duplicated genes that are undergoing gene conversion [46]. This was demonstrated in human red- and green-opsin genes. There is good evidence suggesting that these genes residing ∼24 kb apart from each other were duplicated ∼30–40 mya (million years ago) and that high sequence similarity is maintained by ongoing frequent gene conversion [47–50]. Gene conversion is particularly prevalent in introns, whereas a number of differences have been fixed in some exons. As a result, when the coding sequences are compared, the sequences of different species such as human and macaque are more similar to each other than to the paralogs in the same species (Figure 5). By contrast, when the intronic sequences are compared, the duplicates in the same species are more similar to each other than to their orthologs in other old-world monkeys [49,51,52]. Of particular significance are two amino acid substitutions located close to each other on exon 5, which are largely responsible for the difference in color sensitivity [53]. Interestingly, the divergence increases in exon 5, while being maintained at low levels in the flanking introns, creating a large peak of divergence around these two sites of functionally important changes (Figure 5) [46]. This implies that strong selection restricted gene conversion in this region in order to preserve the newly arisen function. This idea was also used to determine sites where differences are maintained by selection under the pressure of gene conversion in duplicated genes in Drosophila and yeast [12,54].

Bottom Line: A typical pattern is so-called concerted evolution, in which the divergence between duplicates is maintained low for a long time because of frequent exchanges of DNA fragments.In addition, gene conversion affects the DNA evolution of duplicates in various ways especially when selection operates.We also explain how these theories contribute to interpreting real polymorphism and divergence data by using some intriguing examples.

View Article: PubMed Central - PubMed

Affiliation: Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan. fawcett@soken.ac.jp.

ABSTRACT
Gene conversion is one of the major mutational mechanisms involved in the DNA sequence evolution of duplicated genes. It contributes to create unique patters of DNA polymorphism within species and divergence between species. A typical pattern is so-called concerted evolution, in which the divergence between duplicates is maintained low for a long time because of frequent exchanges of DNA fragments. In addition, gene conversion affects the DNA evolution of duplicates in various ways especially when selection operates. Here, we review theoretical models to understand the evolution of duplicates in both neutral and non-neutral cases. We also explain how these theories contribute to interpreting real polymorphism and divergence data by using some intriguing examples.

No MeSH data available.