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The rapid generation of chimerical genes expanding protein diversity in zebrafish.

Fu B, Chen M, Zou M, Long M, He S - BMC Genomics (2010)

Bottom Line: We also found 10 chimerical retrogenes that were created in the last 10 million years, which is 7.14 times the rate of 0.14 chimerical retrogenes per million years in the primate lineage toward human and 6.25 times the rate of 0.16 chimerical genes per million years in Drosophila.There is compelling evidence that much of the extensive transcriptional activity of retrogenes does not represent transcriptional "noise" but indicates the functionality of these retrogenes.Our results indicate that retroposition created a large amount of new genes in the zebrafish genome, which has contributed significantly to the evolution of the fish genome.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P R China.

ABSTRACT

Background: Variation of gene number among species indicates that there is a general process of new gene origination. One of the major mechanism providing raw materials for the origin of new genes is gene duplication. Retroposition, as a special type of gene duplication- the RNA-based duplication, has been found to play an important role in new gene evolution in mammals and plants, but little is known about the process in the teleostei genome.

Results: Here we screened the zebrafish genome for identification of retrocopies and new chimerical retrogenes and investigated their origination and evolution. We identified 652 retrocopies, of which 440 are intact retrogenes and 212 are pseudogenes. Retrocopies have long been considered evolutionary dead ends without functional significance due to the presumption that retrocopies lack the regulatory element needed for expression. However, 437 transcribed retrocopies were identified from all of the retrocopies. This discovery combined with the substitution analysis suggested that the majority of all retrocopies are subject to negative selection, indicating that most of the retrocopies may be functional retrogenes. Moreover, we found that 95 chimerical retrogenes had recruited new sequences from neighboring genomic regions that formed de novo splice sites, thus generating new intron-containing chimeric genes. Based on our analysis of 38 pairs of orthologs between Cyprinus carpio and Danio rerio, we found that the synonymous substitution rate of zebrafish genes is 4.13×10⁻⁹ substitution per silent site per year. We also found 10 chimerical retrogenes that were created in the last 10 million years, which is 7.14 times the rate of 0.14 chimerical retrogenes per million years in the primate lineage toward human and 6.25 times the rate of 0.16 chimerical genes per million years in Drosophila. This is among the most rapid rates of generation of chimerical genes, just next to the rice.

Conclusion: There is compelling evidence that much of the extensive transcriptional activity of retrogenes does not represent transcriptional "noise" but indicates the functionality of these retrogenes. Our results indicate that retroposition created a large amount of new genes in the zebrafish genome, which has contributed significantly to the evolution of the fish genome.

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Ka/Ks ratios in retrogene between the retrogenes and its parental sequences.
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Figure 2: Ka/Ks ratios in retrogene between the retrogenes and its parental sequences.

Mentions: To obtain the age distribution of all the retrocopy formation events, we plotted the Ks distribution of the parental-retrocopy pairs (Figure 2). Based on the divergence time of Danio rerio and Cyprinus carpio of 50 Mya (million years ago) [34], we used 38 pairs of orthologs between the two fishes, and found that the synonymous substitution rate of zebrafish genes is 4.13×10-9 substitution per silent site per year. We found that the majority of retrocopies formed within the past 50 million years, indicating that recent, rapid formation of retrocopies may not have only occurred in primate lineages [29,35].


The rapid generation of chimerical genes expanding protein diversity in zebrafish.

Fu B, Chen M, Zou M, Long M, He S - BMC Genomics (2010)

Ka/Ks ratios in retrogene between the retrogenes and its parental sequences.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3091775&req=5

Figure 2: Ka/Ks ratios in retrogene between the retrogenes and its parental sequences.
Mentions: To obtain the age distribution of all the retrocopy formation events, we plotted the Ks distribution of the parental-retrocopy pairs (Figure 2). Based on the divergence time of Danio rerio and Cyprinus carpio of 50 Mya (million years ago) [34], we used 38 pairs of orthologs between the two fishes, and found that the synonymous substitution rate of zebrafish genes is 4.13×10-9 substitution per silent site per year. We found that the majority of retrocopies formed within the past 50 million years, indicating that recent, rapid formation of retrocopies may not have only occurred in primate lineages [29,35].

Bottom Line: We also found 10 chimerical retrogenes that were created in the last 10 million years, which is 7.14 times the rate of 0.14 chimerical retrogenes per million years in the primate lineage toward human and 6.25 times the rate of 0.16 chimerical genes per million years in Drosophila.There is compelling evidence that much of the extensive transcriptional activity of retrogenes does not represent transcriptional "noise" but indicates the functionality of these retrogenes.Our results indicate that retroposition created a large amount of new genes in the zebrafish genome, which has contributed significantly to the evolution of the fish genome.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P R China.

ABSTRACT

Background: Variation of gene number among species indicates that there is a general process of new gene origination. One of the major mechanism providing raw materials for the origin of new genes is gene duplication. Retroposition, as a special type of gene duplication- the RNA-based duplication, has been found to play an important role in new gene evolution in mammals and plants, but little is known about the process in the teleostei genome.

Results: Here we screened the zebrafish genome for identification of retrocopies and new chimerical retrogenes and investigated their origination and evolution. We identified 652 retrocopies, of which 440 are intact retrogenes and 212 are pseudogenes. Retrocopies have long been considered evolutionary dead ends without functional significance due to the presumption that retrocopies lack the regulatory element needed for expression. However, 437 transcribed retrocopies were identified from all of the retrocopies. This discovery combined with the substitution analysis suggested that the majority of all retrocopies are subject to negative selection, indicating that most of the retrocopies may be functional retrogenes. Moreover, we found that 95 chimerical retrogenes had recruited new sequences from neighboring genomic regions that formed de novo splice sites, thus generating new intron-containing chimeric genes. Based on our analysis of 38 pairs of orthologs between Cyprinus carpio and Danio rerio, we found that the synonymous substitution rate of zebrafish genes is 4.13×10⁻⁹ substitution per silent site per year. We also found 10 chimerical retrogenes that were created in the last 10 million years, which is 7.14 times the rate of 0.14 chimerical retrogenes per million years in the primate lineage toward human and 6.25 times the rate of 0.16 chimerical genes per million years in Drosophila. This is among the most rapid rates of generation of chimerical genes, just next to the rice.

Conclusion: There is compelling evidence that much of the extensive transcriptional activity of retrogenes does not represent transcriptional "noise" but indicates the functionality of these retrogenes. Our results indicate that retroposition created a large amount of new genes in the zebrafish genome, which has contributed significantly to the evolution of the fish genome.

Show MeSH