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The life cycle of Drosophila orphan genes.

Palmieri N, Kosiol C, Schlötterer C - Elife (2014)

Bottom Line: Interestingly, recently emerged orphans are more likely to be lost than older ones.Furthermore, highly expressed orphans with a strong male-bias are more likely to be retained.Since both lost and retained orphans show similar evolutionary signatures of functional conservation, we propose that orphan loss is not driven by high rates of sequence evolution, but reflects lineage-specific functional requirements.

View Article: PubMed Central - PubMed

Affiliation: Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria.

ABSTRACT
Orphans are genes restricted to a single phylogenetic lineage and emerge at high rates. While this predicts an accumulation of genes, the gene number has remained remarkably constant through evolution. This paradox has not yet been resolved. Because orphan genes have been mainly analyzed over long evolutionary time scales, orphan loss has remained unexplored. Here we study the patterns of orphan turnover among close relatives in the Drosophila obscura group. We show that orphans are not only emerging at a high rate, but that they are also rapidly lost. Interestingly, recently emerged orphans are more likely to be lost than older ones. Furthermore, highly expressed orphans with a strong male-bias are more likely to be retained. Since both lost and retained orphans show similar evolutionary signatures of functional conservation, we propose that orphan loss is not driven by high rates of sequence evolution, but reflects lineage-specific functional requirements. DOI: http://dx.doi.org/10.7554/eLife.01311.001.

No MeSH data available.


Related in: MedlinePlus

Conserved and lost orphans differ in their gene expression pattern.Expression intensity and sex bias in D. miranda for orphans conserved in all the obscura species (conserved orphans) vs orphans that pseudogenized in D. lowei and/or D. persimilis (lost orphans). Expression is calculated in males for orphans of age classes 3 and 4. Expression level increases with age for conserved orphans (A), while it decreases for lost orphans (B).DOI:http://dx.doi.org/10.7554/eLife.01311.021
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fig16: Conserved and lost orphans differ in their gene expression pattern.Expression intensity and sex bias in D. miranda for orphans conserved in all the obscura species (conserved orphans) vs orphans that pseudogenized in D. lowei and/or D. persimilis (lost orphans). Expression is calculated in males for orphans of age classes 3 and 4. Expression level increases with age for conserved orphans (A), while it decreases for lost orphans (B).DOI:http://dx.doi.org/10.7554/eLife.01311.021

Mentions: To determine features associated with the differences in disabling mutations among orphans from different age classes, we contrasted orphans lost in D. lowei and/or D. persimilis (lost orphans) vs orphans conserved in all the obscura species (conserved orphans). Genes in both classes evolve at the same rate, are of similar length, and have similar codon usage bias (Figure 15A–E). Conserved orphans have a higher GC content, contain fewer microsatellites, are expressed at a higher level and are more male-biased (Figure 15B,D–F,G,H) compared to lost orphans. Conserved orphans tend to increase their expression level as they become older (Figure 16A), whereas the opposite pattern is true for lost orphans (Figure 16B).10.7554/eLife.01311.020Figure 15.Features of conserved orphans vs lost orphans measured in D. pseudoobscura.


The life cycle of Drosophila orphan genes.

Palmieri N, Kosiol C, Schlötterer C - Elife (2014)

Conserved and lost orphans differ in their gene expression pattern.Expression intensity and sex bias in D. miranda for orphans conserved in all the obscura species (conserved orphans) vs orphans that pseudogenized in D. lowei and/or D. persimilis (lost orphans). Expression is calculated in males for orphans of age classes 3 and 4. Expression level increases with age for conserved orphans (A), while it decreases for lost orphans (B).DOI:http://dx.doi.org/10.7554/eLife.01311.021
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3927632&req=5

fig16: Conserved and lost orphans differ in their gene expression pattern.Expression intensity and sex bias in D. miranda for orphans conserved in all the obscura species (conserved orphans) vs orphans that pseudogenized in D. lowei and/or D. persimilis (lost orphans). Expression is calculated in males for orphans of age classes 3 and 4. Expression level increases with age for conserved orphans (A), while it decreases for lost orphans (B).DOI:http://dx.doi.org/10.7554/eLife.01311.021
Mentions: To determine features associated with the differences in disabling mutations among orphans from different age classes, we contrasted orphans lost in D. lowei and/or D. persimilis (lost orphans) vs orphans conserved in all the obscura species (conserved orphans). Genes in both classes evolve at the same rate, are of similar length, and have similar codon usage bias (Figure 15A–E). Conserved orphans have a higher GC content, contain fewer microsatellites, are expressed at a higher level and are more male-biased (Figure 15B,D–F,G,H) compared to lost orphans. Conserved orphans tend to increase their expression level as they become older (Figure 16A), whereas the opposite pattern is true for lost orphans (Figure 16B).10.7554/eLife.01311.020Figure 15.Features of conserved orphans vs lost orphans measured in D. pseudoobscura.

Bottom Line: Interestingly, recently emerged orphans are more likely to be lost than older ones.Furthermore, highly expressed orphans with a strong male-bias are more likely to be retained.Since both lost and retained orphans show similar evolutionary signatures of functional conservation, we propose that orphan loss is not driven by high rates of sequence evolution, but reflects lineage-specific functional requirements.

View Article: PubMed Central - PubMed

Affiliation: Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria.

ABSTRACT
Orphans are genes restricted to a single phylogenetic lineage and emerge at high rates. While this predicts an accumulation of genes, the gene number has remained remarkably constant through evolution. This paradox has not yet been resolved. Because orphan genes have been mainly analyzed over long evolutionary time scales, orphan loss has remained unexplored. Here we study the patterns of orphan turnover among close relatives in the Drosophila obscura group. We show that orphans are not only emerging at a high rate, but that they are also rapidly lost. Interestingly, recently emerged orphans are more likely to be lost than older ones. Furthermore, highly expressed orphans with a strong male-bias are more likely to be retained. Since both lost and retained orphans show similar evolutionary signatures of functional conservation, we propose that orphan loss is not driven by high rates of sequence evolution, but reflects lineage-specific functional requirements. DOI: http://dx.doi.org/10.7554/eLife.01311.001.

No MeSH data available.


Related in: MedlinePlus