The Discovery of De Novo Gene Evolution

Tautz, Diethard

doi:10.1353/pbm.2014.0006

Cited by 49 publications

(39 citation statements)

References 53 publications

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“…For a long time, de novo emergence was considered to be very unlikely (Tautz 2014) and had therefore initially not been seriously considered as a model of origin of orphan genes (Domazet-Lošo and Tautz 2003). However, it is now clear that de novo gene birth is in fact another important process that can be traced by phylostratigraphy (Tautz and Domazet-Lošo 2011).…”

Section: Introductionmentioning

confidence: 99%

No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution

et al. 2017

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Phylostratigraphy is a computational framework for dating the emergence of DNA and protein sequences in a phylogeny. It has been extensively applied to make inferences on patterns of genome evolution, including patterns of disease gene evolution, ontogeny and de novo gene origination. Phylostratigraphy typically relies on BLAST searches along a species tree, but new simulation studies have raised concerns about the ability of BLAST to detect remote homologues and its impact on phylostratigraphic inferences. Here, we re-assessed these simulations. We found that, even with a possible overall BLAST false negative rate between 11–15%, the large majority of sequences assigned to a recent evolutionary origin by phylostratigraphy is unaffected by technical concerns about BLAST. Where the results of the simulations did cast doubt on previously reported findings, we repeated the original analyses but now excluded all questionable sequences. The originally described patterns remained essentially unchanged. These new analyses strongly support phylostratigraphic inferences, including: genes that emerged after the origin of eukaryotes are more likely to be expressed in the ectoderm than in the endoderm or mesoderm in Drosophila, and the de novo emergence of protein-coding genes from non-genic sequences occurs through proto-gene intermediates in yeast. We conclude that BLAST is an appropriate and sufficiently sensitive tool in phylostratigraphic analysis that does not appear to introduce significant biases into evolutionary pattern inferences.

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Section: Introductionmentioning

confidence: 99%

No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution

et al. 2017

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“…Apart from the emergence of entirely new genes [1–3], diversification of gene function can be achieved either through changes at the regulatory level or by alterations in the coding region of the gene. Most genes have more than one function (pleiotropy), thus changes in their coding region and to a lesser extent in their regulatory regions will not only change a single feature of its function, but usually cause multiple (and mostly negative) effects in different organs or tissues (reviewed in [4, 5]).…”

Section: Introductionmentioning

confidence: 99%

Rapid diversification of homothorax expression patterns after gene duplication in spiders

et al. 2017

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BackgroundGene duplications provide genetic material for the evolution of new morphological and physiological features. One copy can preserve the original gene functions while the second copy may evolve new functions (neofunctionalisation). Gene duplications may thus provide new genes involved in evolutionary novelties.ResultsWe have studied the duplicated homeobox gene homothorax (hth) in the spider species Parasteatoda tepidariorum and Pholcus phalangioides and have compared these data with previously published data from additional spider species. We show that the expression pattern of hth1 is highly conserved among spiders, consistent with the notion that this gene copy preserves the original hth functions. By contrast, hth2 has a markedly different expression profile especially in the prosomal appendages. The pattern in the pedipalps and legs consists of several segmental rings, suggesting a possible role of hth2 in limb joint development. Intriguingly, however, the hth2 pattern is much less conserved between the species than hth1 and shows a species specific pattern in each species investigated so far.ConclusionsWe hypothesise that the hth2 gene has gained a new patterning function after gene duplication, but has then undergone a second phase of diversification of its new role in the spider clade. The evolution of hth2 may thus provide an interesting example for a duplicated gene that has not only contributed to genetic diversity through neofunctionalisation, but beyond that has been able to escape evolutionary conservation after neofunctionalisation thus forming the basis for further genetic diversification.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-1013-0) contains supplementary material, which is available to authorized users.

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“…However, other modes have also been found, such as novel genes arising from non-coding DNA, chimeric fusions, and lateral gene transfers from other organisms [3–7]. Here we use the rapid turnover of venom genes in parasitoid wasps to study how new gene functions evolve.…”

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The Evolution of Venom by Co-option of Single-Copy Genes

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Summary The classic model for the evolution of novel gene function is through gene duplication followed by evolution of a new function by one of the copies (neofunctionalization) [1, 2]. However, other modes have also been found, such as novel genes arising from non-coding DNA, chimeric fusions, and lateral gene transfers from other organisms [3–7]. Here we use the rapid turnover of venom genes in parasitoid wasps to study how new gene functions evolve. In contrast to the classic gene duplication model, we find that a common mode of acquisition of new venom genes in parasitoid wasps is co-option of single copy genes from non-venom progenitors. Transcriptome and proteome sequencing reveal that recruitment and loss of venom genes occur primarily by rapid cis-regulatory expression evolution in the venom gland. Loss of venom genes is primarily due to down-regulation of expression in the gland rather than gene death through coding sequence degradation. While the majority of venom genes have specialized expression in the venom gland, recent losses of venom function occur primarily among genes that show broader expression in development, suggesting that they can more readily switch functional roles. We propose that co-option of single copy genes may be a common but relatively understudied mechanism of evolution for new gene functions, particularly under conditions of rapid evolutionary change.

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The Discovery of De Novo Gene Evolution

Cited by 49 publications

References 53 publications

No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution

No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution

Rapid diversification of homothorax expression patterns after gene duplication in spiders

The Evolution of Venom by Co-option of Single-Copy Genes

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