Faculty Opinions recommendation of Open questions in the study of de novo genes: what, how and why.

Over the last few years, there has been an increasing amount of evidence for the de novo emergence of protein-coding genes, i.e. out of non-coding DNA. Here, we review the current literature and summarize the state of the field. We focus specifically on open questions and challenges in the study of de novo protein-coding genes such as the identification and verification of de novo-emerged genes. The greatest obstacle to date is the lack of high-quality genomic data with very short divergence times which could help precisely pin down the location of origin of a de novo gene. We conclude that, while there is plenty of evidence from a genetics perspective, there is a lack of functional studies of bona fide de novo genes and almost no knowledge about protein structures and how they come about during the emergence of de novo protein-coding genes. We suggest that future studies should concentrate on the functional and structural characterization of de novo protein-coding genes as well as the detailed study of the emergence of functional de novo protein-coding genes.

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Faculty Opinions recommendation of De Novo Genes Arise at a Slow but Steady Rate along the Primate Lineage and Have Been Subject to Incomplete Lineage Sorting.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.726273356.793527096 ◽

2017 ◽

Author(s):

Erich Bornberg-Bauer

Keyword(s):

De Novo ◽

Incomplete Lineage Sorting ◽

Lineage Sorting ◽

Primate Lineage ◽

De Novo Genes ◽

Steady Rate

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Podcast: Mapping childhood mortality, and evolving ‘de novo’ genes

Nature ◽

10.1038/d41586-019-03144-9 ◽

2019 ◽

Keyword(s):

De Novo ◽

Childhood Mortality ◽

De Novo Genes

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De Novo Genes Arise at a Slow but Steady Rate along the Primate Lineage and Have Been Subject to Incomplete Lineage Sorting

Genome Biology and Evolution ◽

10.1093/gbe/evw074 ◽

2016 ◽

Vol 8 (4) ◽

pp. 1222-1232 ◽

Cited By ~ 25

Author(s):

Daniele Guerzoni ◽

Aoife McLysaght

Keyword(s):

De Novo ◽

Incomplete Lineage Sorting ◽

Lineage Sorting ◽

Primate Lineage ◽

De Novo Genes ◽

Steady Rate

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A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster

10.1101/2021.06.10.447990 ◽

2021 ◽

Author(s):

Emily L. Rivard ◽

Andrew G. Ludwig ◽

Prajal H. Patel ◽

Anna Grandchamp ◽

Sarah E. Arnold ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Male Fertility ◽

De Novo ◽

Developmental Process ◽

Chromatin Condensation ◽

Protein Coding ◽

Non Coding Rna ◽

De Novo Genes ◽

History Of ◽

Redundant Role

Comparative genomics has enabled the identification of genes that potentially evolved de novo from non-coding sequences. Many such genes are expressed in male reproductive tissues, but their functions remain poorly understood. To address this, we conducted a functional genetic screen of over 40 putative de novo genes with testis-enriched expression in Drosophila melanogaster and identified one gene, atlas, required for male fertility. Detailed genetic and cytological analyses show that atlas is required for proper chromatin condensation during the final stages of spermatogenesis. Atlas protein is expressed in spermatid nuclei and facilitates the transition from histone- to protamine-based chromatin packaging. Complementary evolutionary analyses revealed the complex evolutionary history of atlas. The protein-coding portion of the gene likely arose at the base of the Drosophila genus on the X chromosome but was unlikely to be essential, as it was then lost in several independent lineages. Within the last ~15 million years, however, the gene moved to an autosome, where it fused with a conserved non-coding RNA and evolved a non-redundant role in male fertility. Altogether, this study provides insight into the integration of novel genes into biological processes, the links between genomic innovation and functional evolution, and the genetic control of a fundamental developmental process, gametogenesis.

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Comparative transcriptomics and ribo-seq: Looking at de novo gene emergence in Saccharomycotina

10.7287/peerj.preprints.3030 ◽

2017 ◽

Author(s):

William Blevins ◽

Mar Albà ◽

Lucas Carey

Keyword(s):

De Novo ◽

Ribosome Profiling ◽

Rna Seq ◽

De Novo Genes ◽

De Novo Gene ◽

Rich Media ◽

Conserved Genes ◽

Different Depths ◽

Yeast Phylogeny ◽

And Oxidative Stress

In de novo gene emergence, a segment of non-coding DNA undergoes a series of changes which enables transcription, potentially leading to a new protein that could eventually acquire a novel function. Due to their recent origins, young de novo genes have no homology with other genes. Furthermore, de novo genes may not initially be under the same selective constraints as other genes. Dozens of de novo genes have recently been identified in many diverse species; however, the mechanisms leading to their appearance are not yet well understood. To study this phenomenon, we have performed deep RNA sequencing (RNA-seq) on 11 species of yeast from the phylum of Ascomycota in both rich media and oxidative stress conditions. Furthermore, we performed ribosome profiling (Ribo-seq) experiments in both conditions with S. cerevisiae. These data have been used to classify the conservation of genes at different depths in the yeast phylogeny. Hundreds of genes in each species were novel (unannotated), and many were identified as putative de novo genes; these candidates were then tested for signals of translation using our Ribo-seq data. We show that putative de novo genes have different properties relative to phylogenetically conserved genes. This comparative phylotranscriptomic analysis advances our understanding of de novo gene origins.

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