Origins, evolution, and phenotypic impact of new genes
Reads0
Chats0
TLDR
The origin and evolution of new genes and their functions in eukaryotes is reviewed, demonstrating that novel genes of the various types significantly impacted the evolution of cellular, physiological, morphological, behavioral, and reproductive phenotypic traits.Abstract:
Ever since the pre-molecular era, the birth of new genes with novel functions has been considered to be a major contributor to adaptive evolutionary innovation. Here, I review the origin and evolution of new genes and their functions in eukaryotes, an area of research that has made rapid progress in the past decade thanks to the genomics revolution. Indeed, recent work has provided initial whole-genome views of the different types of new genes for a large number of different organisms. The array of mechanisms underlying the origin of new genes is compelling, extending way beyond the traditionally well-studied source of gene duplication. Thus, it was shown that novel genes also regularly arose from messenger RNAs of ancestral genes, protein-coding genes metamorphosed into new RNA genes, genomic parasites were co-opted as new genes, and that both protein and RNA genes were composed from scratch (i.e., from previously nonfunctional sequences). These mechanisms then also contributed to the formation of numerous novel chimeric gene structures. Detailed functional investigations uncovered different evolutionary pathways that led to the emergence of novel functions from these newly minted sequences and, with respect to animals, attributed a potentially important role to one specific tissue--the testis--in the process of gene birth. Remarkably, these studies also demonstrated that novel genes of the various types significantly impacted the evolution of cellular, physiological, morphological, behavioral, and reproductive phenotypic traits. Consequently, it is now firmly established that new genes have indeed been major contributors to the origin of adaptive evolutionary novelties.read more
Citations
More filters
Journal ArticleDOI
The evolution of gene expression levels in mammalian organs
David Brawand,Magali Soumillon,Magali Soumillon,Anamaria Necsulea,Anamaria Necsulea,Philippe Julien,Philippe Julien,Gábor Csárdi,Gábor Csárdi,Patrick Harrigan,Manuela Weier,Angélica Liechti,Ayinuer Aximu-Petri,Martin Kircher,Frank W. Albert,Ulrich Zeller,Philipp Khaitovich,Frank Grützner,Sven Bergmann,Sven Bergmann,Rasmus Nielsen,Rasmus Nielsen,Svante Pääbo,Henrik Kaessmann +23 more
TL;DR: It is shown that the rate of gene expression evolution varies among organs, lineages and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation.
Journal ArticleDOI
The evolutionary origin of orphan genes
TL;DR: De novo evolution out of non-coding genomic regions is emerging as an important additional mechanism for the evolution of new gene functions, which can become relevant for lineage-specific adaptations.
Journal ArticleDOI
Genome evolution in filamentous plant pathogens: why bigger can be better
Sylvain Raffaele,Sophien Kamoun +1 more
TL;DR: Cases in which genome plasticity has contributed to the emergence of new virulence traits are illustrated and how genome expansions may have had an impact on the co-evolutionary conflict between these filamentous plant pathogens and their hosts are discussed.
Journal ArticleDOI
Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data
Gregory M. Cooper,Jay Shendure +1 more
TL;DR: Approaches to estimate the deleteriousness of single nucleotide variants (SNVs), which can be used to prioritize disease-causal variants, are reviewed.
Journal ArticleDOI
Proto-genes and de novo gene birth
Anne-Ruxandra Carvunis,Thomas Rolland,Ilan Wapinski,Michael A. Calderwood,Muhammed A. Yildirim,Nicolas Simonis,Nicolas Simonis,Benoit Charloteaux,Benoit Charloteaux,César A. Hidalgo,Justin Barbette,Balaji Santhanam,Gloria A. Brar,Jonathan S. Weissman,Aviv Regev,Aviv Regev,Nicolas Thierry-Mieg,Michael E. Cusick,Marc Vidal +18 more
TL;DR: In this article, the authors formalize an evolutionary model according to which functional genes evolve de novo through transitory proto-genes generated by widespread translational activity in non-genic sequences.
References
More filters
Journal ArticleDOI
RNA-Seq: a revolutionary tool for transcriptomics
TL;DR: The RNA-Seq approach to transcriptome profiling that uses deep-sequencing technologies provides a far more precise measurement of levels of transcripts and their isoforms than other methods.
Journal ArticleDOI
Sequencing technologies-the next generation
TL;DR: A technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments is presented.
Journal ArticleDOI
Long non-coding RNAs: insights into functions
TL;DR: The rapidly advancing field of long ncRNAs is reviewed, describing their conservation, their organization in the genome and their roles in gene regulation, and the medical implications.
Journal ArticleDOI
Origins and Mechanisms of miRNAs and siRNAs
TL;DR: This work has revealed unexpected diversity in their biogenesis pathways and the regulatory mechanisms that they access, which has direct implications for fundamental biology as well as disease etiology and treatment.
Related Papers (5)
The origin of new genes: glimpses from the young and old
Proto-genes and de novo gene birth
Anne-Ruxandra Carvunis,Thomas Rolland,Ilan Wapinski,Michael A. Calderwood,Muhammed A. Yildirim,Nicolas Simonis,Nicolas Simonis,Benoit Charloteaux,Benoit Charloteaux,César A. Hidalgo,Justin Barbette,Balaji Santhanam,Gloria A. Brar,Jonathan S. Weissman,Aviv Regev,Aviv Regev,Nicolas Thierry-Mieg,Michael E. Cusick,Marc Vidal +18 more