Origins, evolution, and phenotypic impact of new genes.

By Henrik Kaessmann. Genome Research, 2010

813 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/041035da165081987afe003c5d8d4127dda55eaf

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Citations in the corpus

Annotation-free quantification of RNA splicing using LeafCutter (2017, positive): “The latter observation is compatible with the “out-of-testis” hypothesis, which proposes that transcription is more permissive in testis and allows novel genes or isoforms to be selected for if beneficial 22,23 .”
Fly Cell Atlas: a single-nucleus transcriptomic atlas of the adult fruit fly (2022, methodology): “The testis has the highest number of specifically expressed genes consistent with previous reports (34), followed by the Malpighian tubule and male reproductive glands (fig.”
Proto-genes and de novo gene birth (2012, methodology): “We optimized three parameters with regard to these two null models: (1) the proportion of ORF length covered in RNA-Seq and footprint reads was fixed at 50% minimum; (2) the factor by which the number of footprint reads per nucleotide in the ORF should be higher than the number of footprint reads pe”
Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data (2011, positive): “For example, humans have acquired many genes 22,23 and regulatory elements 24 in recent evolutionary history; such sequences will have fewer, less divergent orthologues and are therefore given lower .”