ArticlePLoS genetics2021
Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development.
Article in PLoS genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Analysis of the impact of gene evolution on reproductive effects reveals prevalent sexual and germline-soma conflicts.Nature ecology & evolution · 2026Article
- De Novo Genes: Current Status and Future Goals.Genome biology and evolution · 2025Article
- Gene age shapes functional and evolutionary properties of theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Gene regulatory networks and essential transcription factors for de novo-originated genes.Nature ecology & evolution · 2025Article
- Functional innovation through new genes as a general evolutionary process.Nature genetics · 2025Review
- The three-dimensional genome drives the evolution of asymmetric gene duplicates via enhancer capture-divergence.Science advances · 2024Article
- De Novo Genes.Annual review of genetics · 2024Review
- Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.bioRxiv : the preprint server for biology · 2024Article
- The molecular basis of phenotypic evolution: beyond the usual suspects.Trends in genetics : TIG · 2024Review
- Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.Research square · 2023Article
- HP6/Umbrea is dispensable for viability and fertility, suggesting essentiality of newly evolved genes is rare.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- circEIF3I facilitates the recruitment of SMAD3 to early endosomes to promote TGF-β signalling pathway-mediated activation of MMPs in pancreatic cancer.Molecular cancer · 2023Article
- Taxon-specific, phased siRNAs underlie a speciation locus in monkeyflowers.Science (New York, N.Y.) · 2023Article
- Deciphering the Genetic Basis of Silkworm Cocoon Colors Provides New Insights into Biological Coloration and Phenotypic Diversification.Molecular biology and evolution · 2023Article
- Pan-cancer surveys indicate cell cycle-related roles of primate-specific genes in tumors and embryonic cerebrum.Genome biology · 2022Article
- Article
- Rapid Gene Evolution in an Ancient Post-transcriptional and Translational Regulatory System Compensates for Meiotic X Chromosomal Inactivation.Molecular biology and evolution · 2022Article
- Shared evolutionary trajectories of three independent neo-sex chromosomes inGenome research · 2021Article
- Nonadaptive molecular evolution of seminal fluid proteins in Drosophila.Evolution; international journal of organic evolution · 2021Article
- A Rapid Evolving microRNA Cluster Rewires Its Target Regulatory Networks inFrontiers in genetics · 2021Article
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Authors and funding
14 authors.
Funding
Abstract
It is a conventionally held dogma that the genetic basis underlying development is conserved in a long evolutionary time scale. Ample experiments based on mutational, biochemical, functional, and complementary knockdown/knockout approaches have revealed the unexpectedly important role of recently evolved new genes in the development of Drosophila. The recent progress in the genome-wide experimental testing of gene effects and improvements in the computational identification of new genes (< 40 million years ago, Mya) open the door to investigate the evolution of gene essentiality with a phylogenetically high resolution. These advancements also raised interesting issues in techniques and concepts related to phenotypic effect analyses of genes, particularly of those that recently originated. Here we reported our analyses of these issues, including reproducibility and efficiency of knockdown experiment and difference between RNAi libraries in the knockdown efficiency and testing of phenotypic effects. We further analyzed a large data from knockdowns of 11,354 genes (~75% of the Drosophila melanogaster total genes), including 702 new genes (~66% of the species total new genes that aged < 40 Mya), revealing a similarly high proportion (~32.2%) of essential genes that originated in various Sophophora subgenus lineages and distant ancestors beyond the Drosophila genus. The transcriptional compensation effect from CRISPR knockout were detected for highly similar duplicate copies. Knockout of a few young genes detected analogous essentiality in various functions in development. Taken together, our experimental and computational analyses provide valuable data for detection of phenotypic effects of genes in general and further strong evidence for the concept that new genes in Drosophila quickly evolved essential functions in viability during development.
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