Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development
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 ev...
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| creator | Xia, Shengqian VanKuren, Nicholas W Chen, Chunyan Zhang, Li Kemkemer, Clause Shao, Yi Jia, Hangxing Lee, UnJin Advani, Alexander S Gschwend, Andrea Vibranovski, Maria D Chen, Sidi Zhang, Yong E Long, Manyuan |
| description | 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. |
| doi_str_mv | 10.1371/journal.pgen.1009654 |
| format | Article |
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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.</description><identifier>ISSN: 1553-7404</identifier><identifier>ISSN: 1553-7390</identifier><identifier>EISSN: 1553-7404</identifier><identifier>DOI: 10.1371/journal.pgen.1009654</identifier><identifier>PMID: 34242211</identifier><language>eng</language><publisher>San Francisco: Public Library of Science</publisher><subject>Biology and life sciences ; Computer applications ; CRISPR ; Drosophila ; Efficiency ; Engineering and Technology ; Evolution & development ; Evolutionary genetics ; Experiments ; Genes ; Genetic aspects ; Genetic research ; Genetic screening ; Genomes ; Genomic analysis ; Insects ; Methods ; Natural history ; Phylogeny ; Physiological aspects ; Reproducibility ; Research and Analysis Methods ; RNA-mediated interference ; Standard deviation ; Transcription</subject><ispartof>PLoS genetics, 2021-07, Vol.17 (7), p.e1009654-e1009654</ispartof><rights>COPYRIGHT 2021 Public Library of Science</rights><rights>2021 Xia et al. 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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.</description><subject>Biology and life sciences</subject><subject>Computer applications</subject><subject>CRISPR</subject><subject>Drosophila</subject><subject>Efficiency</subject><subject>Engineering and Technology</subject><subject>Evolution & development</subject><subject>Evolutionary genetics</subject><subject>Experiments</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic research</subject><subject>Genetic screening</subject><subject>Genomes</subject><subject>Genomic analysis</subject><subject>Insects</subject><subject>Methods</subject><subject>Natural history</subject><subject>Phylogeny</subject><subject>Physiological 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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. 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| subjects | Biology and life sciences Computer applications CRISPR Drosophila Efficiency Engineering and Technology Evolution & development Evolutionary genetics Experiments Genes Genetic aspects Genetic research Genetic screening Genomes Genomic analysis Insects Methods Natural history Phylogeny Physiological aspects Reproducibility Research and Analysis Methods RNA-mediated interference Standard deviation Transcription |
| title | Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development |
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