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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Autores principales:	Shengqian Xia, Nicholas W VanKuren, Chunyan Chen, Li Zhang, Clause Kemkemer, Yi Shao, Hangxing Jia, UnJin Lee, Alexander S Advani, Andrea Gschwend, Maria D Vibranovski, Sidi Chen, Yong E Zhang, Manyuan Long
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Genetics QH426-470
Acceso en línea:	https://doaj.org/article/1311e241fdee4679af4e4a31677aca39
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spelling	oai:doaj.org-article:1311e241fdee4679af4e4a31677aca392021-12-02T20:02:57ZGenomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development.1553-73901553-740410.1371/journal.pgen.1009654https://doaj.org/article/1311e241fdee4679af4e4a31677aca392021-07-01T00:00:00Zhttps://doi.org/10.1371/journal.pgen.1009654https://doaj.org/toc/1553-7390https://doaj.org/toc/1553-7404It 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.Shengqian XiaNicholas W VanKurenChunyan ChenLi ZhangClause KemkemerYi ShaoHangxing JiaUnJin LeeAlexander S AdvaniAndrea GschwendMaria D VibranovskiSidi ChenYong E ZhangManyuan LongPublic Library of Science (PLoS)articleGeneticsQH426-470ENPLoS Genetics, Vol 17, Iss 7, p e1009654 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Genetics QH426-470
spellingShingle	Genetics QH426-470 Shengqian Xia Nicholas W VanKuren Chunyan Chen Li Zhang Clause Kemkemer Yi Shao Hangxing Jia UnJin Lee Alexander S Advani Andrea Gschwend Maria D Vibranovski Sidi Chen Yong E Zhang Manyuan Long Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development.
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.
format	article
author	Shengqian Xia Nicholas W VanKuren Chunyan Chen Li Zhang Clause Kemkemer Yi Shao Hangxing Jia UnJin Lee Alexander S Advani Andrea Gschwend Maria D Vibranovski Sidi Chen Yong E Zhang Manyuan Long
author_facet	Shengqian Xia Nicholas W VanKuren Chunyan Chen Li Zhang Clause Kemkemer Yi Shao Hangxing Jia UnJin Lee Alexander S Advani Andrea Gschwend Maria D Vibranovski Sidi Chen Yong E Zhang Manyuan Long
author_sort	Shengqian Xia
title	Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development.
title_short	Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development.
title_full	Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development.
title_fullStr	Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development.
title_full_unstemmed	Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development.
title_sort	genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in drosophila development.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/1311e241fdee4679af4e4a31677aca39
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Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development.

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