Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development

• DOI: 10.1371/journal.pgen.1009654
• Publication Date: 2021-07-09T18:04:16Z
• Authors: 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
• Keywords: Gene knockout

It is a conventionally held dogma that the genetic basis underlying development conserved in long evolutionary time scale. Ample experiments based on mutational, biochemical, functional, and complementary knockdown/knockout approaches have revealed unexpectedly important role of recently evolved new genes Drosophila. The recent progress genome-wide experimental testing gene effects improvements computational identification (< 40 million years ago, Mya) open door to investigate evolution essentiality with phylogenetically high resolution. These advancements also raised interesting issues techniques concepts related phenotypic effect analyses genes, particularly those originated. Here we reported our these issues, including reproducibility efficiency knockdown experiment difference between RNAi libraries effects. We further analyzed large data from knockdowns 11,354 (~75% Drosophila melanogaster total genes), 702 (~66% species aged < Mya), revealing similarly proportion (~32.2%) essential originated various Sophophora subgenus lineages distant ancestors beyond genus. transcriptional compensation CRISPR knockout were detected for highly similar duplicate copies. Knockout few young analogous functions development. Taken together, provide valuable detection general strong evidence concept quickly viability during