New gene evolution with subcellular expression patterns detected in PacBio-sequenced genomes of Drosophila genus

Abstract

Previous studies described gene age distributions in the focal species of Drosophila melanogaster. Using third-generation PacBio technology to sequence Drosophila species we investigated gene age distribution in the two subgenera of Drosophila. Our work resulted in several discoveries. First, our data detected abundant new genes in entire Drosophila genus. Second, in analysis of subcellular expression, we found that new genes tend to secret into extracellular matrix and are involved in regulation, environmental adaption, and reproductive functions. We also found that extracellular localization for new genes provides a possible environment to promote their fast evolution. Third, old genes tend to be enriched in mitochondrion and the plasma membrane compared with young genes which may support the endosymbiotic theory that mitochondria originate from bacteria that once lived in primitive eukaryotic cells. Fourth, as gene age becomes older the subcellular compartments in which their products reside broadens suggesting that the evolution of new genes in subcellular location drives functional evolution and diversity in Drosophila species. Additionally, based on the analysis of RNA-Seq of two D. melanogaster populations, we determined a universal paradigm of "from specific to constitutive" expression pattern during the evolutionary process of new genes.