Integrative analysis of young genes, positively selected genes and lncRNAs in the development of Drosophila melanogaster.

He-Qun Liu,David M Irwin,Dong-Dong Wu,Yan Li,Ya-Ping Zhang

doi:10.1186/s12862-014-0241-9

Abstract

BackgroundYoung genes and genes under positive selection commonly contribute to adaptive phenotypic evolution. Early developmental stages are very important for establishing phenotypes, which might be helpful for studying the evolutionary patterns of these rapidly evolving genes.ResultsHere, we performed a weighted gene co-expression network analysis to identify modules of co-expressed genes at different stages of Drosophila melanogaster development. We found that young genes, including duplicated, orphan, and young lncRNA genes, are significantly enriched among modules associated with specific developmental stages. In addition, genes undergoing rapid amino acid sequence evolution driven by positive selection showed a similar proportion of essentiality with other genes, and enrichment in modules for specific developmental stages.ConclusionsOur integrative analysis revealed important roles for the origin of new genes and rapid amino acid sequence evolution in development that may account for specific phenotype evolution in Drosophila melanogaster.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-014-0241-9) contains supplementary material, which is available to authorized users.

Highlights

Young genes and genes under positive selection commonly contribute to adaptive phenotypic evolution
Based on an analysis of gene co-expression networks at different developmental stages, we describe important roles for new genes, and rapid amino acid sequence evolution in genes, in development that might be responsible for specific aspects of phenotypic evolution in Drosophila melanogaster
We found that the expression of new genes, including young protein coding and lncRNA genes, are not randomly distributed during early development, and is significantly enriched in modules that correlate with specific developmental stages

Summary

Introduction

Young genes and genes under positive selection commonly contribute to adaptive phenotypic evolution. Developmental stages are very important for establishing phenotypes, which might be helpful for studying the evolutionary patterns of these rapidly evolving genes. A pioneering study by Chen et al (2010) found that many new genes rapidly evolve to gain essential functions in Drosophila, since knockdown experiments of many of these new genes by RNA interference (RNAi) leads to lethality at various development stages. A functional association between new genes and newly evolved brain structure was observed in humans [22,23] and Drosophila [24]. In the human genome many new genes appear to have been recruited to function in the development of the brain [18,22,23,25]

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