Gemma Johnson

Mentors: Josh Shapiro & Greg Davis



Analysis of RNA-seq data from sexual and asexual fated Acyrthosiphon pisum embryos


Acyrthosiphon pisum (the pea aphid) exhibits an interesting phenotypic plasticity: when exposed to short nights mothers produce asexual embryos, and when exposed to long nights they produce sexual embryos. The nature of the molecular switch that causes the embryos to develop as sexual or asexual is not well characterized, although juvenile hormone (JH) has been implicated in the process. Research this summer will involve analyzing transcriptome data sequenced from A. pisum embryos with different fates, sexual or asexual, at three different stages of development: before specification, during specification, and during differentiation. There are 5 biological replicates of each sample. The RNA was collected by Emily Spica `15, a past student in Greg Davis’ lab, and sequenced by Ambry Genetics. Various computational tools, such as the ballgown software package, will be used to analyze the RNA-seq data. So far, ballgown has been used to test for differential expression within the different stages and across a time series of asexually or sexually fated embryos. The next step is to utilize a more complicated model and test the whole set of samples for differential expression. Alternative methods of resolving transcript splicing and how these methods affect the overall results will also be explored. The overall goal is to find genes that are differentially expressed between asexually and sexually fated embryos. This would then lead to the identification of candidate genes for a further investigation into the nature of the embryonic switch that specifies whether an embryo will be sexual or asexual. Differential expression is expected in the stage where the fates of the embryos are being specified, and in genes that regulate or are downstream targets of JH.