Evolutionary Genomics of Long Intergenic Non-coding RNAs (lincRNAs) in Drosophila

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The importance of non-coding RNAs is becoming increasingly apparent for a wide range of biological processes, but they are still a relatively new topic, and many aspects of their function and evolution remain poorly understood. Long intergenic non-coding (linc) RNAs are perhaps least understood among the non coding RNAs, yet they are known to play roles in dosage compensation, embryonic development, stem cell maintenance and differentiation, and epigenetic regulation of expression. The proposed work is focused on lincRNAs across the species Drosophila pseudoobscura and Drosophila persimilis. RNA-seq will be used to catalog changes in lincRNA expression during development, and these data will be used to evaluate divergence in lincRNA sequence and expression patterns.The specific aims are the following: 1-Identify the lincRNAs in the D. pseudoobscura transcriptome using RNAseq data; 2-Characterize patterns of lincRNA expression in D. pseudoobscura and D. persimilis, with a focus on those lincRNAs that are differentially expressed; 3-Compare levels of intraspecific polymorphism to levels of interspecific divergence using expression and sequence data, and complare patterns for lincRNAs to patterns of protein-coding genes.Broader Impacts include a summer research experience for high school students and teachers. Participant selection will be done in collaboration with minority high schools in the area, and will be facilitated by a Math and Science Partnership grant to the University System of Maryland. Undergraduate research opportunities will also be provided, and recruitment will be done partly through the University of Maryland and partly through the Smithsonian Tropical Research Institute in Panama.