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Alternative pre-mRNA splicing (“AS”) greatly expands proteome diversity, but little is known about the evolutionary landscape of AS in  Drosophila  and how it differs between embryonic and adult stages or males and females. Here we study the transcriptomes from several tissues and developmental stages in males and females from four species across the  Drosophila  genus. We find that 20–37% of multi-exon genes are alternatively spliced. While males generally express a larger number of genes, AS is more prevalent in females, suggesting that the sexes adopt different expression strategies for their specialized function. While the number of total genes expressed increases during early embryonic development, the proportion of expressed genes that are alternatively spliced is highest in the very early embryo, before the onset of zygotic transcription. This indicates that females deposit a diversity of isoforms into the egg, consistent with abundant AS found in ovary. Cluster analysis by gene expression (“GE”) levels shows mostly stage-specific clustering in embryonic samples, and tissue-specific clustering in adult tissues. Clustering embryonic stages and adult tissues based on AS profiles results in stronger species-specific clustering, suggesting that diversification of splicing contributes to lineage-specific evolution in  Drosophila . Most sex-biased AS found in flies is due to AS in gonads, with little sex-specific splicing in somatic tissues.

Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages