GSE126210
De novo transcriptome assembly of the tree swallow (Tachycineta bicolor): tissue-specific expression profiles and positive selection analysis
Tree swallows (Tachycineta bicolor) are one of the most commonly studied wild birds in North America. They have advanced numerous research areas, including life history, physiology, and organismal responses to global change; however, molecular resources are scarce. Thus, we generated a transcriptome for the tree swallow using six tissues (brain, blood, ovary, spleen, liver, and muscle) collected from breeding females. We de novo assembled 207,747 transcripts, which we aligned to 14,717 protein-coding genes. We then characterized tissue-specific expression profiles and applied this transcriptome to two fundamental questions in evolutionary biology and endocrinology. First, we analyzed 3,015 single-copy orthologs and identified 46 genes under positive selection in the tree swallow lineage, including those with putative links to adaptations in this species. Second, we analyzed tissue-specific expression patterns of genes involved in sex steroidogenesis and processing. Enzymes capable of synthesizing these behaviorally relevant hormones were largely limited to the ovary, whereas steroid binding genes were found in nearly all other tissues, highlighting the potential for local regulation of sex steroid-mediated traits. These analyses provide new insights into potential sources of phenotypic variation in a free-living female bird, and in doing so, further advance the utility of this system for biologists across disciplines. Overall design: 6 tissues (blood, liver, spleen, brain, ovary, and muscle) were collected from 2 female tree swallows and total RNA was prepared into equimolar pools for each tissue which were run on both Nextseq and Miseq platforms