Tissue-specific expression profiles and positive selection analysis in the tree swallow (Tachycineta bicolor) using a de novo transcriptome assembly

Abstract

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, transcriptomic resources are scarce. To further advance the utility of this system for biologists across disciplines, 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 207,739 transcripts, which we aligned to 14,717 high confidence protein-coding genes. We then characterized each tissue with regard to its unique genes and processes 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 advance our understanding of fundamental questions in evolutionary and organismal biology.

Design, challenges, and the potential of transcriptomics to understand social behavior

“…Another possibility in such a situation is to assemble a transcriptome de novo without the need to rely on genetic information from a related species as has been demonstrated in other studies ( Vijay et al. 2013 ; Bentz et al. 2019b ).…”

Influence of heat stress on reference genes stability in heart and liver of two chickens genotypes

“…In addition, it is important to highlight that there are genes with tissue-specific expressions, which are under specific regulation, as reported by Bentz et al [41], who found differential genes expression among tissues in swallows. For example, muscle-specific genes were associated with muscle contraction, and spleen-specific genes with immune response.…”

Computational Methods for Prediction of Human Protein-Phenotype Associations: A Review

“…Tissue-selective gene expression is an important mechanism by which the same genome can generate differentiated phenotypes among tissues (Bentz et al 2019). Exploring the pathologic consequences of human genes in specific tissues is typically more essential for insights into disease diagnostics and therapeutics (Barbeira et al 2018;Hekselman and Yeger-Lotem 2020).…”