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ABSTRACT: Multi-omics responses in tree swallow (Tachycineta bicolor) nestlings from the Maumee Area of Concern, Maumee River, Ohio

PROVIDER: PRJNA857430 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR20073509_1.fastq.gz	Fastqsanger.gz
	SRR20073509_2.fastq.gz	Fastqsanger.gz
	SRR20073510_1.fastq.gz	Fastqsanger.gz
	SRR20073510_2.fastq.gz	Fastqsanger.gz
	SRR20073511_1.fastq.gz	Fastqsanger.gz

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Tachycineta bicolor isolate:S2

Project description:Multi-omics responses in tree swallow (Tachycineta bicolor) nestlings from the Maumee Area of Concern, Maumee River, Ohio

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De novo transcriptome assembly of the tree swallow (Tachycineta bicolor): tissue-specific expression profiles and positive selection analysis

Project description: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.

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Project description:A female's behavioral and physiological response to her environment can have lasting effects on the development of her offspring. This type of non-genetic inheritance (or maternal effect) occurs across taxa but is particularly well-studied in birds due to the relative ease of measuring maternal hormones in externally developing eggs. For example, females breeding in areas of high social competition allocate more of the hormone testosterone (T) to their egg yolks. These high-T offspring exhibit numerous phenotypic changes, including faster juvenile growth and enhanced aggression well into adulthood, which are potentially beneficial traits in high-competition areas. Thus, females may be able to communicate the current social environment to their offspring and prepare them for adverse conditions. Yet, the proximate mechanisms underlying how maternal hormones affect offspring are largely ignored, impairing our understanding of an ecologically important source of phenotypic plasticity. Here, we explored the effects of the maternal social environment on yolk T allocation and genome-wide patterns of neural gene expression in male and female tree swallow (Tachycineta bicolor) embryos. We observed a population of free-living tree swallows breeding at sites with variable breeding densities. We performed behavioral observations to record the rate of physical aggression at these sites, which was significantly higher at high density sites. We collected eggs at two developmental timepoints: the day laid to measure maternally derived T concentrations and embryonic day 11 (ED11) to measure gene expression patterns in whole brains using RNA-seq. We took a genome-wide approach to help clarify the potentially diverse mechanisms regulated by early T exposure across variable social environments. We additionally molecularly sexed the embryos to explore sex-specific effects.

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Project description:De novo transcriptome assembly of the tree swallow (Tachycineta bicolor): tissue-specific expression profiles and positive selection analysis

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