Tissue-specific expression profiles and positive selection analysis in the tree swallow (Tachycineta bicolor) using a de novo transcriptome assembly
Tissue-specific expression profiles and positive selection analysis in the tree swallow (Tachycineta bicolor) using a de novo transcriptome assembly
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DOI：
10.1038/s41598-019-52312-4
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发表时间：
2019-11-01
影响因子：
4.6
通讯作者：
Rosvall, Kimberly A.
中科院分区：
文献类型：
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作者：
Bentz, Alexandra B.;Thomas, Gregg W. C.;Rosvall, Kimberly A.
树燕（Tachycineta bicolor）是北美最常被研究的野生鸟类之一。他们已经推进了许多研究领域，包括生命史，生理学和生物体对全球变化的反应;然而，转录组资源是稀缺的。为了进一步推进该系统的跨学科生物学家的效用，我们使用从繁殖雌性收集的六种组织（脑，血液，卵巢，脾脏，肝脏和肌肉）生成了树燕的转录组。我们从头组装了207，739个转录本，我们将其与14，717个高置信度的蛋白质编码基因进行了比对。然后，我们描述了每个组织的独特基因和过程，并将此转录组应用于进化生物学和内分泌学中的两个基本问题。首先，我们分析了3，015个单拷贝直系同源物，并在树燕谱系中确定了46个正选择基因，包括那些与该物种适应性相关的基因。其次，我们分析了性类固醇生成和加工相关基因的组织特异性表达模式。能够合成这些行为相关激素的酶在很大程度上限于卵巢，而类固醇结合基因几乎在所有其他组织中发现，突出了性类固醇介导的性状的局部调节的潜力。这些分析为自由生活的雌鸟的表型变异的潜在来源提供了新的见解，并促进了我们对进化和生物学基本问题的理解。
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.