A novel exome probe set captures phototransduction genes across birds (Aves) enabling efficient analysis of vision evolution
A novel exome probe set captures phototransduction genes across birds (Aves) enabling efficient analysis of vision evolution
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DOI：
10.1111/1755-0998.13496
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发表时间：
2021-10
影响因子：
7.7
通讯作者：
Noor D. White;Zachary A. Batz;E. Braun;M. Braun;K. Carleton;R. Kimball;A. Swaroop
中科院分区：
文献类型：
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作者：
Noor D. White;Zachary A. Batz;E. Braun;M. Braun;K. Carleton;R. Kimball;A. Swaroop
鸟类视觉表型的多样性为一般研究性状多样性的机制，特别是脊椎动物的视觉进化提供了一个框架。以往的研究主要集中在视蛋白上，但要全面了解视觉适应，必须研究完整的光转导级联反应(PTC)。在这里，我们开发了一套探针，捕捉代表PTC和其他光反应的46个基因的外显子区域。对于一个物种子集，我们直接比较了我们的探针集和低覆盖率全基因组测序(WGS)之间的基因捕获，并讨论了在这些方法之间选择的考虑因素。最后，我们开发了一种独特的策略，通过使用“诱饵”参考序列来避免嵌合组装。我们使用探针组成功地捕获了14目46个物种的目标外显子的平均%，并使用WGS数据进行了类似的回收。与WGS或转录本相比，我们的探针组：(1)通过有效地捕获视觉基因来减少测序要求，(2)通过限制所需的组装和否定注释来使用更简单的生物信息学管道，以及(3)消除对新鲜组织的需求，使研究人员能够利用现有的博物馆藏品。然后，我们利用我们的视觉外显子组数据，在两种进化场景中确定了肯定选择的基因-夜间鸟类夜间视觉的进化和山顶蜂科(Pipridae)特有的高速视觉的进化。我们发现在这两种情况下SLC24A1的平行正选择，暗示了杆反应动力学的改变，这可以改善在暗光条件下的颜色辨别和/或促进更高的时间分辨率。
The diversity of avian visual phenotypes provides a framework for studying mechanisms of trait diversification generally, and the evolution of vertebrate vision, specifically. Previous research has focused on opsins, but to fully understand visual adaptation, we must study the complete phototransduction cascade (PTC). Here, we developed a probe set that captures exonic regions of 46 genes representing the PTC and other light responses. For a subset of species, we directly compared gene capture between our probe set and low‐coverage whole genome sequencing (WGS), and we discuss considerations for choosing between these methods. Finally, we developed a unique strategy to avoid chimeric assembly by using “decoy” reference sequences. We successfully captured an average of 64% of our targeted exome in 46 species across 14 orders using the probe set and had similar recovery using the WGS data. Compared to WGS or transcriptomes, our probe set: (1) reduces sequencing requirements by efficiently capturing vision genes, (2) employs a simpler bioinformatic pipeline by limiting required assembly and negating annotation, and (3) eliminates the need for fresh tissues, enabling researchers to leverage existing museum collections. We then utilized our vision exome data to identify positively selected genes in two evolutionary scenarios—evolution of night vision in nocturnal birds and evolution of high‐speed vision specific to manakins (Pipridae). We found parallel positive selection of SLC24A1 in both scenarios, implicating the alteration of rod response kinetics, which could improve color discrimination in dim light conditions and/or facilitate higher temporal resolution.