Why are there so many opsin genes in fish?

在接下来的五年里，作为我对基因复制和分化的长期研究的一部分，我的目标是回答两个重要的问题：1）为什么鱼有这么多的视蛋白基因？2)视蛋白mRNA转录本丰度是视蛋白丰度的良好代表吗？ 在白天，大多数人都是三色的。我们视网膜中不同的光敏感视锥细胞表达短、中或长波长敏感视蛋白基因。这一功能虽然比大多数哺乳动物都要大，但与鱼类相比就相形见绌了。例如，孔雀鱼有九种，斑马鱼有八种不同的视锥细胞视蛋白。鱼类不仅有大量的视蛋白基因，它们还有巨大的多样性。为什么要这样？我们将从比目鱼，孔雀鱼，棘鱼和斑马鱼收集的数据将使我们能够测试四个假设：i）一个大的视蛋白基因“工具包”提高鱼类的能力，使其视觉与光谱环境的变化相匹配。ii）“视觉视蛋白”具有非眼部作用，特别是在皮肤中，其由大的视蛋白库更好地发挥作用。iii）视网膜中存在区域特化的选择（即，在视网膜的不同部分中表达的不同视蛋白）。四.视蛋白复制和发散增强波长辨别和/或波长敏感性。 这些假设中的三个将通过测量视蛋白转录物（mRNA）丰度来测试。 然而，最近的实验表明，mRNA的差异表达捕获最多40%的蛋白质表达的变化。我将使用两个模型物种（斑马鱼和棘鱼），视蛋白基因和两种新技术，数字液滴PCR和基于多反应监测的质谱法或“MRM MS”来回答我的第二个问题。这项研究将对大量量化基因转录本丰度的科学家非常重要（例如，使用qPCR），假设这些数据与基因功能，即与蛋白质丰度相关。

Over the next five years there are two significant questions I aim to answer as part of my long-term study of gene duplication and divergence: 1) Why do fish have so many opsins genes? 2) Is opsin mRNA transcript abundance a good proxy for opsin protein abundance? By day, most humans are trichromatic. Different light-sensitive cone cells in our retinas express short, medium, or long wavelength-sensitive opsin genes. This repertoire, while larger than that of most mammals, pales in comparison to fish. For example, guppies have nine and zebrafish have eight different cone cell opsins. Not only do fish have lots of opsin genes, they have an enormous diversity. Why? The data we will collect from flatfish, guppies, stickleback and zebrafish will allow us to test four hypotheses: i) A large opsin gene 'toolkit' improves the ability of fish to match their vision to variation in their spectral environment. ii) 'Visual opsins' have non-ocular roles, specifically in the skin, that are better served by a large opsin repertoire. iii) There is selection for regional specialization in the retina (i.e., different opsins expressed in different parts of the retina). iv. Opsin duplication and divergence enhances wavelength discrimination and/or wavelength sensitivity. Three of these hypotheses will be tested by measuring opsin transcript (mRNA) abundance. However, recent experiments suggest that the differential expression of mRNA captures at most 40% of the variation of protein expression. I will use two model species (zebrafish and stickleback), opsin genes, and two new technologies, digital droplet PCR and multi reaction monitoring-based mass spectrophotometry or 'MRM MS' to answer my second question. This research will be of great importance to an enormous number of scientists who quantify gene transcript abundance (e.g., using qPCR) under the assumption that these data are correlated with gene function, that is, with protein abundance.