Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America.
Current address: Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America.
PLoS Genet. 2023 Jan 23;19(1):e1010607. doi: 10.1371/journal.pgen.1010607. eCollection 2023 Jan.
With detailed data on gene expression accessible from an increasingly broad array of species, we can test the extent to which our developmental genetic knowledge from model organisms predicts expression patterns and variation across species. But to know when differences in gene expression across species are significant, we first need to know how much evolutionary variation in gene expression we expect to observe. Here we provide an answer by analyzing RNAseq data across twelve species of Hawaiian Drosophilidae flies, focusing on gene expression differences between the ovary and other tissues. We show that over evolutionary time, there exists a cohort of ovary specific genes that is stable and that largely corresponds to described expression patterns from laboratory model Drosophila species. Our results also provide a demonstration of the prediction that, as phylogenetic distance increases, variation between species overwhelms variation between tissue types. Using ancestral state reconstruction of expression, we describe the distribution of evolutionary changes in tissue-biased expression, and use this to identify gains and losses of ovary-biased expression across these twelve species. We then use this distribution to calculate the evolutionary correlation in expression changes between genes, and demonstrate that genes with known interactions in D. melanogaster are significantly more correlated in their evolution than genes with no or unknown interactions. Finally, we use this correlation matrix to infer new networks of genes that share evolutionary trajectories, and we present these results as a dataset of new testable hypotheses about genetic roles and interactions in the function and evolution of the Drosophila ovary.
随着越来越多的物种的基因表达详细数据可供使用，我们可以测试从模式生物获得的发育遗传学知识在多大程度上可以预测物种间的表达模式和变化。但是，要知道物种间基因表达的差异是否显著，我们首先需要知道在基因表达方面，我们预计会观察到多少进化变异。在这里，我们通过分析 12 种夏威夷果蝇科的 RNAseq 数据来回答这个问题，重点研究卵巢和其他组织之间的基因表达差异。我们表明，在进化过程中，存在一组稳定的卵巢特异性基因，这些基因在很大程度上与实验室模式果蝇物种描述的表达模式相对应。我们的研究结果还提供了一个预测的例证，即随着系统发育距离的增加，物种间的变异会超过组织类型间的变异。我们通过表达的祖先状态重建来描述组织偏倚表达的进化变化分布，并利用该分布来识别这 12 个物种中卵巢偏倚表达的增益和损失。然后，我们使用这个分布来计算基因之间表达变化的进化相关性，并证明在 D. melanogaster 中已知相互作用的基因在进化过程中的相关性显著高于没有相互作用或未知相互作用的基因。最后，我们使用这个相关矩阵来推断具有相似进化轨迹的基因的新网络，并将这些结果作为一个新的可测试假设数据集，用于研究果蝇卵巢的功能和进化中的遗传作用和相互作用。
