School of Life Sciences, Arizona State University, Tempe, AZ, United States of America.
Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States of America.
PLoS One. 2021 Jun 10;16(6):e0252457. doi: 10.1371/journal.pone.0252457. eCollection 2021.
In diploid cells, the paternal and maternal alleles are, on average, equally expressed. There are exceptions from this: a small number of genes express the maternal or paternal allele copy exclusively. This phenomenon, known as genomic imprinting, is common among eutherian mammals and some plant species; however, genomic imprinting in species with haplodiploid sex determination is not well characterized. Previous work reported no parent-of-origin effects in the hybrids of closely related haplodiploid Nasonia vitripennis and Nasonia giraulti jewel wasps, suggesting a lack of epigenetic reprogramming during embryogenesis in these species. Here, we replicate the gene expression dataset and observations using different individuals and sequencing technology, as well as reproduce these findings using the previously published RNA sequence data following our data analysis strategy. The major difference from the previous dataset is that they used an introgression strain as one of the parents and we found several loci that resisted introgression in that strain. Our results from both datasets demonstrate a species-of-origin effect, rather than a parent-of-origin effect. We present a reproducible workflow that others may use for replicating the results. Overall, we reproduced the original report of no parent-of-origin effects in the haplodiploid Nasonia using the original data with our new processing and analysis pipeline and replicated these results with our newly generated data.
在二倍体细胞中，父本和母本等位基因的表达通常是均等的。但也存在一些例外情况：少数基因只表达母本或父本等位基因的拷贝。这种现象被称为基因组印记，在真兽类哺乳动物和一些植物物种中很常见；然而，在具有单倍二倍体性别决定的物种中，基因组印记的特征并不明显。以前的工作表明，在亲缘关系密切的单倍二倍体烟夜蛾和 Nasonia giraulti 宝石蜂的杂交种中没有亲本来源效应，这表明在这些物种的胚胎发生过程中缺乏表观遗传重编程。在这里，我们使用不同的个体和测序技术复制了基因表达数据集和观察结果，并且使用之前发表的 RNA 序列数据按照我们的数据分析策略重现了这些发现。与之前数据集的主要区别在于，它们使用了一个渐渗品系作为亲本之一，而我们在该品系中发现了几个抵抗渐渗的基因座。我们来自两个数据集的结果表明存在种源效应，而不是亲本来源效应。我们提出了一个可重复的工作流程，其他人可以使用该流程来复制结果。总的来说，我们使用原始数据和我们新的处理和分析管道复制了在单倍二倍体 Nasonia 中没有亲本来源效应的原始报告，并使用我们新生成的数据复制了这些结果。
