How gene expression can evolve depends on the mechanisms driving gene expression. Gene expression is controlled in different ways in different developmental stages; here we ask whether different developmental stages show different patterns of regulatory evolution. To explore the mode of regulatory evolution, we used the early stages of embryonic development controlled by two different genomes, that of the mother and that of the zygote. During embryogenesis in all animals, initial developmental processes are driven entirely by maternally provided gene products deposited into the oocyte. The zygotic genome is activated later, when developmental control is handed off from maternal gene products to the zygote during the maternal-to-zygotic transition. Using hybrid crosses between sister species of Drosophila (D. simulans, D. sechellia, and D. mauritiana) and transcriptomics, we find that the regulation of maternal transcript deposition and zygotic transcription evolve through different mechanisms. We find that patterns of transcript level inheritance in hybrids, relative to parental species, differ between maternal and zygotic transcripts, and maternal transcript levels are more likely to be conserved. Changes in transcript levels occur predominantly through differences in trans regulation for maternal genes, while changes in zygotic transcription occur through a combination of both cis and trans regulatory changes. Differences in the underlying regulatory landscape in the mother and the zygote are likely the primary determinants for how maternal and zygotic transcripts evolve.

中文翻译：

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果蝇胚胎中母体和合子 mRNA 互补体之间顺式和反式调节的进化差异。


基因表达如何进化取决于驱动基因表达的机制。基因表达在不同的发育阶段以不同的方式受到控制；在这里我们要问的是，不同的发展阶段是否表现出不同的监管演变模式。为了探索调控进化的模式，我们利用了由两个不同基因组（母体基因组和受精卵基因组）控制的胚胎发育的早期阶段。在所有动物的胚胎发生过程中，最初的发育过程完全由母体提供的沉积到卵母细胞中的基因产物驱动。在母体到合子的转变过程中，当发育控制从母体基因产物移交给合子时，合子基因组随后被激活。利用果蝇姐妹物种（ D. simulans、 D. sechellia和D. mauritiana ）之间的杂交和转录组学，我们发现母本转录沉积和合子转录的调节通过不同的机制进化。我们发现，相对于亲本物种，杂种中的转录本水平遗传模式在母本和合子转录本之间有所不同，并且母本转录本水平更有可能保守。转录水平的变化主要通过母体基因反式调节的差异发生，而合子转录的变化通过顺式和反式调节变化的组合发生。母本和受精卵潜在调控环境的差异可能是母本和合子转录本如何进化的主要决定因素。