Cell cycle plays an important role in plant growth and development. Synchronization of cell cycle will help us to elucidate the molecular mechanisms regulating cell cycle and further understand the cell growth and development for various purposes, including crop improvement. However, there are few reports on cell cycle synchronization and its application on transcriptome analysis. In this study, we first developed a cell cycle synchronization technology using flow cytometry technology; then, we deeply sequenced the synchronized cells for studying the gene expression profiling during cell cycle, using cotton as an example, one of the most important fiber and oil crops. Through GO and KEGG enrichment analysis, we obtained some important genes related to cell cycle, including genes associated with hormone and MAPK signal transduction pathways. Our results also showed that tubulin family plays an important role in the cell cycle. This study revealed the differences of gene expression in different cell cycles in cotton for the first time. This study lays a foundation for in-depth understanding of the molecular mechanism and interaction network during cell cycle.

细胞周期在植物生长发育中起着重要作用。细胞周期的同步将有助于我们阐明调节细胞周期的分子机制，并进一步了解细胞生长和发育用于各种目的，包括作物改良。然而，关于细胞周期同步及其在转录组分析中应用的报道却很少。在这项研究中，我们首先开发了一种利用流式细胞仪技术的细胞周期同步技术；然后，我们对同步细胞进行了深度测序，以研究细胞周期中的基因表达谱，以棉花为例，棉花是最重要的纤维和油料作物之一。通过GO和KEGG富集分析，我们获得了一些与细胞周期相关的重要基因，包括与激素和MAPK信号转导通路相关的基因。我们的结果还表明，微管蛋白家族在细胞周期中起着重要作用。该研究首次揭示了棉花不同细胞周期基因表达的差异。本研究为深入了解细胞周期过程中的分子机制和相互作用网络奠定了基础。