Selaginella moellendorffii is a representative of the lycophyte lineage that is studied to understand the evolution of land plant traits such as the vasculature, leaves, stems, roots, and secondary metabolism. However, only a few studies have investigated the expression and transcriptional coordination of Selaginella genes, precluding us from understanding the evolution of the transcriptional programs behind these traits. We present a gene expression atlas comprising all major organs, tissue types, and the diurnal gene expression profiles for S. moellendorffii. We show that the transcriptional gene module responsible for the biosynthesis of lignocellulose evolved in the ancestor of vascular plants and pinpoint the duplication and subfunctionalization events that generated multiple gene modules involved in the biosynthesis of various cell wall types. We demonstrate how secondary metabolism is transcriptionally coordinated and integrated with other cellular pathways. Finally, we identify root-specific genes and show that the evolution of roots did not coincide with an increased appearance of gene families, suggesting that the development of new organs does not coincide with increased fixation of new gene functions. Our updated database at conekt.plant.tools represents a valuable resource for studying the evolution of genes, gene families, transcriptomes, and functional gene modules in the Archaeplastida kingdom.

卷柏（Selaginella moellendorffii）是藻类植物谱系的代表，其研究旨在了解陆地植物性状的演变，例如脉管系统，叶片，茎，根和次生代谢。然而，只有少数研究调查了卷柏基因的表达和转录协调，这使我们无法理解这些特性背后的转录程序的演变。我们提出了一个基因表达图谱，包括所有主要器官，组织类型和S. moellendorffii的昼夜基因表达谱。我们表明负责木质纤维素生物合成的转录基因模块在维管植物的祖先中进化，并指出了重复和亚功能化事件，该事件产生了涉及多种细胞壁类型的生物合成的多个基因模块。我们演示了次级代谢如何在转录上与其他细胞途径协调并整合在一起。最后，我们确定了根特定基因，并表明根的进化与基因家族的出现并不吻合，这表明新器官的发育与新基因功能的固定化并不吻合。我们更新的数据库锥子.plant.tools提供了宝贵的资源，可用于研究基因，基因家族，转录组，