The lycophyte Selaginella moellendorffii represents early vascular plants and is studied to understand the evolution of higher plant traits such as the vasculature, leaves, stems, roots, and secondary metabolism. However, little is known about the gene expression and transcriptional coordination of Selaginella genes, which precludes us from understanding the evolution of transcriptional programs behind these traits.
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Introduction:The lycophyte Selaginella moellendorffii is an important model organism for plant evolutionary studies and comparative genomics, as it represents lycophytes, a clade of one of the oldest still existing vascular plants on earth. It is characterised by adaxial sporangia, a root system (roots or rhizophores), a vasculature and leaf-like structures with a single vein, called microphylls. S. moellendorffii has a genome size of only about 100 Mbp, which is one of the smallest reported plant genomes 1 . Lycophytes appeared about 400 Myr ago during the Silurian period and were particularly abundant during the Devonian to mid-Carboniferous period, peaking around 310 Myr ago in Euramerican coal swamps 2 . During the Carboniferous period, many lycophytes were tall, fast-growing trees, and their remains now exist as coal. As 70% of the biomass responsible for the Bashkirian and Moscovian coal formations in Euramerica came from lycophytes 3 , they are an important source of fossil fuels. Despite their decreasing abundance at the end of the Carboniferous period, the impact of lycophytes on the climate was significant, as their role as carbon sinks most likely contributed to the dramatic decline in atmospheric CO 2 4 .Lycophytes produce spores for reproduction that are dispersed by wind and water. One means to increase spore dispersal and outcompete neighbors in light capture, and thus facilitate the colonization of land, is to increase the height of the sporophyte. This required the evolution of specialized vasculature (xylem and phloem) for the transport of nutrients, water, and various signaling molecules and the reinforcement of cell walls by lignification 5 . This lignification, in turn, was associated with the evolution of the phenylpropanoid metabolic pathway to synthesize and polymerize the heterogeneous aromatic lignin in the xylem cell walls 6 .To provide water and structural support to the larger sporophytes, land plants also evolved roots. Despite their morphological and evolutionary diversity, all roots have the capacity to acquire and transport water and nutrients, grow in a downward direction, and form branch roots, and they all possess a root cap (set of terminal protective cells), a root apical meristem (a self-sustaining stem cell population) and a radial organization of cell types (from outermost epidermis tissue to innermost vascular tissue). Root morphology in extant plants and fossil records...