Expression atlas of Selaginella moellendorffii provides insights into the evolution of vasculature, secondary metabolism and roots

Selaginella moellendorffii is a representative of the lycophyte lineage
and is studied to understand the evolution of land plant traits such as
the vasculature, leaves, stems, roots, and secondary metabolism. However,
only few studies investigated about the gene expression and
transcriptional coordination of Selaginella genes, precluding us from
understanding the evolution of 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 provides a unique resource to study the evolution of
genes, gene families, transcriptomes, and functional gene modules in the
Archaeplastida kingdom.