From the T2T cotton genome to a tripartite regulatory module governing embryo folding

Human civilization relies heavily on the nutritional resources provided either directly or indirectly by angiosperm seeds and their associated structures. Angiosperm embryos with storage cotyledons can be classified into four distinct foliate axile types (Martin, 1946). Cotton, as an economically vital crop that belongs to a monophyletic clade including Gossypium and 8 other genera with over 100 species (Huang et al., 2021), is distinguished by its complex folded foliate axile 3-type embryos (Figure 1A). These embryos are among the most fully developed and intricate of any angiosperm, with the complex folding significantly increasing the surface area, which, in turn, enhances the storage capacity for nutritional resources (Fryxell, 1978). This complex structure is closely tied to the evolution of seed germination and dormancy by improving the plant's ability to adapt to environmental conditions. However, the morphogenetic mechanisms and developmental process of the complex embryonic cotyledons remain unexplored. Since the publication of the Gossypium raimondii genome (one of the two ancestral genomes made of the allotetraploid cotton) in 2012 (Paterson et al., 2012; Wang et al., 2012), substantial progress has been achieved in cotton genomics, fueling functional genomic research and providing insights into the resolution of complex traits (Huang et al., 2021; Li et al., 2023; Lin et al., 2023).Figure 1Shown are cotton embryos with complex folded cotyledons(A) and the siRNA-based tripartite regulatory module(B) responsible for complex embryo folding.