Extended Data Fig. 6: The regulatory network involved in Arabidopsis leaf initiation and development, and P. guangdongensis and G. elata contraction (loss) genes of involved in leaf initiation and development.

The regulatory network was modified according to three review papers^6,7,9. The transition of cells in the shoot apical meristem (SAM) from a pluripotent fate to a determinate fate is necessary for plant leaf initiation. SAM is maintained by the class I KNOX homeodomain transcription factor through the activation of cytokinin signalling and repression of asymmetric leaves1 (AS1) and AS2, which are involved in organogenesis. The leaf organ initiates from the sites where the expression of KNOX is downregulated and auxin maxima are established via polar localization of PIN1, the auxin efflux carrier. Light is necessary for leaf initiation. Without light, polar localization of PIN1 is lost, and leaf production ceases⁷. The PLETHORA (PLT) transcription factors PLT3, PLT5, and PLT7, have been reported to be required for proper expression of PIN1¹⁰ and YUC1/4¹¹. AS1 and AS2 form a complex and repress the expression of Yabby, KAN, and miR165/166. Yabby gene expression is essential for the switch of the SAM program to the leaf-specific program⁹. In addition, Yabby interacts with LUG to promote the expression of Class II TCP genes which are involved in lamina development. The AS1 and CUC genes are regulated by Class II TCPs to control lamina development⁷. The Arabidopsis genes regulating leaf initiation and development in this figure were used as queries to identify orthologous genes in the genomes of P. guangdongensis, P. zijinensis, G. elata, A. shenzhenica, D. catenatum, and Pha. equestris (Supplementary Table 30). The genes indicated in red are lost or contracted in P. guangdongensis and G. elata, whereas those in blue are lost in G. elata. ARF: auxin-responsive factor; CUC: CUP-SHAPED COTYLEDON; KAN: KANADI; KNOX: KNOT-TED-like homeobox (STM, BP/KNAT1, KNAT2, KNAT6); LUG: LEUNIG; PIN1: PIN-FORMED 1; YUC: YUCCA.