Functional Dimorphism Analysis of Sporotrophophyll Leaves and Nest Leaves of Drynaria roosii with Their Connected Rhizomes Based on Multi-Omics Analysis

<b>Background</b>: <i>Drynaria roosii</i> is a typically epiphytic fern characterized by the intriguing phenomenon that nest leaves (NLs) and sporotrophophyll leaves (SLs) are metatypical, with NLs persisting in a hardened form. Few reports have concentrated on the physiological characteristics of these two leaf types and the metabolite differences in their associated rhizomes (NRs and ORs). <b>Methods</b>: A comparative analysis of the two leaf types and their connected rhizomes was conducted based on photosynthetic parameters, leaf ultrastructure, Illumina HiSeqTM 2000 transcriptome sequencing, widely targeted metabolomics, and the spatial distribution of flavonoid components. <b>Results</b>: The results indicated that SLs exhibited significant advantages in photosynthetic parameters, with a net photosynthetic rate exceeding that of NLs by 228%. A total of 7236 differentially expressed genes (DEGs) were identified between SLs and NLs, with the majority of DEGs involved in developmental processes (491 DEGs), stress response (420 DEGs), and responses to abiotic stimuli (337 DEGs). A total of 1409 components were detected and authenticated, revealing that ORs contained relatively high levels of flavonoids, quinones, tannins, alkaloids, terpenoids, and vitamins. Furthermore, the spatial distribution of flavonoid components indicated a dispersive distribution in both NRs and ORs. <b>Conclusions</b>: This comprehensive study of NLs and SLs, along with their connected rhizomes, provides vital reference for scientific cultivation management and rational harvesting prior to medicinal use.