Fig. 6. The potential molecular mechanisms of mycoheterotrophy in orchids.

a, Initial mycoheterotrophy. The seeds of orchids do not have endosperms and their germination depends on absorbing carbohydrates, such as trehalose, from their associated fungi. Trehalose is a disaccharide in fungi that has similar roles to sucrose in plants. In contrast to other sequenced plant genomes, most orchid genomes have multiple copies of trehalase genes (Supplementary Table 34), which digest a molecule of trehalose into two molecules of glucose (d-1). The seeds develop into protocorms, which keep using the carbohydrates from fungi until they can perform photosynthesis. b, Full mycoheterotrophy. Leaflessness of P. guangdongensis may be related to the loss of most photoreceptor genes and auxin efflux transporters such as PINs, because light signals are essential for leaf initiation and positioning through redistribution of auxin to the incipient primordia. The development of roots also relies on light signals and photosynthesis. In addition, transcription factors involved in root development, such as CPC, TRY and ETC1-like genes, are missing in P. guangdongensis, which may correlate with its rootless phenotype. c, Partial mycoheterotrophy. In contrast to full mycoheterotrophy, partially mycoheterotrophic orchids have similar numbers of photoreceptors and auxin efflux transporters, which are important for the development of leaves, to Pha. equestris and D. catenatum. P. zijinensis has all the transcription factors involved in root development as well as the AGL12 genes. d, Obtaining nutrients from fungi. Fully mycoheterotrophic orchids keep expressing trehalase genes as protocorms to digest trehalose into glucose (Glc), which is further converted into sucrose and transported by SUTs throughout the plant body (d-1). Mycoheterotrophic orchids also have fewer nitrogen and phosphorus transmembrane transporters, such as AMT, NRT2 and PHT1/2, than Pha. equestris and D. catenatum. Furthermore, NIA and NIR genes are missing in the G. elata genome and have low expression in P. guangdongensis, suggesting that these orchids may only obtain nitrogen in the forms of ammonium (${\mathrm{NH}}_4^{+}$) and/or glutamine (Gln) and amino acid (AA) from fungi but cannot absorb nitrate (${\mathrm{NO}}_3^{-}$) from soil (d-2). As a partially mycoheterotrophic orchid, P. zijinensis can perform photosynthesis and obtains trehalose from its associated fungi (d-3).