Several plant lineages have wholly or partly lost their photosynthetic ability and instead rely on carbon acquired from soil fungal associations, to varying degrees. One manifestation of this mycoheterotrophic lifestyle is in the gametophytes of several fern and lycophyte groups. In contrast to their photosynthetic sporophyte generation, these gametophytes rely solely on fungal carbon for nutrition throughout their life. Thus, their independently living haploid and diploid generations effectively switch trophically, a form of initial mycoheterotrophy in which only the haploid stage is fully mycoheterotrophic. Initial mycoheterotrophy has arisen independently multiple times across ferns and lycophytes and critical genetic changes accompanying this shift have yet to be explored. We are generating transcriptomes from photosynthetic sporophytes and mycoheterotrophic gametophytes of ferns (Psilotaceae, Ophioglossaceae, Gleicheniaceae, Schizaeaceae) and lycophytes (Lycopodiaceae). We will then contrast gene expression between generations of the same species and between mycoheterotrophic gametophytes and those of completely photosynthetic taxa.  We will use these datasets to better understand: (1) the genetic and molecular changes that accompany trophic switching between generations within species, and (2) the evolution of mycoheterotrophy in fern and lycophyte lineages, by comparing changes in gene expression among sporophytes and gametophytes with different or similar trophic status. Our study will provide insights into the evolution of mycoheterotrophy, the genetic basis of trophic switching across generations, and nuclear genome evolution in relation to plant-fungi interactions.