Adaptive evolution of carnivory in Nepenthes pitcher plants: a comparative transcriptomics and proteomics perspective

While trait diversity associated with evolutionary radiations is easily recognized, their function and adaptive relevance often remain elusive. Here we study the evolution of carnivory genes in Nepenthes, an iconic radiation of carnivorous pitcher plants. We investigate 13 species chosen to represent the diversity of nutrient acquisition strategies, geography and climates covered by the genus. Using a combination of proteomics and transcriptomics, we discovered that Nepenthes secrete hundreds of enzymes and antimicrobial proteins into their digestive fluids. Further genes related to plant carnivory were uncovered by analyses of gene expression changes induced by experimental feeding of starved Nepenthes traps. Feeding status appears to affect the relative abundance of nearly 35% of all expressed genes, and may be accompanied by a strong physiological shift away from photosynthesis towards heterotrophy, proteolysis, and protein synthesis. Among the many thousand genes showing signatures of adaptive evolution in sequence or expression level within the Nepenthes radiation, the secreted pitcher fluid proteins and the carnivory-related genes were over-represented. A bias towards carnivory genes, and towards trap-expressed genes versus leaf-expressed genes, was also observed among the genes differing in expression in a young pair of sister species. Together, our results suggest that the molecular basis of the carnivorous syndrome was disproportionally targeted by positive selection during the Nepenthes radiation. This study demonstrates how the evolutionary relevance of putative key traits can be tested at the level of underlying genes.