Phytochrome interacting factors in tomato: diversity, evolutionary history and expres-sion profiling during different developmental processes.

Light signals are fundamental for plant physiology, providing not only energy for photosynthesis, but also environmental cues for the maintenance of daily rhythms and developmental progression through the life cycle. Phytochrome-interacting factors (PIFs) are basic helix-loop-helix (bHLH) transcription factors that play a key role in light signal transduction being part of the regulatory network of a wide range of developmental processes. After germination, PIF proteins accumulate in the dark inducing hypocotyl elongation and inhibiting chlorophyll biosynthesis and chloroplast development. When exposed to light, as PIF levels decrease, seedlings turn green and photomorphogenic growth begins. In adult plants, PIFs induce nocturnal daily growth and regulate dark-induced leaf senescence, activating many senescence associated genes and leading to chlorophyll breakdown and plastid degradation. Chloroplast maintenance in source leaves and chloroplast to chromoplast transition during fruit ripening are important to determine crop yield and quality of fleshy fruits. In this context and considering the poorly available knowledge about PIF genes in tomato, we performed a comprehensive characterization of this gene family in S. lycopersicum. In particular, we identified eight PIF loci in the tomato genome. The phylogenetic and evolutionary analysis allowed us to reconstruct the evolutionary history of PIF genes in S. lycopersicum and closely related Solanaceae species, the wild tomato S. pennellii and S. tuberosum. To evaluate the functional diversity of tomato PIF genes, we further explored the transcriptional profile in different physiological contexts, such as deetiolation, dark-induced senescence, daily cycle and fruit ripening. Interestingly, PIF genes displayed oscillation in the mRNA accumulation pattern at least along one of the analyzed experimental conditions and the expression profiles identified suggest that they have undergone functional specification.