A de novo transcriptome analysis revealed that photomorphogenic genes are required for carotenoid synthesis in the dark-
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ORIGINAL ARTICLE
A de novo transcriptome analysis revealed that photomorphogenic genes are required for carotenoid synthesis in the dark‑grown carrot taproot Daniela Arias1 · Jonathan Maldonado2 · Herman Silva2 · Claudia Stange1 Received: 31 December 2019 / Accepted: 3 July 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Carotenoids are terpenoid pigments synthesized by all photosynthetic and some non-photosynthetic organisms. In plants, these lipophilic compounds are involved in photosynthesis, photoprotection, and phytohormone synthesis. In plants, carotenoid biosynthesis is induced by several environmental factors such as light including photoreceptors, such as phytochromes (PHYs) and negatively regulated by phytochrome interacting factors (PIFs). Daucus carota (carrot) is one of the few plant species that synthesize and accumulate carotenoids in the storage root that grows in darkness. Contrary to other plants, light inhibits secondary root growth and carotenoid accumulation suggesting the existence of new mechanisms repressed by light that regulate both processes. To identify genes induced by dark and repressed by light that regulate carotenoid synthesis and carrot root development, in this work an RNA-Seq analysis was performed from dark- and light-grown carrot roots. Using this high-throughput sequencing methodology, a de novo transcriptome model with 63,164 contigs was obtained, from which 18,488 were differentially expressed (DEG) between the two experimental conditions. Interestingly, light-regulated genes are preferably expressed in dark-grown roots. Enrichment analysis of GO terms with DEGs genes, validation of the transcriptome model and DEG analysis through qPCR allow us to hypothesize that genes involved in photomorphogenesis and light perception such as PHYA, PHYB, PIF3, PAR1, CRY2, FYH3, FAR1 and COP1 participate in the synthesis of carotenoids and carrot storage root development. Keywords Carrot · De novo transcriptome · Carotenoid biosynthesis · Photomorphogenic genes · Carrot storage root
Introduction Carotenoids are the second most abundant natural pigments worldwide with more than 750 structurally different compounds (Nisar et al. 2015). In photosynthetic tissues, carotenoids accumulate in chloroplasts and participate in Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00438-020-01707-4) contains supplementary material, which is available to authorized users. * Claudia Stange [email protected] 1
Facultad de Ciencias, Centro de Biología Molecular Vegetal, Universidad de Chile, Las Palmeras, 3425 Ñuñoa, Santiago, Chile
Laboratorio de Genómica Funcional & Bioinformática, Facultad de Ciencias Agronómicas, Universidad de Chile, Av. Santa Rosa 11315, 8820808 La Pintana, Santiago, Chile
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photosynthesis, light harvesting and photoprotection (Grotewold 2006; DellaPenna and Pogson 2006; Johnson et al. 2007; Rosas and Stange 2016) and are the essential precursors of the phytohormones abscisic acid (ABA, Walter an
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