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A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

Massimo Iorizzo, Shelby Ellison, Douglas Senalik, Peng Zeng, Pimchanok Satapoomin, Jiaying Huang, Megan Bowman, Marina Iovene, Walter Sanseverino, Pablo Cavagnaro, Mehtap Yildiz, Alicja Macko-Podgórni, Emilia Moranska, Ewa Grzebelus, Dariusz Grzebelus, Hamid Ashrafi, Zhijun Zheng, Shifeng Cheng, David Spooner, Allen Van Deynze, Philipp Simon
Nature genetics 2016 v.48 no.6 pp. 657-666
Daucus carota, biosynthesis, carotenes, carrots, color, diet, evolution, flavor, flowering, gene overexpression, genes, genome assembly, loci, nucleotide sequences, transcriptome
We report a chromosome-scale assembly and analysis of the Daucus carota genome, an important source of provitamin A in the human diet and the first sequenced genome among members of the Euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Euasterid I clade, clarifying the evolutionary scenario before and after the radiation of the two main Asterid clades. Large- and small-scale lineage-specific duplications contributed to the expansion of gene families including those with roles in flowering time, defense response, flavor, and pigment accumulation. We demonstrated that the primary genetic locus underlying carotenoid accumulation in the carrot root, that is the foundation of the orange color of modern carrots, is not directly controlled at the biosynthetic level. A candidate gene was identified, and transcriptome data suggested that high carotenoid accumulation involves overexpression of several light-induced genes operating in photosystem development and function. These results provide a resource for crop improvement, for comparative genome analysis in the Asterid lineage, and for the discovery of novel genetic mechanisms regulating carotene biosynthesis and accumulation in plants.