title: A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution.
abstract: We report a high-quality chromosome-scale assembly and analysis of the carrot (Daucus carota) genome, the first sequenced genome to include a comparative evolutionary analysis among members of the euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Asterales order, clarifying the evolutionary scenario before and after radiation of the two main asterid clades. Large- and small-scale lineage-specific duplications have contributed to the expansion of gene families, including those with roles in flowering time, defense response, flavor, and pigment accumulation. We identified a candidate gene, DCAR_032551, that conditions carotenoid accumulation (Y) in carrot taproot and is coexpressed with several isoprenoid biosynthetic genes. The primary mechanism regulating carotenoid accumulation in carrot taproot is not at the biosynthetic level. We hypothesize that DCAR_032551 regulates upstream photosystem development and functional processes, including photomorphogenesis and root de-etiolation.
authors.affiliation: Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin, USA.
authors.forename: Massimo
authors.initials: M
authors.lastname: Iorizzo
authors.affiliation: Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin, USA.
authors.forename: Shelby
authors.initials: S
authors.lastname: Ellison
authors.affiliation: Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin, USA.|Vegetable Crops Research Unit, US Department of Agriculture-Agricultural Research Service, Madison, Wisconsin, USA.
authors.forename: Douglas
authors.identifier: 0000-0001-8526-0554
authors.initials: D
authors.lastname: Senalik
authors.affiliation: Beijing Genomics Institute-Shenzhen, Shenzhen, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Zeng
authors.affiliation: Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin, USA.
authors.forename: Pimchanok
authors.initials: P
authors.lastname: Satapoomin
authors.affiliation: Beijing Genomics Institute-Shenzhen, Shenzhen, China.
authors.forename: Jiaying
authors.initials: J
authors.lastname: Huang
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA.
authors.forename: Megan
authors.initials: M
authors.lastname: Bowman
authors.affiliation: Institute of Biosciences and Bioresources, National Research Council, Bari, Italy.
authors.forename: Marina
authors.initials: M
authors.lastname: Iovene
authors.affiliation: Sequentia Biotech, Bellaterra, Barcelona, Spain.
authors.forename: Walter
authors.initials: W
authors.lastname: Sanseverino
authors.affiliation: National Scientific and Technical Research Council (CONICET), Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Cuyo, Argentina.|Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria La Consulta, La Consulta, Argentina.
authors.forename: Pablo
authors.initials: P
authors.lastname: Cavagnaro
authors.affiliation: Department of Agricultural Biotechnology, Faculty of Agriculture, Yuzuncu Yil University, Van, Turkey.
authors.forename: Mehtap
authors.initials: M
authors.lastname: Yildiz
authors.affiliation: Institute of Plant Biology and Biotechnology, University of Agriculture in Krakow, Krakow, Poland.
authors.forename: Alicja
authors.initials: A
authors.lastname: Macko-Podgórni
authors.affiliation: Institute of Plant Biology and Biotechnology, University of Agriculture in Krakow, Krakow, Poland.
authors.forename: Emilia
authors.initials: E
authors.lastname: Moranska
authors.affiliation: Institute of Plant Biology and Biotechnology, University of Agriculture in Krakow, Krakow, Poland.
authors.forename: Ewa
authors.initials: E
authors.lastname: Grzebelus
authors.affiliation: Institute of Plant Biology and Biotechnology, University of Agriculture in Krakow, Krakow, Poland.
authors.forename: Dariusz
authors.initials: D
authors.lastname: Grzebelus
authors.affiliation: Seed Biotechnology Center, University of California, Davis, Davis, California, USA.
authors.forename: Hamid
authors.initials: H
authors.lastname: Ashrafi
authors.affiliation: Beijing Genomics Institute-Shenzhen, Shenzhen, China.
authors.forename: Zhijun
authors.initials: Z
authors.lastname: Zheng
authors.affiliation: Beijing Genomics Institute-Shenzhen, Shenzhen, China.
authors.forename: Shifeng
authors.initials: S
authors.lastname: Cheng
authors.affiliation: Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin, USA.|Vegetable Crops Research Unit, US Department of Agriculture-Agricultural Research Service, Madison, Wisconsin, USA.
authors.forename: David
authors.initials: D
authors.lastname: Spooner
authors.affiliation: Seed Biotechnology Center, University of California, Davis, Davis, California, USA.
authors.forename: Allen
authors.initials: A
authors.lastname: Van Deynze
authors.affiliation: Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin, USA.|Vegetable Crops Research Unit, US Department of Agriculture-Agricultural Research Service, Madison, Wisconsin, USA.
authors.forename: Philipp
authors.initials: P
authors.lastname: Simon
mesh_terms: D005075:Biological Evolution; D002338:Carotenoids / Q000378:metabolism*; D018552:Daucus carota / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D005809:Genes, Regulator; D008040:Genetic Linkage; D005819:Genetic Markers; D018745:Genome, Plant; D010802:Phylogeny; D018517:Plant Roots / Q000378:metabolism
chemical_list: D005819:Genetic Markers; D002338:Carotenoids