A High-Quality Carrot Genome Assembly Provides New Insights Into Carotenoid Accumulation and Asterid Genome Evolution
| dc.contributor.author | Iorizzo, Massimo | |
| dc.contributor.author | Ellison, Shelby | |
| dc.contributor.author | Senalik, Douglas | |
| dc.contributor.author | Zeng, Peng | |
| dc.contributor.author | Satapoomin, Pimchanok | |
| dc.contributor.author | Huang, Jiaying | |
| dc.contributor.author | Simon, Philipp | |
| dc.date.accessioned | 2025-05-10T17:40:38Z | |
| dc.date.available | 2025-05-10T17:40:38Z | |
| dc.date.issued | 2016 | |
| dc.description | Bowman, Megan/0000-0001-5742-1779; Jiaying, Huang/0000-0002-4711-158X; Yildiz, Mehtap/0000-0001-6534-5286; Iovene, Marina/0000-0002-5992-8677; Ashrafi, Hudson/0000-0002-2094-2367; Simon, Philipp/0000-0001-6978-6062; Grzebelus, Dariusz/0000-0001-6999-913X; Macko-Podgorni, Alicja/0000-0003-2416-2808; Zeng, Peng/0000-0002-5460-2256; Cavagnaro, Pablo/0000-0001-5838-0876; Zheng, Zhijun/0000-0003-0104-4550; Senalik, Douglas/0000-0001-8526-0554; Sanseverino, Walter/0000-0003-3324-5912; Iorizzo, Massimo/0000-0002-0032-8247; Grzebelus, Ewa/0000-0003-2067-585X | en_US |
| dc.description.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. | en_US |
| dc.description.sponsorship | carrot industry; Bejo; Carosem; Monsanto; Nunhems; |Sumika; Takii; Vilmorin; National Science Foundation [1202666]; projects RGV-FAO [D.M.3824]; Polish National Science Center [2012/05/B/NZ9/03401]; Polish Ministry of Science and Higher Education to Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow; [PONa3_00025-BIOforIU]; Direct For Biological Sciences; Division Of Integrative Organismal Systems [1202666] Funding Source: National Science Foundation; ARS [813495, ARS-0425034] Funding Source: Federal RePORTER | en_US |
| dc.description.sponsorship | The authors appreciate the financial support of the carrot industry and the following vegetable seed companies-Bejo, Carosem, Monsanto, Nunhems, Rijk Zwaan (RZ), Sumika, Takii, and Vilmorin-with additional thanks to RZ for providing DH1, BAC libraries, and BES. S.E. was supported by the National Science Foundation under grant 1202666. M. Iovene thanks the projects RGV-FAO (D.M.3824) for partial financial support and PONa3_00025-BIOforIU for funding the acquisition of a fluorescence microscope. A.M.-P., E.M., E.G., and D.G. were supported by the Polish National Science Center, project 2012/05/B/NZ9/03401, and the statutory funds for science granted by the Polish Ministry of Science and Higher Education to the Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow. The authors thank H. Ruess for assembly and annotation of the plastid genome and R. Kane for support in the development of plant materials. | en_US |
| dc.identifier.doi | 10.1038/ng.3565 | |
| dc.identifier.issn | 1061-4036 | |
| dc.identifier.issn | 1546-1718 | |
| dc.identifier.scopus | 2-s2.0-84966671734 | |
| dc.identifier.uri | https://doi.org/10.1038/ng.3565 | |
| dc.identifier.uri | https://hdl.handle.net/20.500.14720/15270 | |
| dc.language.iso | en | en_US |
| dc.publisher | Nature Portfolio | en_US |
| dc.rights | info:eu-repo/semantics/openAccess | en_US |
| dc.title | A High-Quality Carrot Genome Assembly Provides New Insights Into Carotenoid Accumulation and Asterid Genome Evolution | en_US |
| dc.type | Article | en_US |
| dspace.entity.type | Publication | |
| gdc.author.id | Bowman, Megan/0000-0001-5742-1779 | |
| gdc.author.id | Jiaying, Huang/0000-0002-4711-158X | |
| gdc.author.id | Yildiz, Mehtap/0000-0001-6534-5286 | |
| gdc.author.id | Iovene, Marina/0000-0002-5992-8677 | |
| gdc.author.id | Ashrafi, Hudson/0000-0002-2094-2367 | |
| gdc.author.id | Simon, Philipp/0000-0001-6978-6062 | |
| gdc.author.id | Grzebelus, Ewa/0000-0003-2067-585X | |
| gdc.author.scopusid | 54889841100 | |
| gdc.author.scopusid | 55682186000 | |
| gdc.author.scopusid | 6506954898 | |
| gdc.author.scopusid | 56274470300 | |
| gdc.author.scopusid | 57189237068 | |
| gdc.author.scopusid | 57193319785 | |
| gdc.author.scopusid | 6603401656 | |
| gdc.author.wosid | Sanseverino, Walter/Aax-5254-2021 | |
| gdc.author.wosid | Ashrafi, Hamid/C-9202-2009 | |
| gdc.author.wosid | Van Deynze, Allen/Afk-4820-2022 | |
| gdc.author.wosid | Yildiz, Mehtap/Abu-1488-2022 | |
| gdc.author.wosid | Iovene, Marina/J-5593-2015 | |
| gdc.author.wosid | Grzebelus, Dariusz/I-8832-2014 | |
| gdc.author.wosid | Grzebelus, Ewa/Aae-8271-2019 | |
| gdc.coar.access | open access | |
| gdc.coar.type | text::journal::journal article | |
| gdc.description.department | T.C. Van Yüzüncü Yıl Üniversitesi | en_US |
| gdc.description.departmenttemp | [Iorizzo, Massimo; Ellison, Shelby; Senalik, Douglas; Satapoomin, Pimchanok; Spooner, David; Simon, Philipp] Univ Wisconsin, Dept Hort, 1575 Linden Dr, Madison, WI 53706 USA; [Senalik, Douglas; Spooner, David; Simon, Philipp] USDA ARS, Vegetable Crops Res Unit, Madison, WI USA; [Zeng, Peng; Huang, Jiaying; Zheng, Zhijun; Cheng, Shifeng] Beijing Genom Inst Shenzhen, Shenzhen, Peoples R China; [Bowman, Megan] Michigan State Univ, Dept Plant Biol, E Lansing, MI 48824 USA; [Iovene, Marina] CNR, Inst Biosci & Bioresources, Bari, Italy; [Sanseverino, Walter] Sequentia Biotech, Barcelona, Spain; [Cavagnaro, Pablo] Univ Nacl Cuyo, Fac Ciencias Agr, Natl Sci & Tech Res Council CONICET, Cuyo, Argentina; [Cavagnaro, Pablo] Inst Nacl Tecnol Agr, Estn Expt Agr Consulta, La Consulta, Argentina; [Yildiz, Mehtap] Yuzuncu Yil Univ, Fac Agr, Dept Agr Biotechnol, Van, Turkey; [Macko-Podgorni, Alicja; Moranska, Emilia; Grzebelus, Ewa; Grzebelus, Dariusz] Agr Univ Krakow, Inst Plant Biol & Biotechnol, Krakow, Poland; [Ashrafi, Hamid; Van Deynze, Allen] Univ Calif Davis, Seed Biotechnol Ctr, Davis, CA 95616 USA; [Iorizzo, Massimo; Ashrafi, Hamid] N Carolina State Univ, Dept Hort Sci, Plants Human Hlth Inst, Kannapolis, NC USA; [Ashrafi, Hamid] N Carolina State Univ, Dept Hort Sci, Raleigh, NC 27695 USA | en_US |
| gdc.description.endpage | + | en_US |
| gdc.description.issue | 6 | en_US |
| gdc.description.publicationcategory | Makale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı | en_US |
| gdc.description.scopusquality | Q1 | |
| gdc.description.startpage | 657 | en_US |
| gdc.description.volume | 48 | en_US |
| gdc.description.woscitationindex | Science Citation Index Expanded | |
| gdc.description.wosquality | Q1 | |
| gdc.identifier.pmid | 27158781 | |
| gdc.identifier.wos | WOS:000376744200014 | |
| gdc.index.type | WoS | |
| gdc.index.type | Scopus | |
| gdc.index.type | PubMed |