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

Autores
Iorizzo, Massimo; Ellison, Shelby L.; Senalik, Douglas A.; Peng, Zeng; Satapoomin, Pimchanok; Jiaying, Huang; Bowman, Megan; Iovene, Marina; Sanseverino, Walter; Cavagnaro, Pablo; Yildiz, Mehtap; Macko-Podgórni, Alicja; Moranska, Emilia; Grzebelus, Ewa; Grzebelus, Dariusz; Ashrafi, Hamid; Zhijun, Zheng; Shifeng, Cheng; Spooner, David M.; Deynze, Allen Van; Simon, Philipp W.
Año de publicación
2016
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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.
EEA La Consulta
Fil: Iorizzo, Massimo. University of Wisconsin. Department of Horticulture; Estados Unidos. North Carolina State University. Plants for Human Health Institute, Department of Horticultural Science; Estados Unidos
Fil: Ellison, Shelby L. University of Wisconsin. Department of Horticulture; Estados Unidos
Fil: Senalik, Douglas A. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados Unidos
Fil: Peng, Zeng. Beijing Genomics Institute–Shenzhen; China
Fil: Satapoomin, Pimchanok. University of Wisconsin. Department of Horticulture; Estados Unidos
Fil: Jiaying, Huang. Beijing Genomics Institute–Shenzhen; China
Fil: Bowman, Megan. Michigan State University. Department of Plant Biology; Estados Unidos
Fil: Iovene, Marina. Consiglio Nazionale delle Ricerche. Istituto di Bioscienze e Biorisorse; Italia
Fil: Sanseverino, Walter. Sequentia Biotech; España
Fil: Cavagnaro, Pablo Federico. . Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria La Consulta; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Yildiz, Mehtap. Yuzuncu Yil University. Faculty of Agriculture. Department of Agricultural Biotechnology; Turquía
Fil: Macko-Podgórni, Alicja. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; Polonia
Fil: Moranska, Emilia. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; Polonia
Fil: Grzebelus, Ewa. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; Polonia
Fil: Grzebelus, Dariusz. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; Polonia
Fil: Ashrafi, Hamid. University of California. Seed Biotechnology Center; Estados Unidos. North Carolina State University. Plants for Human Health Institute, Department of Horticultural Science; Estados Unidos
Fil: Zhijun, Zheng. Beijing Genomics Institute–Shenzhen; China
Fil: Shifeng, Cheng. Beijing Genomics Institute–Shenzhen; China
Fil: Spooner, David M. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados Unidos
Fil: Deynze, Allen Van. University of California. Seed Biotechnology Center; Estados Unidos
Fil: Simon, Philipp W. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados Unidos
Fuente
Nature genetics 48 (6) : 657–666. (June 2016)
Materia
Zanahoria
Genomas
Carotenoides
Carrots
Genomes
Carotenoids
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/1162
Acceder
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oai_identifier_str oai:localhost:20.500.12123/1162
network_acronym_str INTADig
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network_name_str INTA Digital (INTA)
spelling A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolutionIorizzo, MassimoEllison, Shelby L.Senalik, Douglas A.Peng, ZengSatapoomin, PimchanokJiaying, HuangBowman, MeganIovene, MarinaSanseverino, WalterCavagnaro, PabloYildiz, MehtapMacko-Podgórni, AlicjaMoranska, EmiliaGrzebelus, EwaGrzebelus, DariuszAshrafi, HamidZhijun, ZhengShifeng, ChengSpooner, David M.Deynze, Allen VanSimon, Philipp W.ZanahoriaGenomasCarotenoidesCarrotsGenomesCarotenoidsWe 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.EEA La ConsultaFil: Iorizzo, Massimo. University of Wisconsin. Department of Horticulture; Estados Unidos. North Carolina State University. Plants for Human Health Institute, Department of Horticultural Science; Estados UnidosFil: Ellison, Shelby L. University of Wisconsin. Department of Horticulture; Estados UnidosFil: Senalik, Douglas A. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados UnidosFil: Peng, Zeng. Beijing Genomics Institute–Shenzhen; ChinaFil: Satapoomin, Pimchanok. University of Wisconsin. Department of Horticulture; Estados UnidosFil: Jiaying, Huang. Beijing Genomics Institute–Shenzhen; ChinaFil: Bowman, Megan. Michigan State University. Department of Plant Biology; Estados UnidosFil: Iovene, Marina. Consiglio Nazionale delle Ricerche. Istituto di Bioscienze e Biorisorse; ItaliaFil: Sanseverino, Walter. Sequentia Biotech; EspañaFil: Cavagnaro, Pablo Federico. . Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria La Consulta; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Yildiz, Mehtap. Yuzuncu Yil University. Faculty of Agriculture. Department of Agricultural Biotechnology; TurquíaFil: Macko-Podgórni, Alicja. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; PoloniaFil: Moranska, Emilia. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; PoloniaFil: Grzebelus, Ewa. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; PoloniaFil: Grzebelus, Dariusz. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; PoloniaFil: Ashrafi, Hamid. University of California. Seed Biotechnology Center; Estados Unidos. North Carolina State University. Plants for Human Health Institute, Department of Horticultural Science; Estados UnidosFil: Zhijun, Zheng. Beijing Genomics Institute–Shenzhen; ChinaFil: Shifeng, Cheng. Beijing Genomics Institute–Shenzhen; ChinaFil: Spooner, David M. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados UnidosFil: Deynze, Allen Van. University of California. Seed Biotechnology Center; Estados UnidosFil: Simon, Philipp W. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados Unidos2017-09-07T13:06:48Z2017-09-07T13:06:48Z2016info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/1162https://www.nature.com/ng/journal/v48/n6/pdf/ng.3565.pdf1061-4036 (Print)1546-1718 (Online)doi:10.1038/ng.3565Nature genetics 48 (6) : 657–666. (June 2016)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-09-11T10:22:09Zoai:localhost:20.500.12123/1162instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-11 10:22:10.199INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution
title A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution
spellingShingle A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution
Iorizzo, Massimo
Zanahoria
Genomas
Carotenoides
Carrots
Genomes
Carotenoids
title_short A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution
title_full A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution
title_fullStr A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution
title_full_unstemmed A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution
title_sort A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution
dc.creator.none.fl_str_mv Iorizzo, Massimo
Ellison, Shelby L.
Senalik, Douglas A.
Peng, Zeng
Satapoomin, Pimchanok
Jiaying, Huang
Bowman, Megan
Iovene, Marina
Sanseverino, Walter
Cavagnaro, Pablo
Yildiz, Mehtap
Macko-Podgórni, Alicja
Moranska, Emilia
Grzebelus, Ewa
Grzebelus, Dariusz
Ashrafi, Hamid
Zhijun, Zheng
Shifeng, Cheng
Spooner, David M.
Deynze, Allen Van
Simon, Philipp W.
author Iorizzo, Massimo
author_facet Iorizzo, Massimo
Ellison, Shelby L.
Senalik, Douglas A.
Peng, Zeng
Satapoomin, Pimchanok
Jiaying, Huang
Bowman, Megan
Iovene, Marina
Sanseverino, Walter
Cavagnaro, Pablo
Yildiz, Mehtap
Macko-Podgórni, Alicja
Moranska, Emilia
Grzebelus, Ewa
Grzebelus, Dariusz
Ashrafi, Hamid
Zhijun, Zheng
Shifeng, Cheng
Spooner, David M.
Deynze, Allen Van
Simon, Philipp W.
author_role author
author2 Ellison, Shelby L.
Senalik, Douglas A.
Peng, Zeng
Satapoomin, Pimchanok
Jiaying, Huang
Bowman, Megan
Iovene, Marina
Sanseverino, Walter
Cavagnaro, Pablo
Yildiz, Mehtap
Macko-Podgórni, Alicja
Moranska, Emilia
Grzebelus, Ewa
Grzebelus, Dariusz
Ashrafi, Hamid
Zhijun, Zheng
Shifeng, Cheng
Spooner, David M.
Deynze, Allen Van
Simon, Philipp W.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Zanahoria
Genomas
Carotenoides
Carrots
Genomes
Carotenoids
topic Zanahoria
Genomas
Carotenoides
Carrots
Genomes
Carotenoids
dc.description.none.fl_txt_mv 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.
EEA La Consulta
Fil: Iorizzo, Massimo. University of Wisconsin. Department of Horticulture; Estados Unidos. North Carolina State University. Plants for Human Health Institute, Department of Horticultural Science; Estados Unidos
Fil: Ellison, Shelby L. University of Wisconsin. Department of Horticulture; Estados Unidos
Fil: Senalik, Douglas A. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados Unidos
Fil: Peng, Zeng. Beijing Genomics Institute–Shenzhen; China
Fil: Satapoomin, Pimchanok. University of Wisconsin. Department of Horticulture; Estados Unidos
Fil: Jiaying, Huang. Beijing Genomics Institute–Shenzhen; China
Fil: Bowman, Megan. Michigan State University. Department of Plant Biology; Estados Unidos
Fil: Iovene, Marina. Consiglio Nazionale delle Ricerche. Istituto di Bioscienze e Biorisorse; Italia
Fil: Sanseverino, Walter. Sequentia Biotech; España
Fil: Cavagnaro, Pablo Federico. . Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria La Consulta; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Yildiz, Mehtap. Yuzuncu Yil University. Faculty of Agriculture. Department of Agricultural Biotechnology; Turquía
Fil: Macko-Podgórni, Alicja. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; Polonia
Fil: Moranska, Emilia. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; Polonia
Fil: Grzebelus, Ewa. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; Polonia
Fil: Grzebelus, Dariusz. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; Polonia
Fil: Ashrafi, Hamid. University of California. Seed Biotechnology Center; Estados Unidos. North Carolina State University. Plants for Human Health Institute, Department of Horticultural Science; Estados Unidos
Fil: Zhijun, Zheng. Beijing Genomics Institute–Shenzhen; China
Fil: Shifeng, Cheng. Beijing Genomics Institute–Shenzhen; China
Fil: Spooner, David M. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados Unidos
Fil: Deynze, Allen Van. University of California. Seed Biotechnology Center; Estados Unidos
Fil: Simon, Philipp W. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados Unidos
description 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.
publishDate 2016
dc.date.none.fl_str_mv 2016
2017-09-07T13:06:48Z
2017-09-07T13:06:48Z
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/1162
https://www.nature.com/ng/journal/v48/n6/pdf/ng.3565.pdf
1061-4036 (Print)
1546-1718 (Online)
doi:10.1038/ng.3565
url http://hdl.handle.net/20.500.12123/1162
https://www.nature.com/ng/journal/v48/n6/pdf/ng.3565.pdf
identifier_str_mv 1061-4036 (Print)
1546-1718 (Online)
doi:10.1038/ng.3565
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv Nature genetics 48 (6) : 657–666. (June 2016)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
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instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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