The genome of Chenopodium quinoa

Handle URI:
http://hdl.handle.net/10754/622874
Title:
The genome of Chenopodium quinoa
Authors:
Jarvis, David Erwin ( 0000-0002-0072-9112 ) ; Ho, Yung Shwen; Lightfoot, Damien ( 0000-0003-3824-8856 ) ; Schmöckel, Sandra M.; Li, Bo; Borm, Theo J. A.; Ohyanagi, Hajime; Mineta, Katsuhiko ( 0000-0002-4727-045X ) ; Michell, Craig; Saber, Noha; Kharbatia, Najeh M.; Rupper, Ryan R.; Sharp, Aaron R.; Dally, Nadine; Boughton, Berin A.; Woo, Yong; Gao, Ge; Schijlen, Elio G. W. M.; Guo, Xiujie; Momin, Afaque Ahmad Imtiyaz; Negrão, Sónia; Al-Babili, Salim ( 0000-0003-4823-2882 ) ; Gehring, Christoph A. ( 0000-0003-4355-4591 ) ; Roessner, Ute; Jung, Christian; Murphy, Kevin; Arold, Stefan T. ( 0000-0001-5278-0668 ) ; Gojobori, Takashi ( 0000-0001-7850-1743 ) ; Linden, C. Gerard van der; Loo, Eibertus N. van; Jellen, Eric N.; Maughan, Peter J.; Tester, Mark A. ( 0000-0002-5085-8801 )
Abstract:
Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Red Sea Research Center (RSRC); Analytical Core Lab
Citation:
Jarvis DE, Ho YS, Lightfoot DJ, Schmöckel SM, Li B, et al. (2017) The genome of Chenopodium quinoa. Nature: 1–6. Available: http://dx.doi.org/10.1038/nature21370.
Publisher:
Springer Nature
Journal:
Nature
Issue Date:
8-Feb-2017
DOI:
10.1038/nature21370
Type:
Article
ISSN:
0028-0836; 1476-4687
Sponsors:
Research reported in this publication was supported by the King Abdullah University of Science and Technology (KAUST), by USDA/NIFA-REEIS grant #2012-51300-20100 (WSU/BYU), by NSF grant #1339412, and by a grant from the German Research Foundation, DFG (grant no. JU205/24-1). We thank T. Ramaraj from the National Center for Genomic Resources (Santa Fe) for his bioinformatics assistance, O. Mohammed Eid Alharbi at the KAUST Imaging and Characterization Laboratory for generating SEM images, K. Zemmouri at the KAUST Greenhouse for plant care, and H. Ho (Heno) Hwang and I. D. Gromicho at the KAUST Academic Writing Department for assistance with quinoa illustrations and photographs. We also thank H. Štorchová, F. Morton, D. Bertero, F. Fuentes and D. Brenner of USDA-ARS-NPGS for their assistance in providing seeds.
Additional Links:
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature21370.html
Appears in Collections:
Articles; Red Sea Research Center (RSRC); Analytical Core Lab; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorJarvis, David Erwinen
dc.contributor.authorHo, Yung Shwenen
dc.contributor.authorLightfoot, Damienen
dc.contributor.authorSchmöckel, Sandra M.en
dc.contributor.authorLi, Boen
dc.contributor.authorBorm, Theo J. A.en
dc.contributor.authorOhyanagi, Hajimeen
dc.contributor.authorMineta, Katsuhikoen
dc.contributor.authorMichell, Craigen
dc.contributor.authorSaber, Nohaen
dc.contributor.authorKharbatia, Najeh M.en
dc.contributor.authorRupper, Ryan R.en
dc.contributor.authorSharp, Aaron R.en
dc.contributor.authorDally, Nadineen
dc.contributor.authorBoughton, Berin A.en
dc.contributor.authorWoo, Yongen
dc.contributor.authorGao, Geen
dc.contributor.authorSchijlen, Elio G. W. M.en
dc.contributor.authorGuo, Xiujieen
dc.contributor.authorMomin, Afaque Ahmad Imtiyazen
dc.contributor.authorNegrão, Sóniaen
dc.contributor.authorAl-Babili, Salimen
dc.contributor.authorGehring, Christoph A.en
dc.contributor.authorRoessner, Uteen
dc.contributor.authorJung, Christianen
dc.contributor.authorMurphy, Kevinen
dc.contributor.authorArold, Stefan T.en
dc.contributor.authorGojobori, Takashien
dc.contributor.authorLinden, C. Gerard van deren
dc.contributor.authorLoo, Eibertus N. vanen
dc.contributor.authorJellen, Eric N.en
dc.contributor.authorMaughan, Peter J.en
dc.contributor.authorTester, Mark A.en
dc.date.accessioned2017-02-12T13:38:49Z-
dc.date.available2017-02-12T13:38:49Z-
dc.date.issued2017-02-08en
dc.identifier.citationJarvis DE, Ho YS, Lightfoot DJ, Schmöckel SM, Li B, et al. (2017) The genome of Chenopodium quinoa. Nature: 1–6. Available: http://dx.doi.org/10.1038/nature21370.en
dc.identifier.issn0028-0836en
dc.identifier.issn1476-4687en
dc.identifier.doi10.1038/nature21370en
dc.identifier.urihttp://hdl.handle.net/10754/622874-
dc.description.abstractChenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.en
dc.description.sponsorshipResearch reported in this publication was supported by the King Abdullah University of Science and Technology (KAUST), by USDA/NIFA-REEIS grant #2012-51300-20100 (WSU/BYU), by NSF grant #1339412, and by a grant from the German Research Foundation, DFG (grant no. JU205/24-1). We thank T. Ramaraj from the National Center for Genomic Resources (Santa Fe) for his bioinformatics assistance, O. Mohammed Eid Alharbi at the KAUST Imaging and Characterization Laboratory for generating SEM images, K. Zemmouri at the KAUST Greenhouse for plant care, and H. Ho (Heno) Hwang and I. D. Gromicho at the KAUST Academic Writing Department for assistance with quinoa illustrations and photographs. We also thank H. Štorchová, F. Morton, D. Bertero, F. Fuentes and D. Brenner of USDA-ARS-NPGS for their assistance in providing seeds.en
dc.publisherSpringer Natureen
dc.relation.urlhttp://www.nature.com/nature/journal/vaop/ncurrent/full/nature21370.htmlen
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported licence. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons licence, users will need to obtain permission from the licence holder to reproduce the material. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-sa/3.0/.en
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/3.0/en
dc.titleThe genome of Chenopodium quinoaen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.contributor.departmentAnalytical Core Laben
dc.identifier.journalNatureen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionWageningen University and Research, Wageningen UR Plant Breeding, Wageningen, The Netherlands.en
dc.contributor.institutionBrigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, Utah 84602, USA.en
dc.contributor.institutionPlant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24118 Kiel, Germany.en
dc.contributor.institutionMetabolomics Australia, The School of Biosciences, The University of Melbourne, Parkville, Victoria 3010, Australia.en
dc.contributor.institutionPRI Bioscience, Plant Research International, Wageningen UR, Wageningen, The Netherlands.en
dc.contributor.institutionWashington State University, Department of Crop and Soil Sciences, College of Agricultural, Human, and Natural Resource Sciences, Pullman, Washington 99164-6420, USA.en
kaust.authorJarvis, David Erwinen
kaust.authorHo, Yung Shwenen
kaust.authorLightfoot, Damienen
kaust.authorSchmöckel, Sandra M.en
kaust.authorLi, Boen
kaust.authorOhyanagi, Hajimeen
kaust.authorMineta, Katsuhikoen
kaust.authorMichell, Craigen
kaust.authorSaber, Nohaen
kaust.authorWoo, Yongen
kaust.authorGao, Geen
kaust.authorGuo, Xiujieen
kaust.authorMomin, Afaque Ahmad Imtiyazen
kaust.authorNegrão, Sóniaen
kaust.authorAl-Babili, Salimen
kaust.authorGehring, Christoph A.en
kaust.authorMurphy, Kevinen
kaust.authorArold, Stefan T.en
kaust.authorGojobori, Takashien
kaust.authorTester, Mark A.en
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