The genome of Chenopodium quinoa

David Erwin Jarvis; Ho Shwen; Damien Lightfoot; Sandra M. Schmöckel; Bo Li; Theo J. A. Borm; Hajime Ohyanagi; Katsuhiko Mineta; Craig Michell; Noha Saber; Najeh M. Kharbatia; Ryan R. Rupper; Aaron R. Sharp; Nadine Dally; Berin A. Boughton; Yong Woo; Ge Gao; Elio G. W. M. Schijlen; Xiujie Guo; Afaque Ahmad Imtiyaz Momin; Sónia Negrão; Salim Al-Babili; Christoph A Gehring; Ute Roessner; Christian Jung; Kevin Murphy; Stefan T. Arold; Takashi Gojobori; C. Gerard van der Linden; Eibertus N. van Loo; Eric N. Jellen; Peter J. Maughan; Mark A. Tester

doi:10.1038/nature21370

The genome of Chenopodium quinoa

David Erwin Jarvis, Ho Shwen, Damien Lightfoot, Sandra M. Schmöckel, Bo Li, Theo J. A. Borm, Hajime Ohyanagi, Katsuhiko Mineta, Craig Michell, Noha Saber, Najeh M. Kharbatia, Ryan R. Rupper, Aaron R. Sharp, Nadine Dally, Berin A. Boughton, Yong Woo, Ge Gao, Elio G. W. M. Schijlen, Xiujie Guo, Afaque Ahmad Imtiyaz MominSónia Negrão, Salim Al-Babili, Christoph A Gehring, Ute Roessner, Christian Jung, Kevin Murphy, Stefan T. Arold, Takashi Gojobori, C. Gerard van der Linden, Eibertus N. van Loo, Eric N. Jellen, Peter J. Maughan, Mark A. Tester

Research output: Contribution to journal › Article › peer-review

243 Scopus citations

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.

Original language	English (US)
Pages (from-to)	307-312
Number of pages	6
Journal	Nature
Volume	542
Issue number	7641
DOIs	https://doi.org/10.1038/nature21370
State	Published - Feb 8 2017

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This output contributes to the following Sustainable Development Goal(s)

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10.1038/nature21370

https://repository.kaust.edu.sa/bitstream/10754/622874/1/nature21370.pdf

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Chenopodium pallidicaule isolate:PI_478407 Genome sequencing and assembly
Jarvis, D. E. (Creator), Lightfoot, D. (Creator), Schmöckel, S. M. (Creator), Li, B. (Creator), Borm, T. J. A. (Creator), Ohyanagi, H. (Creator), Mineta, K. (Creator), Michell, C. (Creator), Saber, N. (Creator), Kharbatia, N. M. (Creator), Rupper, R. R. (Creator), Sharp, A. R. (Creator), Dally, N. (Creator), Boughton, B. A. (Creator), Woo, Y. (Creator), Gao, G. (Creator), Schijlen, E. G. W. M. (Creator), Guo, X. (Creator), Momin, A. A. I. (Creator), Negrão, S. (Creator), Al-Babili, S. (Creator), Gehring, C. A. (Creator), Roessner, U. (Creator), Jung, C. (Creator), Murphy, K. (Creator), Arold, S. (Creator), Gojobori, T. (Creator), Linden, C. G. V. D. (Creator), Loo, E. N. V. (Creator), Jellen, E. N. (Creator), Maughan, P. J. (Creator), Tester, M. A. (Creator), Shwen, H. (Creator), Jarvis, D. E. (Creator), Lightfoot, D. (Creator), Borm, T. J. A. (Creator), Michell, C. (Creator), Kharbatia, N. M. (Creator), Rupper, R. R. (Creator), Sharp, A. R. (Creator), Dally, N. (Creator), Boughton, B. A. (Creator), Woo, Y. (Creator), Schijlen, E. G. W. M. (Creator), Momin, A. A. I. (Creator), Gehring, C. A. (Creator), Roessner, U. (Creator), Jung, C. (Creator), Murphy, K. (Creator), Linden, C. G. V. D. (Creator), Loo, E. N. V. (Creator), Jellen, E. N. (Creator), Maughan, P. J. (Creator), Tester, M. A. (Creator) & Shwen, H. (Creator), NCBI, Jul 18 2016
http://hdl.handle.net/10754/666729
Dataset
Chenopodium quinoa cultivar:QQ74 Genome sequencing and assembly
Jarvis, D. E. (Creator), Lightfoot, D. (Creator), Schmöckel, S. M. (Creator), Li, B. (Creator), Borm, T. J. A. (Creator), Ohyanagi, H. (Creator), Mineta, K. (Creator), Michell, C. (Creator), Saber, N. (Creator), Kharbatia, N. M. (Creator), Rupper, R. R. (Creator), Sharp, A. R. (Creator), Dally, N. (Creator), Boughton, B. A. (Creator), Woo, Y. (Creator), Gao, G. (Creator), Schijlen, E. G. W. M. (Creator), Guo, X. (Creator), Momin, A. A. I. (Creator), Negrão, S. (Creator), Al-Babili, S. (Creator), Gehring, C. A. (Creator), Roessner, U. (Creator), Jung, C. (Creator), Murphy, K. (Creator), Arold, S. (Creator), Gojobori, T. (Creator), Linden, C. G. V. D. (Creator), Loo, E. N. V. (Creator), Jellen, E. N. (Creator), Maughan, P. J. (Creator), Tester, M. A. (Creator), Shwen, H. (Creator), Jarvis, D. E. (Creator), Lightfoot, D. (Creator), Borm, T. J. A. (Creator), Michell, C. (Creator), Kharbatia, N. M. (Creator), Rupper, R. R. (Creator), Sharp, A. R. (Creator), Dally, N. (Creator), Boughton, B. A. (Creator), Woo, Y. (Creator), Schijlen, E. G. W. M. (Creator), Momin, A. A. I. (Creator), Gehring, C. A. (Creator), Roessner, U. (Creator), Jung, C. (Creator), Murphy, K. (Creator), Linden, C. G. V. D. (Creator), Loo, E. N. V. (Creator), Jellen, E. N. (Creator), Maughan, P. J. (Creator), Tester, M. A. (Creator) & Shwen, H. (Creator), NCBI, Jul 11 2016
http://hdl.handle.net/10754/666420
Dataset
Chenopodium suecicum isolate:BYU_1480 Genome sequencing and assembly
Jarvis, D. E. (Creator), Lightfoot, D. (Creator), Schmöckel, S. M. (Creator), Li, B. (Creator), Borm, T. J. A. (Creator), Ohyanagi, H. (Creator), Mineta, K. (Creator), Michell, C. (Creator), Saber, N. (Creator), Kharbatia, N. M. (Creator), Rupper, R. R. (Creator), Sharp, A. R. (Creator), Dally, N. (Creator), Boughton, B. A. (Creator), Woo, Y. (Creator), Gao, G. (Creator), Schijlen, E. G. W. M. (Creator), Guo, X. (Creator), Momin, A. A. I. (Creator), Negrão, S. (Creator), Al-Babili, S. (Creator), Gehring, C. A. (Creator), Roessner, U. (Creator), Jung, C. (Creator), Murphy, K. (Creator), Arold, S. (Creator), Gojobori, T. (Creator), Linden, C. G. V. D. (Creator), Loo, E. N. V. (Creator), Jellen, E. N. (Creator), Maughan, P. J. (Creator), Tester, M. (Creator), Shwen, H. (Creator), Jarvis, D. E. (Creator), Lightfoot, D. (Creator), Borm, T. J. A. (Creator), Michell, C. (Creator), Kharbatia, N. M. (Creator), Rupper, R. R. (Creator), Sharp, A. R. (Creator), Dally, N. (Creator), Boughton, B. A. (Creator), Woo, Y. (Creator), Schijlen, E. G. W. M. (Creator), Momin, A. A. I. (Creator), Gehring, C. A. (Creator), Roessner, U. (Creator), Jung, C. (Creator), Murphy, K. (Creator), Linden, C. G. V. D. (Creator), Loo, E. N. V. (Creator), Jellen, E. N. (Creator), Maughan, P. J. (Creator) & Shwen, H. (Creator), NCBI, Jul 18 2016
http://hdl.handle.net/10754/666415
Dataset

Cite this

Jarvis, D. E., Shwen, H., Lightfoot, D., Schmöckel, S. M., Li, B., Borm, T. J. A., Ohyanagi, H., Mineta, K., Michell, C., Saber, N., Kharbatia, N. M., Rupper, R. R., Sharp, A. R., Dally, N., Boughton, B. A., Woo, Y., Gao, G., Schijlen, E. G. W. M., Guo, X., ... Tester, M. A. (2017). The genome of Chenopodium quinoa. Nature, 542(7641), 307-312. https://doi.org/10.1038/nature21370

Jarvis, David Erwin ; Shwen, Ho ; Lightfoot, Damien ; Schmöckel, Sandra M. ; Li, Bo ; Borm, Theo J. A. ; Ohyanagi, Hajime ; Mineta, Katsuhiko ; 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 ; Gehring, Christoph A ; Roessner, Ute ; Jung, Christian ; Murphy, Kevin ; Arold, Stefan T. ; Gojobori, Takashi ; Linden, C. Gerard van der ; Loo, Eibertus N. van ; Jellen, Eric N. ; Maughan, Peter J. ; Tester, Mark A. / The genome of Chenopodium quinoa. In: Nature. 2017 ; Vol. 542, No. 7641. pp. 307-312.

@article{669a84f05a3b45f3869e954259cfb83b,

title = "The genome of Chenopodium quinoa",

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.",

author = "Jarvis, {David Erwin} and Ho Shwen and Damien Lightfoot and Schm{\"o}ckel, {Sandra M.} and Bo Li and Borm, {Theo J. A.} and Hajime Ohyanagi and Katsuhiko Mineta and Craig Michell and Noha Saber and Kharbatia, {Najeh M.} and Rupper, {Ryan R.} and Sharp, {Aaron R.} and Nadine Dally and Boughton, {Berin A.} and Yong Woo and Ge Gao and Schijlen, {Elio G. W. M.} and Xiujie Guo and Momin, {Afaque Ahmad Imtiyaz} and S{\'o}nia Negr{\~a}o and Salim Al-Babili and Gehring, {Christoph A} and Ute Roessner and Christian Jung and Kevin Murphy and Arold, {Stefan T.} and Takashi Gojobori and Linden, {C. Gerard van der} and Loo, {Eibertus N. van} and Jellen, {Eric N.} and Maughan, {Peter J.} and Tester, {Mark A.}",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: 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. {\v S}torchov{\'a}, F. Morton, D. Bertero, F. Fuentes and D. Brenner of USDA-ARS-NPGS for their assistance in providing seeds.",

year = "2017",

month = feb,

day = "8",

doi = "10.1038/nature21370",

language = "English (US)",

volume = "542",

pages = "307--312",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "7641",

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Jarvis, DE, Shwen, H, Lightfoot, D, Schmöckel, SM, Li, B, Borm, TJA, Ohyanagi, H, Mineta, K, Michell, C, Saber, N, Kharbatia, NM, Rupper, RR, Sharp, AR, Dally, N, Boughton, BA, Woo, Y, Gao, G, Schijlen, EGWM, Guo, X, Momin, AAI, Negrão, S, Al-Babili, S , Gehring, CA, Roessner, U, Jung, C, Murphy, K, Arold, ST , Gojobori, T, Linden, CGVD, Loo, ENV, Jellen, EN, Maughan, PJ & Tester, MA 2017, 'The genome of Chenopodium quinoa', Nature, vol. 542, no. 7641, pp. 307-312. https://doi.org/10.1038/nature21370

The genome of Chenopodium quinoa. / Jarvis, David Erwin; Shwen, Ho; Lightfoot, Damien; Schmöckel, Sandra M.; Li, Bo; Borm, Theo J. A.; Ohyanagi, Hajime; Mineta, Katsuhiko; 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 ; Gehring, Christoph A; Roessner, Ute; Jung, Christian; Murphy, Kevin; Arold, Stefan T.; Gojobori, Takashi; Linden, C. Gerard van der; Loo, Eibertus N. van; Jellen, Eric N.; Maughan, Peter J.; Tester, Mark A.

In: Nature, Vol. 542, No. 7641, 08.02.2017, p. 307-312.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - The genome of Chenopodium quinoa

AU - Jarvis, David Erwin

AU - Shwen, Ho

AU - Lightfoot, Damien

AU - Schmöckel, Sandra M.

AU - Li, Bo

AU - Borm, Theo J. A.

AU - Ohyanagi, Hajime

AU - Mineta, Katsuhiko

AU - Michell, Craig

AU - Saber, Noha

AU - Kharbatia, Najeh M.

AU - Rupper, Ryan R.

AU - Sharp, Aaron R.

AU - Dally, Nadine

AU - Boughton, Berin A.

AU - Woo, Yong

AU - Gao, Ge

AU - Schijlen, Elio G. W. M.

AU - Guo, Xiujie

AU - Momin, Afaque Ahmad Imtiyaz

AU - Negrão, Sónia

AU - Al-Babili, Salim

AU - Gehring, Christoph A

AU - Roessner, Ute

AU - Jung, Christian

AU - Murphy, Kevin

AU - Arold, Stefan T.

AU - Gojobori, Takashi

AU - Linden, C. Gerard van der

AU - Loo, Eibertus N. van

AU - Jellen, Eric N.

AU - Maughan, Peter J.

AU - Tester, Mark A.

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: 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.

PY - 2017/2/8

Y1 - 2017/2/8

N2 - 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.

AB - 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.

UR - http://hdl.handle.net/10754/622874

UR - http://www.nature.com/nature/journal/vaop/ncurrent/full/nature21370.html

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U2 - 10.1038/nature21370

DO - 10.1038/nature21370

M3 - Article

C2 - 28178233

VL - 542

SP - 307

EP - 312

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7641

ER -

The genome of Chenopodium quinoa

Abstract

UN SDGs

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Other files and links

Chenopodium pallidicaule isolate:PI_478407 Genome sequencing and assembly

Chenopodium quinoa cultivar:QQ74 Genome sequencing and assembly

Chenopodium suecicum isolate:BYU_1480 Genome sequencing and assembly

Cite this