Nature Plants, volume 4, issue 7, pages 473-484

A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits

Hibrand Saint Oyant L ¹

Ruttink Tom ²

Hamama L ¹

Kirov I ^{2, 3}

Lakhwani D ¹

Zhou N N ¹

Bourke P M ⁴

Daccord N ¹

Leus L. ²

Schulz D. ⁵

Van De Geest H ⁶

Hesselink T ⁶

Van Laere K. ²

Debray K. ¹

Balzergue S. ¹

Thouroude T ¹

Chastellier A ¹

Jeauffre J ¹

Voisine L ¹

GAILLARD S. ¹

Borm T J A ⁴

Arens P ⁴

Voorrips R E ⁴

MALIEPAARD C. ⁴

Neu E. ⁵

Linde M. ⁵

Le Paslier M C ⁷

Berard A. ⁷

Bounon R ⁷

Clotault J ¹

Choisne N ⁸

Quesneville H ⁸

Kawamura K. ⁹

Aubourg S ¹

Sakr S. ¹

Smulders M.J.M. ⁴

Schijlen E ⁶

Bucher Etienne ¹

Debener T ⁵

De Riek J ²

Foucher Fabrice ¹

Hide authors affiliations Show authors affiliations: 9 affiliations

IRHS, Agrocampus-Ouest, INRA, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France |

ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium |

Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia |

⁴

Plant Breeding, Wageningen University & Research, Wageningen, the Netherlands |

⁵

Leibniz Universität, Hannover, Germany |

⁶

Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands |

⁷

INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France |

⁸

URGI, INRA, Université Paris-Saclay, Versailles, France |

⁹

Osaka Institute of Technology, Osaka, Japan |

Publication type: Journal Article

Publication date: 2018-06-11

Springer Nature

Journal: Nature Plants

Quartile SCImago

Quartile WOS

Impact factor: 18

ISSN: 2055026X, 20550278

DOI: 10.1038/s41477-018-0166-1

Copy DOI

PubMed ID: 29892093

Plant Science

Abstract

Rose is the world’s most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line (‘HapOB’) from Rosa chinensis ‘Old Blush’ and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1–96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.A high-quality reference genome of rose is generated by sequencing a doubled haploid line. The researchers analysed the genome structure and uncovered candidate genes associated with major ornamental traits through integrated genetic and genomic analyses.

By date By citations

Citations by journals

	5 10 15 20
Horticulture Research	Horticulture Research, 20, 9.52% Horticulture Research 20 publications, 9.52%
Frontiers in Plant Science	Frontiers in Plant Science, 18, 8.57% Frontiers in Plant Science 18 publications, 8.57%
Acta Horticulturae	Acta Horticulturae, 15, 7.14% Acta Horticulturae 15 publications, 7.14%
Plants	Plants, 8, 3.81% Plants 8 publications, 3.81%
Scientia Horticulturae	Scientia Horticulturae, 6, 2.86% Scientia Horticulturae 6 publications, 2.86%
Theoretical And Applied Genetics	Theoretical And Applied Genetics, 5, 2.38% Theoretical And Applied Genetics 5 publications, 2.38%
Genes	Genes, 4, 1.9% Genes 4 publications, 1.9%
Scientific Reports	Scientific Reports, 4, 1.9% Scientific Reports 4 publications, 1.9%
BMC Genomics	BMC Genomics, 4, 1.9% BMC Genomics 4 publications, 1.9%
Plant Journal	Plant Journal, 4, 1.9% Plant Journal 4 publications, 1.9%
International Journal of Molecular Sciences	International Journal of Molecular Sciences, 3, 1.43% International Journal of Molecular Sciences 3 publications, 1.43%
Plant Cell, Tissue and Organ Culture	Plant Cell, Tissue and Organ Culture, 3, 1.43% Plant Cell, Tissue and Organ Culture 3 publications, 1.43%
BMC Plant Biology	BMC Plant Biology, 3, 1.43% BMC Plant Biology 3 publications, 1.43%
Horticultural Plant Journal	Horticultural Plant Journal, 3, 1.43% Horticultural Plant Journal 3 publications, 1.43%
Industrial Crops and Products	Industrial Crops and Products, 3, 1.43% Industrial Crops and Products 3 publications, 1.43%
Journal of Experimental Botany	Journal of Experimental Botany, 3, 1.43% Journal of Experimental Botany 3 publications, 1.43%
Biomolecules	Biomolecules, 2, 0.95% Biomolecules 2 publications, 0.95%
Horticulturae	Horticulturae, 2, 0.95% Horticulturae 2 publications, 0.95%
Biology	Biology, 2, 0.95% Biology 2 publications, 0.95%
Diversity	Diversity, 2, 0.95% Diversity 2 publications, 0.95%
Pathogens	Pathogens, 2, 0.95% Pathogens 2 publications, 0.95%
Frontiers in Genetics	Frontiers in Genetics, 2, 0.95% Frontiers in Genetics 2 publications, 0.95%
Journal of Plant Growth Regulation	Journal of Plant Growth Regulation, 2, 0.95% Journal of Plant Growth Regulation 2 publications, 0.95%
Plant Molecular Biology	Plant Molecular Biology, 2, 0.95% Plant Molecular Biology 2 publications, 0.95%
Nature Communications	Nature Communications, 2, 0.95% Nature Communications 2 publications, 0.95%
Plant Diversity	Plant Diversity, 2, 0.95% Plant Diversity 2 publications, 0.95%
Plant Physiology and Biochemistry	Plant Physiology and Biochemistry, 2, 0.95% Plant Physiology and Biochemistry 2 publications, 0.95%
IOP Conference Series: Earth and Environmental Science	IOP Conference Series: Earth and Environmental Science, 2, 0.95% IOP Conference Series: Earth and Environmental Science 2 publications, 0.95%
PLoS ONE	PLoS ONE, 2, 0.95% PLoS ONE 2 publications, 0.95%

	5 10 15 20

Citations by publishers

	10 20 30 40 50 60
Springer Nature	Springer Nature, 57, 27.14% Springer Nature 57 publications, 27.14%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 29, 13.81% Multidisciplinary Digital Publishing Institute (MDPI) 29 publications, 13.81%
Frontiers Media S.A.	Frontiers Media S.A., 21, 10% Frontiers Media S.A. 21 publications, 10%
Elsevier	Elsevier, 21, 10% Elsevier 21 publications, 10%
International Society for Horticultural Science (ISHS)	International Society for Horticultural Science (ISHS), 15, 7.14% International Society for Horticultural Science (ISHS) 15 publications, 7.14%
Oxford University Press	Oxford University Press, 14, 6.67% Oxford University Press 14 publications, 6.67%
Wiley	Wiley, 8, 3.81% Wiley 8 publications, 3.81%
Taylor & Francis	Taylor & Francis, 4, 1.9% Taylor & Francis 4 publications, 1.9%
KeAi Communications Co.	KeAi Communications Co., 2, 0.95% KeAi Communications Co. 2 publications, 0.95%
IOP Publishing	IOP Publishing, 2, 0.95% IOP Publishing 2 publications, 0.95%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 2, 0.95% Public Library of Science (PLoS) 2 publications, 0.95%
Crop Science Society of America	Crop Science Society of America, 2, 0.95% Crop Science Society of America 2 publications, 0.95%
Genetics Society of America	Genetics Society of America, 2, 0.95% Genetics Society of America 2 publications, 0.95%
American Society of Plant Biologists	American Society of Plant Biologists, 2, 0.95% American Society of Plant Biologists 2 publications, 0.95%
Fundacion Romulo Raggio	Fundacion Romulo Raggio, 1, 0.48% Fundacion Romulo Raggio 1 publication, 0.48%
Pensoft Publishers	Pensoft Publishers, 1, 0.48% Pensoft Publishers 1 publication, 0.48%
Social Science Electronic Publishing	Social Science Electronic Publishing, 1, 0.48% Social Science Electronic Publishing 1 publication, 0.48%
Cambridge University Press	Cambridge University Press, 1, 0.48% Cambridge University Press 1 publication, 0.48%
Annual Reviews	Annual Reviews, 1, 0.48% Annual Reviews 1 publication, 0.48%
CAIRN	CAIRN, 1, 0.48% CAIRN 1 publication, 0.48%
	10 20 30 40 50 60

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GOST Copy

Hibrand Saint Oyant L. et al. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits // Nature Plants. 2018. Vol. 4. No. 7. pp. 473-484.

GOST all authors (up to 50) Copy

Hibrand Saint Oyant L., Ruttink T., Hamama L., Kirov I., Lakhwani D., Zhou N. N., Bourke P. M., Daccord N., Leus L., Schulz D., Van De Geest H., Hesselink T., Van Laere K., Debray K., Balzergue S., Thouroude T., Chastellier A., Jeauffre J., Voisine L., GAILLARD S., Borm T. J. A., Arens P., Voorrips R. E., MALIEPAARD C., Neu E., Linde M., Le Paslier M. C., Berard A., Bounon R., Clotault J., Choisne N., Quesneville H., Kawamura K., Aubourg S., Sakr S., Smulders M., Schijlen E., Bucher E., Debener T., De Riek J., Foucher F. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits // Nature Plants. 2018. Vol. 4. No. 7. pp. 473-484.

RIS |

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RIS Copy

TY - JOUR

DO - 10.1038/s41477-018-0166-1

UR - https://doi.org/10.1038%2Fs41477-018-0166-1

TI - A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits

T2 - Nature Plants

AU - Hibrand Saint Oyant, L

AU - Ruttink, Tom

AU - Hamama, L

AU - Kirov, I

AU - Lakhwani, D

AU - Zhou, N N

AU - Bourke, P M

AU - Daccord, N

AU - Leus, L.

AU - Schulz, D.

AU - Van De Geest, H

AU - Hesselink, T

AU - Van Laere, K.

AU - Debray, K.

AU - Balzergue, S.

AU - Thouroude, T

AU - Chastellier, A

AU - Jeauffre, J

AU - Voisine, L

AU - GAILLARD, S.

AU - Borm, T J A

AU - Arens, P

AU - Voorrips, R E

AU - MALIEPAARD, C.

AU - Neu, E.

AU - Linde, M.

AU - Le Paslier, M C

AU - Berard, A.

AU - Bounon, R

AU - Clotault, J

AU - Choisne, N

AU - Quesneville, H

AU - Kawamura, K.

AU - Aubourg, S

AU - Sakr, S.

AU - Smulders, M.J.M.

AU - Schijlen, E

AU - Bucher, Etienne

AU - Debener, T

AU - De Riek, J

AU - Foucher, Fabrice

PY - 2018

DA - 2018/06/11 00:00:00

PB - Springer Nature

SP - 473-484

IS - 7

VL - 4

PMID - 29892093

SN - 2055-026X

SN - 2055-0278

ER -

BibTex |

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BibTex Copy

@article{2018_Hibrand Saint Oyant,

author = {L Hibrand Saint Oyant and Tom Ruttink and L Hamama and I Kirov and D Lakhwani and N N Zhou and P M Bourke and N Daccord and L. Leus and D. Schulz and H Van De Geest and T Hesselink and K. Van Laere and K. Debray and S. Balzergue and T Thouroude and A Chastellier and J Jeauffre and L Voisine and S. GAILLARD and T J A Borm and P Arens and R E Voorrips and C. MALIEPAARD and E. Neu and M. Linde and M C Le Paslier and A. Berard and R Bounon and J Clotault and N Choisne and H Quesneville and K. Kawamura and S Aubourg and S. Sakr and M.J.M. Smulders and E Schijlen and Etienne Bucher and T Debener and J De Riek and Fabrice Foucher},

title = {A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits},

journal = {Nature Plants},

year = {2018},

volume = {4},

publisher = {Springer Nature},

month = {jun},

url = {https://doi.org/10.1038%2Fs41477-018-0166-1},

number = {7},

pages = {473--484},

doi = {10.1038/s41477-018-0166-1}

}

MLA

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MLA Copy

Hibrand Saint Oyant, L., et al. “A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits.” Nature Plants, vol. 4, no. 7, Jun. 2018, pp. 473-484. https://doi.org/10.1038%2Fs41477-018-0166-1.

Found error?

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Springer Nature

Journal

Nature Plants

Quartile SCImago

Quartile WOS

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2055026X (Print)
20550278 (Electronic)

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Kirov, Ilya V