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

L. Hibrand Saint-Oyant, T. Ruttink, L. Hamama, I. Kirov, D. Lakhwani, N.N. Zhou, P.M. Bourke, N. Daccord, L. Leus, D. Schulz, H. van de Geest, T. Hesselink, K. Van Laere, K. Debray, S. Balzergue, T. Thouroude, A. Chastellier, J. Jeauffre, L. Voisine, S. Gaillard & 21 others T.J.A. Borm, P. Arens, R.E. Voorrips, C. Maliepaard, E. Neu, M. Linde, M.C. Le Paslier, A. Bérard, R. Bounon, J. Clotault, N. Choisne, H. Quesneville, K. Kawamura, S. Aubourg, S. Sakr, M.J.M. Smulders, E. Schijlen, E. Bucher, T. Debener, J. De Riek, F. Foucher

Research output: Contribution to journalArticleAcademicpeer-review

28 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)473-484
JournalNature Plants
Volume4
Early online date11 Jun 2018
DOIs
Publication statusPublished - 2018

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Rosa chinensis
Rosa
genome
plant spines
doubled haploids
corolla
tetraploidy
diploidy
Fragaria vesca
genome assembly
container-grown plants
cut flowers
Rosaceae
fluorescence in situ hybridization
ploidy
ornamental plants
meiosis
transposons
haploidy
gardens

Cite this

Hibrand Saint-Oyant, L., Ruttink, T., Hamama, L., Kirov, I., Lakhwani, D., Zhou, N. N., ... Foucher, F. (2018). A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. Nature Plants, 4, 473-484. https://doi.org/10.1038/s41477-018-0166-1
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. ; Bérard, A. ; Bounon, R. ; Clotault, J. ; Choisne, N. ; Quesneville, H. ; Kawamura, K. ; Aubourg, S. ; Sakr, S. ; Smulders, M.J.M. ; Schijlen, E. ; Bucher, E. ; Debener, T. ; De Riek, J. ; Foucher, F. / A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. In: Nature Plants. 2018 ; Vol. 4. pp. 473-484.
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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.",
author = "{Hibrand Saint-Oyant}, L. and T. 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 {van de Geest}, H. and T. Hesselink and {Van Laere}, K. 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 {Le Paslier}, M.C. and A. B{\'e}rard 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 E. Bucher and T. Debener and {De Riek}, J. and F. Foucher",
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Hibrand Saint-Oyant, L, Ruttink, T, Hamama, L, Kirov, I, Lakhwani, D, Zhou, NN, Bourke, PM, 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, TJA, Arens, P, Voorrips, RE, Maliepaard, C, Neu, E, Linde, M, Le Paslier, MC, Bérard, A, Bounon, R, Clotault, J, Choisne, N, Quesneville, H, Kawamura, K, Aubourg, S, Sakr, S, Smulders, MJM, Schijlen, E, Bucher, E, Debener, T, De Riek, J & Foucher, F 2018, 'A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits' Nature Plants, vol. 4, pp. 473-484. https://doi.org/10.1038/s41477-018-0166-1

A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. / 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.; Bérard, A.; Bounon, R.; Clotault, J.; Choisne, N.; Quesneville, H.; Kawamura, K.; Aubourg, S.; Sakr, S.; Smulders, M.J.M.; Schijlen, E.; Bucher, E.; Debener, T.; De Riek, J.; Foucher, F.

In: Nature Plants, Vol. 4, 2018, p. 473-484.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits

AU - Hibrand Saint-Oyant, L.

AU - Ruttink, T.

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 - Bérard, 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, E.

AU - Debener, T.

AU - De Riek, J.

AU - Foucher, F.

PY - 2018

Y1 - 2018

N2 - 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.

AB - 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.

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DO - 10.1038/s41477-018-0166-1

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EP - 484

JO - Nature Plants

JF - Nature Plants

SN - 2055-026X

ER -

Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN et al. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. Nature Plants. 2018;4:473-484. https://doi.org/10.1038/s41477-018-0166-1