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The Rosa genome provides new insights into the domestication of modern roses.

ABSTRACT: Roses have high cultural and economic importance as ornamental plants and in the perfume industry. We report the rose whole-genome sequencing and assembly and resequencing of major genotypes that contributed to rose domestication. We generated a homozygous genotype from a heterozygous diploid modern rose progenitor, Rosa chinensis 'Old Blush'. Using single-molecule real-time sequencing and a meta-assembly approach, we obtained one of the most comprehensive plant genomes to date. Diversity analyses highlighted the mosaic origin of 'La France', one of the first hybrids combining the growth vigor of European species and the recurrent blooming of Chinese species. Genomic segments of Chinese ancestry identified new candidate genes for recurrent blooming. Reconstructing regulatory and secondary metabolism pathways allowed us to propose a model of interconnected regulation of scent and flower color. This genome provides a foundation for understanding the mechanisms governing rose traits and should accelerate improvement in roses, Rosaceae and ornamentals.

SUBMITTER: Raymond O

PROVIDER: S-EPMC5984618 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

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The Rosa genome provides new insights into the domestication of modern roses.

Raymond Olivier O Gouzy Jérôme J Just Jérémy J Badouin Hélène H Verdenaud Marion M Lemainque Arnaud A Vergne Philippe P Moja Sandrine S Choisne Nathalie N Pont Caroline C Carrère Sébastien S Caissard Jean-Claude JC Couloux Arnaud A Cottret Ludovic L Aury Jean-Marc JM Szécsi Judit J Latrasse David D Madoui Mohammed-Amin MA François Léa L Fu Xiaopeng X Yang Shu-Hua SH Dubois Annick A Piola Florence F Larrieu Antoine A Perez Magali M Labadie Karine K Perrier Lauriane L Govetto Benjamin B Labrousse Yoan Y Villand Priscilla P Bardoux Claudia C Boltz Véronique V Lopez-Roques Céline C Heitzler Pascal P Vernoux Teva T Vandenbussche Michiel M Quesneville Hadi H Boualem Adnane A Bendahmane Abdelhafid A Liu Chang C Le Bris Manuel M Salse Jérôme J Baudino Sylvie S Benhamed Moussa M Wincker Patrick P Bendahmane Mohammed M

Nature genetics 20180430 6

Roses have high cultural and economic importance as ornamental plants and in the perfume industry. We report the rose whole-genome sequencing and assembly and resequencing of major genotypes that contributed to rose domestication. We generated a homozygous genotype from a heterozygous diploid modern rose progenitor, Rosa chinensis 'Old Blush'. Using single-molecule real-time sequencing and a meta-assembly approach, we obtained one of the most comprehensive plant genomes to date. Diversity analys ...[more]

PMID: 29713014

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Project description:Rosa chinensis var. spontanea, an endemic and endangered plant of China, is one of the key ancestors of modern roses and a source for famous traditional Chinese medicines against female diseases, such as irregular menses and dysmenorrhea. In this study, the complete chloroplast (cp) genome of R. chinensis var. spontanea was sequenced, analyzed, and compared to congeneric species. The cp genome of R. chinensis var. spontanea is a typical quadripartite circular molecule of 156,590 bp in length, including one large single copy (LSC) region of 85,910 bp and one small single copy (SSC) region of 18,762 bp, separated by two inverted repeat (IR) regions of 25,959 bp. The GC content of the whole genome is 37.2%, while that of LSC, SSC, and IR is 42.8%, 35.2% and 31.2%, respectively. The genome encodes 129 genes, including 84 protein-coding genes (PCGs), 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Seventeen genes in the IR regions were found to be duplicated. Thirty-three forward and five inverted repeats were detected in the cp genome of R. chinensis var. spontanea. The genome is rich in SSRs. In total, 85 SSRs were detected. A genome comparison revealed that IR contraction might be the reason for the relatively smaller cp genome size of R. chinensis var. spontanea compared to other congeneric species. Sequence analysis revealed that the LSC and SSC regions were more divergent than the IR regions within the genus Rosa and that a higher divergence occurred in non-coding regions than in coding regions. A phylogenetic analysis showed that the sampled species of the genus Rosa formed a monophyletic clade and that R. chinensis var. spontanea shared a more recent ancestor with R. lichiangensis of the section Synstylae than with R. odorata var. gigantea of the section Chinenses. This information will be useful for the conservation genetics of R. chinensis var. spontanea and for the phylogenetic study of the genus Rosa, and it might also facilitate the genetics and breeding of modern roses.

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The Rosa genome provides new insights into the domestication of modern roses.

Publications

The Rosa genome provides new insights into the domestication of modern roses.

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