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

作者：Laurence Hibrand Saint-Oyant, Tom Ruttink, Latifa Hamama, Ilya Kirov, Deepika Lakhwani, Ningning Zhou, Peter M. Bourke, Nicolas Daccord, Leen Leus, Dietmar Schulz, Henri van de Geest, Thamara Hesselink, Katrijn Van Laere, Kévin Debray, Sandrine Balzergue, Tatiana Thouroude, Annie Chastellier, Julien Jeauffre, Linda Voisine, Sylvain Gaillard, Theo Borm, Paul Arens, Roeland E. Voorrips, Chris Maliepaard, Enzo Neu, Marcus Linde, Marie Christine Le Paslier, Aurélie Berard, Rémi Bounon, Jérémy Clotault, Nathalie Choisne, Hadi Quesneville, Kôji Kawamura, Santiago P. Aubourg, Soulaïman Sakr, M.J.M. Smulders, Elio Schijlen, Etienne Bucher, Thomas Debener, Jan De Riek, Fabrice Foucher · 发表于：Nature Plants · 年份：2018 · DOI：10.1038/s41477-018-0166-1 · 被引用次数：371 · 研究领域：Plant Reproductive Biology、Plant Gene Expression Analysis、Chromosomal and Genetic Variations

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 ...