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

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 chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes

“…We have reported a highly contiguous genome assembly of B. juncea variety Varuna, an oleiferous type belonging to the Indian gene pool of mustard, using long-read SMRT sequencing and optical mapping. The B. juncea assembly reported here has given contig N50 value of >5Mb, comparable to the other recent SMRT based genome assemblies [9][10][11][12][13][14] . We found recursive optical mapping with three different labeling reactions to be highly useful for correcting mis-assemblies.…”

“…Recent genome sequencing efforts have relied exclusively on high coverage SMRT sequencing, both for the de-novo genome assemblies and for improving earlier assembled draft genomes that used the second-generation technologies [8][9][10][11][12][13] . Amongst the Brassica species -assembly of B. rapa Chiifu has been improved by additional data from ~57x SMRT sequencing, BioNano optical mapping, and Hi-C reads 14 .…”

Phylogenomic analysis of UDP‐dependent glycosyltransferases provides insights into the evolutionary landscape of glycosylation in plant metabolism

“…With the exception of Brassicales and Cucumis sativus (Cucurbitaceae), group Q UGTs can be found throughout the rosids (Vitales, malvids and fabids), suggesting that group Q was present in the common ancestor of Malvales ( T. cacao ) and Brassicales in the malvids, but was lost in Brassicales (Figure ). In addition, group Q UGTs are absent in the syntenic chromosomal regions of A. thaliana , but present in those of other rosids ( V. vinifera , E. grandis and R. chinensis ), providing further support to the loss of group Q UGTs in Brassicales (Figure ; the syntenic relationships among different chromosomal regions were reported in Amborella Genome Project, ; Proost et al ., ; Hibrand Saint‐Oyant et al ., ; Jung et al ., ). Similarly, two group Q UGTs in Musa acuminata (Zingiberales) share an ancestry with the other angiosperm group Q UGTs.…”

Draft Genome Assembly and Annotation of Red Raspberry Rubus Idaeus

“…Fragaria vesca (woodland strawberry) (Edger et al, 2018;Shulaev et al, 2011), Potentilla 42 micranthia (mock strawberry) (Buti et al, 2018), and Rosa chinensis (Chinese rose) (Hibrand 43 Saint-Oyant et al, 2018;Raymond et al, 2018). Due to the small genome size, wide variety of 44 fruit types (pomes, drupes, achenes, hips, follicles and capsules), and plant growth habits 45 (ranging from herbaceous to cane, bush and tree forms), Rosaceous genomes offer one of the 46 best systems for the comparative studies in genome evolution and development (Xiang et al, 3 2017).…”