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

Rose is the worlds most important ornamental plant with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Rose has a complex genome with high heterozygosity and various ploidy levels. Our objectives were (i) to develop the first high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short read sequencing, and anchoring to a high-density genetic map and (ii) to study the genome structure and the genetic basis of major ornamental traits. We produced a haploid rose line from R. chinensis "Old Blush" and generated the first rose genome sequence at the pseudo-molecule scale (512 Mbp with N50 of 3.4 Mb and L75 of 97). The sequence was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features including the pericentromeric regions through annotation of TE families and positioned centromeric repeats using FISH. Genetic diversity was analysed by resequencing eight Rosa species. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and number of flower petals. A rose APETALA2 homologue is proposed to be the major regulator of petals number in rose. This reference sequence is an important resource for studying polyploidisation, meiosis and developmental processes as we demonstrated for flower and prickle development. This reference sequence 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

Role of the Polymerase ϵ sub-unit DPB2 in DNA replication, cell cycle regulation and DNA damage response in Arabidopsis

Faithful DNA replication maintains genome stability in dividing cells and from one generation to the next. This is particularly important in plants because the whole plant body and reproductive cells originate from meristematic cells that retain their proliferative capacity throughout the life cycle of the organism. DNA replication involves large sets of proteins whose activity is strictly regulated, and is tightly linked to the DNA damage response to detect and respond to replication errors or defects. Central to this interconnection is the replicative polymerase DNA Polymerase ϵ (Pol ϵ) which participates in DNA replication per se, as well as replication stress response in animals and in yeast. Surprisingly, its function has to date been little explored in plants, and notably its relationship with DNA Damage Response (DDR) has not been investigated. Here, we have studied the role of the largest regulatory sub-unit of Arabidopsis DNA Pol ϵ DPB2, using an over-expression strategy. We demonstrate that excess accumulation of the protein impairs DNA replication and causes endogenous DNA stress. Furthermore, we show that Pol ϵ dysfunction has contrasting outcomes in vegetative and reproductive cells and leads to the activation of distinct DDR pathways in the two cell types. © 2016 The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research

The GrapeReSeq 18k Vitis genotyping chip

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Physical mapping and re-sequencing of a set of resistance related genes in grapevine

Physical mapping and re-sequencing of a set of resistance related genes in grapevine. 17. Conference Plant and Animal Genome

Nucleotide variation at the Vitis chloroplast genome based on high-throughput sequencing and SNP genotyping

International audienc

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

International audienceRose is the queen of flowers, holding great symbolic and cultural value. Roses appeared as decoration on 5,000-year-old Asian pottery 1 , and Romans cultivated roses for their flowers and essential oil 2. Today, no ornamental plants have greater economic importance than roses. They are cultivated worldwide and are sold as garden plants, in pots or as cut flowers, the latter accounting for approximately 30% of the market. Roses are also used for scent production and for culinary purposes 3. Despite their genetic complexity and lack of biotechnological resources, rose represents a model for ornamental plant species, allowing the investigation of traits such as bloom seasonality or flower morphology. Furthermore, rose displays a range of unique features as a result of its complex evolutionary and breeding history , including interspecific hybridization events and polyploidi-zation 4-6. Roses belong to the genus Rosa (Rosoideae, Rosaceae), which contains more than 150 species 7 of varying ploidy levels, ranging from 2n = 2× to 10× 8,9. Many modern roses are tetra-ploid and can be genetically classified as 'segmental' allopolyploids (a mixture between allopolyploidy and autopolyploidy) 10 , whereas dog-roses display unequal meiosis to maintain pentaploidy 11,12. Rose breeding has a long and generally unresolved history in Europe and Asia, most likely involving several interspecific hybridization events. Importantly, many very-old varieties are still maintained in private and public rose gardens and are a living historical archive of rose breeding and selection 13. Large and well-documented her-barium collections, combined with genomic advances, offer excellent opportunities to reconstruct phylogenetic relationships within the species. Roses have been subject to selection for several traits that are not usually encountered in other crops. In particular, aesthetic criteria have been a principal focus of rose breeding over the past 250 years, next to plant vigour and resistances to biotic and abiotic stresses. Among the aesthetic traits, flower colour and architecture (from 5-petalled 'simple' flowers to 100-petalled 'double' flowers), floral scent and prickle formation on the stem and leaves have been the main targets of the breeders' eyes (and noses). Although these traits can be interpreted as signs of the domestication process, they originally evolved through adaptation to natural conditions. 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 resequenc-ing 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. NATuRE PLANTS | www.nature.com/natureplant

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

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