Search

Arabidopsis stranded 150 bp paired end RNA sequencing data (Illumina) of plants that were submitted to heat stress for the manuscript "Generation of transcriptional novelty by transposable element insertions in Arabidopsis" Heat stress trial for RNA seq Sequenced F4 seeds were sterilized for 10 minutes in 10% bleach, rinsed, and stratified at 4°C for four days in the dark before being sown on 0.5x Murashige & Skoog media (Duschefa cat# M0222) and transferred to growth chambers under long day conditions (16h of light at 24°C followed by 8h of darkness at 21°C; 20 seeds per plate, 6 replicate plates). Ten days after sowing, plants were subjected to 6°C for 24 hours and heat stressed plants were placed at 37°C for 24 hours before harvesting (3 replicate plates per condition). RNA extraction and sequencing Seedlings were harvested and RNA extractions were done on pools of 5 plants. RNA extractions were performed for 3 biological replicate samples for each line in each condition (n=96) using the Macherey-Nagel NucleoSpin RNA kit (cat# 740955.50). Samples were sent to Novogene for Illumina 150bp paired-end sequencing using a stranded poly-A library. Files description: Forward and reverse strand RNA seq data are combined in one file. The numbering at the end ("_1") denominates the biological replicate number., This dataset is corrupt in the main uploaded dataset. That is why it has been added separately.

International audience

Arabidopsis stranded 150 bp paired end RNA sequencing data (Illumina) of plants that were submitted to heat stress for the manuscript "Generation of transcriptional novelty by transposable element insertions in Arabidopsis" Heat stress trial for RNA seq Sequenced F4 seeds were sterilized for 10 minutes in 10% bleach, rinsed, and stratified at 4°C for four days in the dark before being sown on 0.5x Murashige & Skoog media (Duschefa cat# M0222) and transferred to growth chambers under long day conditions (16h of light at 24°C followed by 8h of darkness at 21°C; 20 seeds per plate, 6 replicate plates). Ten days after sowing, plants were subjected to 6°C for 24 hours and heat stressed plants were placed at 37°C for 24 hours before harvesting (3 replicate plates per condition). RNA extraction and sequencing Seedlings were harvested and RNA extractions were done on pools of 5 plants. RNA extractions were performed for 3 biological replicate samples for each line in each condition (n=96) using the Macherey-Nagel NucleoSpin RNA kit (cat# 740955.50). Samples were sent to Novogene for Illumina 150bp paired-end sequencing using a stranded poly-A library. Files description: Forward and reverse strand RNA seq data are combined in one file. The numbering at the end ("_1") denominates the biological replicate number.

of Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements

Chapitre 10; Fleshy fruits, which are only found in Angiosperms, are of high economic importance as they represent an essential component of the human daily diet. True fruits derive from carpels, a leaf-like organ, and their development requires major reprogrammings of gene expression patterns of which we are just starting to grasp the importance of epigenetic regulations. Starting at fruit set, fruit development can be subdivided in two main steps, cell division and cell enlargement, that are followed by ripening in the case of fleshy fruits, whereas dry fruits enter a lignification phase before dehiscence occurs. Here, we summarize the state of the art in epigenetic regulation of fruit initiation, development and ripening with a focus on fleshy fruits. We present evidence that stable epigenetic variations, also called epimutations can affect fruit phenotype and discuss the role of DNA methylation and specific histone post translational modifications at the different fruit developmental phases. Indeed most works so far have been performed on tomato, the model for fleshy fruit studies, but recent works also indicate that epigenetic regulations might be of primary importance in other fruits, although the precise mechanisms might differ. Future research directions required to answer key remaining questions are discussed with the idea to develop breeding strategies that will integrate the epigenetic dimension.

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.