Project description:Rhododendron hybridum Hort. (Ericaceae) is an important ornamental species with striking continuous flowering feature. However, few genomic resources are currently available in this species, and the breeding programs were handicapped by the lack of basic genetic information. Here, we established a transcriptomic profiling study from four different tissues using RNA-Seq to gain insight on the functional genes and to isolate EST-SSR markers for breeding and conservation purposes. In total 38,050,296 high-quality sequence reads were obtained, and 56,120 unigenes (with N50 = 1,236bp) were assembled. Of which, 32,580 (58.05 %) and 8,788 (15.66 %) were annotated to GO and KEGG database, respectively. Additionally, 38,775 (69.09 %) and 37,409 (66.66 %) R. hybridum unigenes were aligned to the Arabidopsis thaliana and Oryza sativa genome, respectively. A total of 21,103 simple sequence repeat (SSR) motifs were identified in 15,050 contigs. Among them, dinucleotide repeats account for the largest proportion for 49.27%, followed by mono- (35.94%) and trinucleotide (21.5%). This study represents the first transcriptome data of R. hybridum and confirms that the transcriptome assembly data are a useful resource for EST-SSR loci development. Such vast sequence data and markers will be robust tools for genomic research and breeding of R. hybridum and related species.

2020-04-11 | GSE97630 | GEO

Pandanus amaryllifolius drought stress and recovery LC-MSMS TMT-Labelled

Project description:The aim of this project is to determine the protein changes of P. amaryllifolius in response to drought stress and during recovery. The protein changes between drought-stressed, well-watered, and recovered plants were evaluated using tandem mass tags (TMT)-based quantitative proteomics. The proteins were extracted from sample by using TCA/Acetone method and digested with trypsin. The digested proteins were then labelled with 10-plex TMT labelling prior fractionation with 12.5%, 17.5%, and 50% ACN with 0.1% triethylamine. The prepared proteins were then subjected to 1D data dependent acquisition (DDA) with nano LC column ionization source was set as positive ion mode, whereby 350-1850 m/z peptide precursors were scanned at 70,000 resolutions. The raw data generated was then searched against Viridiplantae protein sequences downloaded from UniProt. Of the 1,415 differentially abundant proteins, 74 were significantly altered. The majority of proteins differing between them were related to carbon metabolism, photosynthesis, stress response, and antioxidant activity. This is the first study that reports the protein changes in response to drought stress in Pandanus. The data generated provide an insight into the drought-responsive mechanisms in P. amaryllifolius.

2022-02-16 | PXD028784 | Pride

Project description:EST-SSR Marker Development and Polymorphism Analysis of Miben Pumpkin

| PRJNA900560 | ENA