title: Genome Survey Sequencing for the Characterization of the Genetic Background of Rosa roxburghii Tratt and Leaf Ascorbate Metabolism Genes.
abstract: Rosa roxburghii Tratt is an important commercial horticultural crop in China that is recognized for its nutritional and medicinal values. In spite of the economic significance, genomic information on this rose species is currently unavailable. In the present research, a genome survey of R. roxburghii was carried out using next-generation sequencing (NGS) technologies. Total 30.29 Gb sequence data was obtained by HiSeq 2500 sequencing and an estimated genome size of R. roxburghii was 480.97 Mb, in which the guanine plus cytosine (GC) content was calculated to be 38.63%. All of these reads were technically assembled and a total of 627,554 contigs with a N50 length of 1.484 kb and furthermore 335,902 scaffolds with a total length of 409.36 Mb were obtained. Transposable elements (TE) sequence of 90.84 Mb which comprised 29.20% of the genome, and 167,859 simple sequence repeats (SSRs) were identified from the scaffolds. Among these, the mono-(66.30%), di-(25.67%), and tri-(6.64%) nucleotide repeats contributed to nearly 99% of the SSRs, and sequence motifs AG/CT (28.81%) and GAA/TTC (14.76%) were the most abundant among the dinucleotide and trinucleotide repeat motifs, respectively. Genome analysis predicted a total of 22,721 genes which have an average length of 2311.52 bp, an average exon length of 228.15 bp, and average intron length of 401.18 bp. Eleven genes putatively involved in ascorbate metabolism were identified and its expression in R. roxburghii leaves was validated by quantitative real-time PCR (qRT-PCR). This is the first report of genome-wide characterization of this rose species.
authors: Agricultural College, Guizhou University, Guiyang, Guizhou, China.
authors: Min
authors: M
authors: Lu
authors: Agricultural College, Guizhou University, Guiyang, Guizhou, China.|Guizhou Engineering Research Center for Fruit Crops, Guiyang, Guizhou, China.
authors: Huaming
authors: H
authors: An
authors: Agricultural College, Guizhou University, Guiyang, Guizhou, China.|Guizhou Engineering Research Center for Fruit Crops, Guiyang, Guizhou, China.
authors: Liangliang
authors: L
authors: Li
mesh_terms: D001205:Ascorbic Acid / Q000378:metabolism*; D001482:Base Composition; D019295:Computational Biology / Q000379:methods; D017343:Genes, Plant; D056726:Genetic Association Studies; D059646:Genome Size; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D053858:Metabolic Networks and Pathways; D058977:Molecular Sequence Annotation; D018515:Plant Leaves / Q000235:genetics* / Q000378:metabolism*; D012091:Repetitive Sequences, Nucleic Acid; D027826:Rosa / Q000235:genetics* / Q000378:metabolism*
chemical_list: D001205:Ascorbic Acid