De novo assembly and characterization of Rhododendron hybridum Hort. (Ericaceae) global transcriptome using Illumina sequencing

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. Overall design: Fresh roots, leaves, flowers and stem tissues were collected from one adult R. hybridum tree located at the Baotianman National Nature Reserve. All tissues were immediately frozen in liquid nitrogen and stored at -80°C until future use. Total RNA was extracted from four tissues using RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany) and quantified with an Agilent 2100 Bioanalyzer RNA Nanochip Kit (QIAGEN, Hilden, Germany). An equal amount of RNA from each sample was pooled, and the mixed RNA (~10 µg) was subjected to Illumina HiSeq X TEN sequencing.