PJB-2018-1601
De novo assembly and characterization of Rhododendron hybridum Hort. (Ericaceae) global transcriptome using Illumina sequencing
Shiping Cheng, Yuxia Zong, Minghui Chen, Jiansheng Wang, Mengjie Liao and Fei Liu
Abstract
Rhododendron hybridum Hort. (Ericaceae) is an important ornamental species with striking continuous flowering features. However, few genomic resources are currently available for the species; thus, breeding programs are blocked by a lack of genetic information. Here, we document our transcriptomic profiling of four different R. hybridum tissues using whole transcriptome shotgun sequencing (RNA-Seq) to gain insight on functional genes, and to isolate expressed sequence tag-simple sequence repeat (EST-SSR) markers for breeding and conservation purposes. In total 38,050,296 high-quality sequence reads were obtained, and 56,120 unigenes (contiguous sequence assemblies representing transcripts, with N50 = 1,236 bp) were assembled. Of these, 32,580 (58.05%) and 8,788 (15.66%) were annotated to the GO and KEGG databases, respectively. Additionally, 38,775 (69.09%) and 37,409 (66.66%) of the R. hybridum unigenes aligned to the Arabidopsis thaliana and Oryza sativa genomes, respectively. A total of 21,103 SSR motifs were identified in 15,050 of the unigenes. Among them, dinucleotide repeats account for the largest proportion (49.27%), followed by mono- (35.94%) and trinucleotide repeats (21.5%). This is the first comprehensive transcriptome dataset for R. hybridum, and RNA-Seq technology is proven to be useful approach for EST-SSR development. Such a vast quantity of sequence data and microsatellite markers should prove to be robust tools for subsequent genomic research and breeding programs in R. hybridum and related species.
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