Abstract
Rhododendron lapponicum L. is a familiar ornamental plant worldwide with important ornamental and economic value. However, a full-length R. lapponicum transcriptome is still lacking. In the present study, we used the Pacific Biosciences single-molecule real-time sequencing technology to generate the R. lapponicum transcriptome. A total of 346,270 full-length non-chimeric reads were generated, from which we obtained 75,002 high-quality full-length transcripts. We identified 55,255 complete open reading frames, 7,140 alternative splicing events and 2,011 long non-coding RNAs. In gene annotation analyses, 71,155, 33,653, 30,359 and 31,749 transcripts were assigned to the Nr, GO, COG and KEGG databases, respectively. Additionally, 3,150 transcription factors were detected. KEGG pathway analysis showed that 96 transcripts were identified coding for the enzymes associated with anthocyanin synthesis. Furthermore, we identified 64,327 simple sequence repeats from 45,319 sequences, and 150 pairs of primers were randomly selected to develop SSR markers. This study provides a large number of full-length transcripts, which will facilitate the further study of the genetics of R. lapponicum.
Highlights
Rhododendron lapponicum L. is a familiar ornamental plant worldwide with important ornamental and economic value
The transcriptome data generated from this study provide valuable resources for genome annotation that may establish an important basis for future molecular biology research on Rhododendron species
We identified unique transcripts without protein-coding potential as candidate long non-coding RNAs (lncRNA) with four analysis tools: the coding-non-coding index (CNCI)[21], the coding potential assessment tool (CPAT)[22], the coding potential calculator (CPC)[23], and Pfam protein structure domain analysis[24]
Summary
Rhododendron lapponicum L. is a familiar ornamental plant worldwide with important ornamental and economic value. PacBio single-molecule real-time (SMRT) sequencing technology has served as a better alternative for obtaining full-length transcripts[10,11]. Based on the obtained transcripts, alternative splicing (AS) analysis, long non-coding RNAs (lncRNA) prediction, transcription factor (TF) classification, open reading frame (ORF) prediction, transcript functional annotation and SSR analysis were performed. This is the first systematic report to characterize the full-length transcriptome of R. lapponicum via SMRT sequencing. The transcriptome data generated from this study provide valuable resources for genome annotation that may establish an important basis for future molecular biology research on Rhododendron species
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