Single-molecule long-read sequencing of the full-length transcriptome of Rhododendron lapponicum L.

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.Rhododendron is the largest genus in Ericaceae, with more than 1000 species of woody plants, either evergreen or deciduous 1 . Rhododendron species are widely cultivated around the world ranging from tropical to polar climates, and serve as a potential genetic resource for the development of new plant cultivars adapted to different environmental conditions 2 . Rhododendron is a familiar ornamental plant worldwide, and is decorative shrub with beautiful flowers that are widespread around the world. There are a remarkably broad range of rhododendron flower colours, including red, white, yellow, and green and so on. Rhododendron lapponicum L., a Rhododendron species found in subarctic regions around the world, is a common ornamental plant worldwide 3 . Recent advances in sequencing technology have facilitated genome and transcriptome studies in many species. However, genome and transcriptome sequencing in R. lapponicum has lagged behind that in other species, and information about the sequence and structure of its genes is limited. Therefore, the generation of a transcriptome data may establish a very important molecular biology basis for the research of R. lapponicum.The transcriptome reflects the number and type of genes expressed in different cell types and reveals underlying metabolic pathways and genetic mechanisms 4 . Transcriptome sequencing is an efficient and feasible approach for generating a large amount of sequence data, and a large number of cDNA sequences provides a useful resource for genomic and genetic research 5-9 . Thus, third-generation long-read transcriptome sequencing platforms such as the Pacific Biosciences (PacBio), Nanopore and Moleculo platforms were developed. Recently, PacBio single-molecule real-time (SMRT) sequencing technology has served as a better alternative for obtaining full-length transcripts 10,11 . The ...

Full-length SMRT transcriptome sequencing and microsatellite characterization in Paulownia catalpifolia

“…We annotated 25,602 HQ P. catalpifolia transcripts using five public databases. The annotated HQ transcripts accounted for 98.59% of all HQ transcripts, a similar rate to those of transcriptomics studies in R. lapponicum 39 and Medicago sativa 46 . The 367 HQ transcripts with no predicted functions are likely to be species-specific or unknown genes in P. catalpifolia .…”

“…The frequency of the SSRs was 28.37%, and the average distribution distance was 5.59 kb. Among the 6604 complete SSRs, the most abundant and frequent mononucleotide, dinucleotide and trinucleotide motifs were A/T, AG/CT and GAA/TTC, respectively; studies examining SSRs in Hevea brasiliensis 49 , Chinese cabbage 50 and R. lapponicum 39 produced similar results. A/T was the most abundant mononucleotide motif (2816, 95.43%), which was consistent with a study performed by Lagercrantz et al 51 .…”

“…In this study, we used the SMRT technique to perform full-length transcriptome sequencing in P. catalpifolia using PacBio RS II platform. In total, 28.83 Gb sequencing data were obtained including 349,745 full-length non-chimeric sequence reads, which was similar to the number of FLNC reads in Rhododendron lapponicum 39 . After subjecting the reads to clustering, error correction and redundant sequence removal, a total of 25,969 HQ transcripts were finally obtained.…”

“…A/T was the most abundant mononucleotide motif (2816, 95.43%), which was consistent with a study performed by Lagercrantz et al 51 . AG/CT (807, 36.09%) and GA/TC (636, 28.44%) were the most abundant dinucleotide motifs, and CT repeats usually existed in transcriptional regions that might take part in antisense transcription and have an effect on gene regulation 39 , 52 . There were differences in SSR abundance of different plant species in diverse researches, and repeat number of 6, 10, 5, 11, and 12 occupied 59.30% of the total complete SSR loci in our study.…”

PacBio single molecule real-time sequencing-based full-length transcriptome of tree tomato (Solanum betaceum Cav.) and mining of simple sequence repeat (SSR) markers

“…In addition, transcriptome pro ling has proved an effective approach for genome-wide development of simple sequence repeat (SSR) markers in many non-model plants at a large scale and low cost [15,[24][25][26]. SSRs are good DNA ngerprinting markers to assess genetic diversity and population structure and to distinguish closely-related cultivars because of the advantages of single locus, multiple allele variations and abundant polymorphism [27].…”