De novo transcriptome analysis of Rhododendron molle G. Don flowers by Illumina sequencing

Xiao, Zheng; JiaLe, Su; Sun, Xin; Li, Chang; He, Lin; Cheng, Shangping; Liu, Xiaoqing

doi:10.1007/s13258-018-0662-8

Cited by 27 publications

(20 citation statements)

References 41 publications

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“…Besides, transcriptomes also serve as invaluable resource for discovery of SSRs. In the present study, a total of 10,828 SSRs were identified which are slightly more than the SSRs (8,266) discovered in Xiao's work [21]. The distribution and frequency of the classified SSRs between two studies were also different.…”

Section: Discussioncontrasting

confidence: 61%

“…genes involved in the biosynthetic pathways of these complicated compounds, including grayanane diterpenoids, are not clear. Recently, Xiao et al[21] conducted the transcriptome sequencing analysis of mixed RNA separately extracted from flowers at four developmental stages of R. molle. About 20 millions clean reads were generated and assembled into 66,026 unigenes with mean length of 698 bp, among which 31,542 unigenes were annotated in public databases, a total of 55,456 CDSs were also predicted.…”

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confidence: 99%

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De novo transcriptome sequencing of Rhododendron molle and identification of genes involved in the biosynthesis of secondary metabolites

Zhou

Zhu²

2020

Preprint

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Background: Rhododendron molle (Ericaceae) is a traditional Chinese medicinal plant, its flower and root have been widely used to treat rheumatism and relieve pain for thousands of years in China. Chemical studies have revealed that R. molle contains abundant secondary metabolites such as terpenoinds, flavonoids and lignans, some of which have exhibited various bioactivities including antioxidant, hypotension and analgesic activity. In spite of immense pharmaceutical importance, the mechanism underlying the biosynthesis of secondary metabolites remains unknown and the genomic information is unavailable. Results: To gain molecular insight into this plant, especially on the pharmaceutically important secondary metabolic information, we conducted deep transcriptome sequencing for R. molle flower and root using the Illumina Hiseq platform. In total, 100,603 unigenes were generated through de novo assembly with mean length of 778 bp, 57.1% of these unigenes were annotated in public databases and 17,906 of those unigenes showed significant match in the KEGG database. Unigenes involved in the biosynthesis of secondary metabolites were annotated, including the TPSs and CYPs that were potentially responsible for the biosynthesis of grayanoids. Moreover, 3,376 transcription factors and 10,828 simple sequence repeats (SSRs) were also identified. Additionally, we further performed differential gene expression (DEG) analysis of the flower and root transcriptome libraries and identified numerous genes that were specifically expressed or up-regulated in flower.Conclusions: To the best of our knowledge, this is the first time to generate and thoroughly analyze the transcriptome data of both R. molle flower and root. This study provided an important genetic resource which will shed light on elucidating various secondary metabolite biosynthetic pathways in R. molle, especially for those with medicinal value and allow for drug development in this plant.

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Section: Discussioncontrasting

confidence: 61%

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confidence: 99%

De novo transcriptome sequencing of Rhododendron molle and identification of genes involved in the biosynthesis of secondary metabolites

Zhou

Zhu²

2020

Preprint

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“…In this study, the average length of the R. lapponicum transcripts was 2,509 bp, which was longer than those obtained in seashore paspalum (970 bp) 38 , sweet potato (581 bp) 39 , and sesame (629 bp) 40 by Illumina sequencing technology. Furthermore, we found that 58.66% of all transcripts were longer than 2,000 bp in this study, and much higher than that in Rhododendron molle (7.23%) 41 and Neottopteris nidus (13.63%) 6 using Illumina sequencing technology. These results indicated that PacBio SMRT sequencing technology is an efficient approach to capture the transcript sequences, especially for long transcript sequences.…”

Section: Discussionmentioning

confidence: 46%

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

Jia

Tang

Mei

et al. 2020

Sci Rep

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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 ...

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“…However, many putative genes involved in the biosynthetic pathways of these complicated compounds, including grayanane diterpenoids, are not clear. Recently, Xiao et al [21] conducted the transcriptome sequencing analysis of mixed RNA separately extracted from owers at four developmental stages of R. molle. About 20 millions clean reads were generated and assembled into 66,026 unigenes with mean length of 698 bp, among which 31,542 unigenes were annotated in public databases, a total of 55,456 CDSs were also predicted.…”

Section: Discussionmentioning

confidence: 99%

De novo transcriptome sequencing of Rhododendron molle and identification of genes involved in the biosynthesis of secondary metabolites

Zhou

Zhu²

2020

Preprint

View full text Add to dashboard Cite

Background: Rhododendron molle (Ericaceae) is a traditional Chinese medicinal plant, its flower and root have been widely used to treat rheumatism and relieve pain for thousands of years in China. Chemical studies have revealed that R. molle contains abundant secondary metabolites such as terpenoinds, flavonoids and lignans, some of which have exhibited various bioactivities including antioxidant, hypotension and analgesic activity. In spite of immense pharmaceutical importance, the mechanism underlying the biosynthesis of secondary metabolites remains unknown and the genomic information is unavailable. Results: To gain molecular insight into this plant, especially on the information of pharmaceutically important secondary metabolites including grayanane diterpenoids, we conducted deep transcriptome sequencing for R. molle flower and root using the Illumina Hiseq platform. In total, 100,603 unigenes were generated through de novo assembly with mean length of 778 bp, 57.1% of these unigenes were annotated in public databases and 17,906 of those unigenes showed significant match in the KEGG database. Unigenes involved in the biosynthesis of secondary metabolites were annotated, including the TPSs and CYPs that were potentially responsible for the biosynthesis of grayanoids. Moreover, 3,376 transcription factors and 10,828 simple sequence repeats (SSRs) were also identified. Additionally, we further performed differential gene expression (DEG) analysis of the flower and root transcriptome libraries and identified numerous genes that were specifically expressed or up-regulated in flower.Conclusions: To the best of our knowledge, this is the first time to generate and thoroughly analyze the transcriptome data of both R. molle flower and root. This study provided an important genetic resource which will shed light on elucidating various secondary metabolite biosynthetic pathways in R. molle, especially for those with medicinal value and allow for drug development in this plant.

show abstract

De novo transcriptome analysis of Rhododendron molle G. Don flowers by Illumina sequencing

Cited by 27 publications

References 41 publications

De novo transcriptome sequencing of Rhododendron molle and identification of genes involved in the biosynthesis of secondary metabolites

De novo transcriptome sequencing of Rhododendron molle and identification of genes involved in the biosynthesis of secondary metabolites

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

De novo transcriptome sequencing of Rhododendron molle and identification of genes involved in the biosynthesis of secondary metabolites

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