ArticleBMC genomics2019
A survey of transcriptome complexity using PacBio single-molecule real-time analysis combined with Illumina RNA sequencing for a better understanding of ricinoleic acid biosynthesis in Ricinus communis.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 36 citations in OpenAlex.
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- Full-length transcriptome from different life stages of cobia (Rachycentron canadum, Rachycentridae).Scientific data · 2023Article
- Microsatellite analysis and polymorphic marker development based on the full-length transcriptome of Camellia chekiangoleosa.Scientific reports · 2022Article
- A Global Analysis of Alternative Splicing ofCurrent genomics · 2022Article
- Integrated SMRT and Illumina Sequencing Provide New Insights into Crocin Biosynthesis ofInternational journal of molecular sciences · 2022Article
- An integrated omics analysis reveals the gene expression profiles of maize, castor bean, and rapeseed for seed oil biosynthesis.BMC plant biology · 2022Article
- Full-length transcriptome sequencing and comparative transcriptome analysis ofFrontiers in cellular and infection microbiology · 2022Article
- SMRT sequencing of full-length transcriptome and gene expression analysis in two chemical types ofPeerJ · 2022Article
- Application of third-generation sequencing in cancer research.Medical review (2021) · 2021Article
- Targeted transcriptome analysis using synthetic long read sequencing uncovers isoform reprograming in the progression of colon cancer.Communications biology · 2021Article
- PacBio Single-Molecule Long-Read Sequencing Provides New Light on the Complexity of Full-Length Transcripts in Cattle.Frontiers in genetics · 2021Article
- Integrative expression network analysis of microRNA and gene isoforms in sacred lotus.BMC genomics · 2020Article
- Research Progress on Plant Long Non-Coding RNA.Plants (Basel, Switzerland) · 2020Review
- Integrated metabolomic and transcriptomic profiling reveals the tissue-specific flavonoid compositions and their biosynthesis pathways inChinese medicine · 2020Article
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Authors and funding
7 authors at 4 institutions in 1 country.
Funding
Abstract
backgroundRicinus communis is a highly economically valuable oil crop plant from the spurge family, Euphorbiaceae. However, the available reference genomes are incomplete and to date studies on ricinoleic acid biosynthesis at the transcriptional level are limited.
resultsIn this study, we combined PacBio single-molecule long read isoform and Illumina RNA sequencing to identify the alternative splicing (AS) events, novel isoforms, fusion genes, long non-coding RNAs (lncRNAs) and alternative polyadenylation (APA) sites to unveil the transcriptomic complexity of castor beans and identify critical genes related to ricinoleic acid biosynthesis. Here, we identified 11,285 AS-variants distributed in 21,448 novel genes and detected 520 fusion genes, 320 lncRNAs and 9511 (APA-sites). Furthermore, a total of 6067, 5983 and 4058 differentially expressed genes between developing beans of the R. communis lines 349 and 1115 with extremely different oil content were identified at 7, 14 and 21 days after flowering, respectively. Specifically, 14, 18 and 11 DEGs were annotated encoding key enzymes related to ricinoleic acid biosynthesis reflecting the higher castor oil content of 1115 compared than 349. Quantitative real-time RT-PCR further validated fifteen of these DEGs at three-time points.
conclusionOur results significantly improved the existed gene models of R. communis, and a putative model of key genes was built to show the differences between strains 349 and 1115, illustrating the molecular mechanism of castor oil biosynthesis. A multi-transcriptome database and candidate genes were provided to further improve the level of ricinoleic acid in transgenic crops.
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