Full-Length Transcriptome from Camellia oleifera Seed Provides Insight into the Transcript Variants Involved in Oil Biosynthesis

Abstract

Camellia oleifera Abel., belonging to the genus Camellia of Theaceae, has been widely used as a cooking oil, lubricant, and in cosmetics. Because of complicated polyploidization and large genomes, reference genome information is still lacking. Systematic characterization of gene models based on transcriptome data is a fast and economical approach for C. oleifera. Pacific Biosciences single-molecule long-read isoform sequencing (Iso-Seq) and Illumina RNA-Seq combined with gas chromatography were performed for exploration of oil biosynthesis, accumulation, and comprehensive transcriptome analysis in C. oleifera seeds at five different developmental stages. We report the first full-length transcriptome data set of C. oleifera seeds comprising 40,143 deredundant high-quality isoforms. Among these isoforms, 37,982 were functionally annotated, and 271 (2.43%) belonged to fatty acid metabolism. A total of 8,344 full-length unique transcript models were obtained, and 8,151 (97.69%) of them produced more than two isoforms, suggesting a high degree of transcriptome complexity in C. oleifera seeds. A total of 783 alternative splicing (AS) events were identified, among which the retained intron was the most abundant. We also obtained 1,910 long noncoding RNAs (lncRNAs) and found that AS events occurred in these lncRNAs. Potential transcript variants of genes involved in oil biosynthesis were also investigated. After performing weighted correlation network analysis, we found seven “gene modules” and hub genes for each module showing a significant association with oil content. The series test of clusters classified these modules into four significant profiles based on gene expression patterns. Protein–protein interaction network analysis showed that upregulated WRI1 interacted with 17 genes encoding the enzymes playing key roles in oil synthesis. MYB and ZIP transcriptional factors also showed significant interactions with key genes involved in oil synthesis. Collectively, our data advance the knowledge of RNA isoform diversity in seeds at different developmental stages and provide a rich resource for functional studies on oil synthesis in C. oleifera.

Comparative study on fruit development and oil synthesis in two cultivars of Camellia oleifera

“…The area of oil bodies in cells are positively correlated with the oil content in seeds [ 28 – 30 ]. We were unable to detect oil or oil bodies in C. oleifera ‘Huashuo’ seeds in July, this is similar to the previous research [ 36 ]. This indicated that there was no oil body synthesis in ‘Huashuo’ fruits before July.…”

“…By using C. oleifera 'Huashuo' as the test material and analyzing transcriptome data, Jiang et al [34] found that PLA2, FAD2 and FAD3 could regulate the synthesis of α-linolenic acid in C. oleifera seeds, Zeng et al [35] found that the mRNA levels of CoFBA and CoSAD were closely related to the oil content in oil-tea tree seeds. Gong et al [36] explored the oil biosynthesis and accumulation of C. oleifera seeds at five different developmental stages. Moreover, Peng et al [37] and Lin et al [38] used RNA-seq technology to study seeds development and lipid synthesis in different C. oleifera cultivars, which provide a new insight into the lipid biosynthesis and fatty acid accumulation mechanism.…”

Transcriptomic Analysis Reveals Key Genes Involved in Oil and Linoleic Acid Biosynthesis during Artemisia sphaerocephala Seed Development

“…The key TFs that regulated the biosynthesis of oil varied by species and different organizations: GRF5, WRI1, FUS3 were hub TFs in the oil biosynthesis regulatory network in B. rape seed [39]. WRI1, MYB and ZIP played key roles in the biosynthesis of oil in C. oleifera [40]; PBS and RAP played a critical role in the oil biosynthesis regulatory network in avocado (Persea americana) mesocarp and seed, respectively [41]. For this study, a total of 1440 differentially expressed TFs belonging to 83 different gene families were identified from the seed transcriptome of A. sphaerocephala at different developmental stages.…”

The genome of oil-Camellia and population genomics analysis provide insights into seed oil domestication

“…Oil-Camellia, in a broad sense, refers to more than 60 shrubs of the genus Camellia (Theaceae) whose seed kernels produce high-quality edible oils [ 4 ]. Currently, Camellia oleifera is the dominant species that is cultivated for Camellia oil production in China [ 5 , 6 ].…”