Transcriptome analysis revealed the dynamic oil accumulation in Symplocos paniculata fruit

Abstract

Background Symplocos paniculata, asiatic sweetleaf or sapphire berry, is a widespread shrub or small tree from Symplocaceae with high oil content and excellent fatty acid composition in fruit. It has been used as feedstocks for biodiesel and cooking oil production in China. Little transcriptome information is available on the regulatory molecular mechanism of oil accumulation at different fruit development stages.ResultsThe transcriptome at four different stages of fruit development (10, 80,140, and 170 days after flowering) of S. paniculata were analyzed. Approximately 28 million high quality clean reads were generated. These reads were trimmed and assembled into 182,904 non-redundant putative transcripts with a mean length of 592.91 bp and N50 length of 785 bp, respectively. Based on the functional annotation through Basic Local Alignment Search Tool (BLAST) with public protein database, the key enzymes involved in lipid metabolism were identified, and a schematic diagram of the pathway and temporal expression patterns of lipid metabolism was established. About 13,939 differentially expressed unigenes (DEGs) were screened out using differentially expressed sequencing (DESeq) method. The transcriptional regulatory patterns of the identified enzymes were highly related to the dynamic oil accumulation along with the fruit development of S. paniculata. In addition, quantitative real-time PCR (qRT-PCR) of six vital genes was significantly correlated with DESeq data.ConclusionsThe transcriptome sequences obtained and deposited in NCBI would enrich the public database and provide an unprecedented resource for the discovery of the genes associated with lipid metabolism pathway in S. paniculata. Results in this study will lay the foundation for exploring transcriptional regulatory profiles, elucidating molecular regulatory mechanisms, and accelerating genetic engineering process to improve the yield and quality of seed oil of S. paniculata.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3275-0) contains supplementary material, which is available to authorized users.

Transcriptome analysis of metabolic pathways associated with oil accumulation in developing seed kernels of Styrax tonkinensis, a woody biodiesel species

“…Subsequently, a final contigs assembly produced 168,205 unigenes (N50: 1437) with a mean length of 854 bp. The number of unigenes assembled in this study was comparable to numbers assembled in studies of kernel development in other woody plants [29][30][31][32]. Of the unigenes we found, 42.25% (71,071) were 200-400 bp in length, 32.17% (54,119) were 400-1000 bp, 15.62% (26,268) were 1000-2000 bp, and 9.96% (6747) exceeded 2000 bp (Table 2).…”

“…It provides a readily available, cheap, and comprehensive method to acquire large-scale genomic and transcriptomic data for non-model plant species and has been used to analyze the transcriptomic profiles and construct summary overviews of FA and TAG biosynthesis during oil accumulation in woody oil plants, such as Elaeis guineensis Jacq., Prunus sibirica L., Pistacia chinensis Bunge, Symplocos paniculata Miq., and Lindera glauca (Siebold & Zucc.) Blume [28][29][30][31][32]. However, functional gene expression and regulatory profiles of oil biosynthesis and metabolism in S. tonkinensis have not yet been analyzed.…”

Deciphering key proteins of oil palm (Elaeis guineensis Jacq.) fruit mesocarp development by proteomics and chemometrics

“…The highly expressed proteins associated with lipid biosynthesis correspond to an increase in transcriptome and proteome levels throughout mesocarp development . This finding is in parallel with the FAS enzyme activities in lipid biosynthesis which regulates the oil yield and quality in developing fruits .…”

Identification of Key Genes Involved in Embryo Development and Differential Oil Accumulation in Two Contrasting Maize Genotypes

“…In addition to the acyl-CoA based pathway for TAG biosynthesis, oil seed crops have an alternate pathway for TAG biosynthesis, which is independent of acyl-CoA pool [28,52]. This is catalyzed by PDAT enzymes which convert phosphatidylcholine (PC) into TAG via polyunsaturated fatty acids.…”

“…Transcriptome approaches such as RNA sequencing (RNA-seq) and micro-array have the potential to greatly accelerate the rate of genes' mining for desired phenotypes [3,26]. Several transcriptome studies on important oil seed crops have identified key candidate genes and molecular pathways related to seed oil biosynthesis [27][28][29][30]. However, transcriptome studies focused on identifying important regulators and processes required for embryo development and/or seed oil biosynthesis in maize based on a genome-wide transcriptional profile are scarce [3,31].…”