Transcriptomic analysis of Perilla frutescens seed to insight into the biosynthesis and metabolic of unsaturated fatty acids
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Perilla frutescens is well known for its high α-linolenic acid (ALA) accumulation in seeds and medicinal values as well as a source of edible and general-purpose oils. However, the regulatory mechanisms of the biosynthesis of fatty acid in its seeds remain poorly understood due to the lacking of sequenced genome. For better understanding the regulation of lipid metabolism and further increase its oil content or modify oil composition, time-course transcriptome and lipid composition analyses were performed.
Analysis of fatty acid content and composition showed that the α-linolenic acid and oleic acid accumulated rapidly from 5 DAF to 15 DAF and then kept relatively stable. However, the amount of palmitic acid and linoleic acid decreased quickly from 5 DAF to 15DAF. No significant variation of stearic acid content was observed from 5 DAF to 25DAF. Our transcriptome data analyses revealed that 110,176 unigenes were generated from six seed libraries at 5, 10, 20 DAF. Of these, 53 (31 up, 22 down) and 653 (259 up, 394 down) genes showed temporal and differentially expression during the seed development in 5 DAF vs 10 DAF, 20 vs 10 DAF, respectively. The differentially expressed genes were annotated and found to be involved in distinct functional categories and metabolic pathways. Deep mining of transcriptome data led to the identification of key genes involved in fatty acid and triacylglycerol biosynthesis and metabolism. Thirty seven members of transcription factor family AP2, B3 and NFYB putatively involved in oil synthesis and deposition were differentially expressed during seed development. The results of qRT-PCR for selected genes showed a strong positive correlation with the expression abundance measured in RNA-seq analysis.
The present study provides valuable genomic resources for characterizing Perilla seed gene expression at the transcriptional level and will extend our understanding of the complex molecular and cellular events of oil biosynthesis and accumulation in oilseed crops.
KeywordsPerilla frutescens Fatty acid biosynthesis RNA-seq Seed development Gene expression profiling
Abscisic Acid Insensitive3
days after flowering
Fatty acid desaturase
Kyoto Encyclopedia of Genes and Genomes)
Eukaryotic orthologous groups
Perilla is a self-pollinating plant and widely distributed in East Asian countries and considered as a food supply and natural medicine resource [1, 2]. Perilla frutescens belongs to the Lamiaceae family and encompasses many natural varieties . P. frutescens var. frutescens seed has potential application in pharmaceutical and food industry due to the high accumulation of unsaturated acids, such as α-linolenic acid (ALA, 18:3) (> 60% of total FA in seeds) [4, 5]. With the exception of flaxseed oil, such high levels of ALA are uncommon in seed oils. However, the variety P. frutescens var. crispa has been used as a Chinese medicine or spicy vegetable crop [6, 7].
ALA content in most common edible oils, including peanut oil, sesame oil, sunflower oil and olive oil, is less than 3% [8, 9] . High ALA content in Perilla seeds, ranging from 60 to 70% depending on the varieties, is not only beneficial to human health but also important for stress responses, pathogen defense-related signaling and cell maturation processes. Therefore, it is a good model plant to dissect the biosynthesis pathways of unsaturated fatty acids. Although, few genes encoding enzymes involved in fatty acid biosynthesis, such as FAD3, 3-ketoacyl-ACP synthases, KAS (I, II, and III), have been characterized in Perilla [10, 11], the molecular regulatory mechanisms underlying the biosynthesis and metabolism of FA in Perilla seed have not yet been intensively studied, largely due to a dearth of genetic resources. To insight into the conserved and diverse aspects of lipid metabolism across multiple species, it is useful to expand the genomic and transcriptomic datasets available for non-model species to facilitate comparative analyses. Without the genome sequence of Perilla, transcriptome sequencing is an effective approach to identify the genes involved in specific biological processes.
As an initial step to understand the expression patterns of genes associated with fatty acid biosynthesis in Perilla, an cDNA library of P. fruescens  was constructed and 1056 expressed sequence tags were identified . Subsequently, comparative expression profiles within cultivar variety P. frutescens var. frutescens Britt and wildtype P. frutescens var. crispa were performed through the de novo transcriptome sequencing approach, candidate genes causing the different leaf color and seed size were identified and their expression patterns were compared . These datasets provided a large number of targeted gene information and could be referenced for functional transcriptome studies of Perilla. However, due to the temporal and spatial characteristics of transcriptome, from these studies it is not clear how fatty acid and TAG biosynthesis pathways were regulated and how they affect the oil content, composition and accumulation during seed development. Therefore, it is necessary to explore the transcriptome of developing seeds for further understanding of the regulation of lipid metabolism. To accomplish this objective, FA content and compositions in developing seeds were analyzed and a time-series analysis of transcriptomic data was performed. The approach used here is helpful to systematically identify the core biological process involved in oil synthesis and the new identified transcription factors will help us to further explore the molecular regulatory mechanisms of oil biosynthesis and metabolism in developing seeds.
Results and discussion
Major fatty acid content and composition differ from developing seeds
Transcriptome sequencing and de novo assembly
To gain a comprehensive transcriptional profile of Perilla seeds, sample collecting at the optimal developmental stage is crucial. It was rationalized that gene expressions and their regulations would precede the presence of enzymes and their products. Therefore, seeds at 5 DAF, 10 DAF and 20 DAF were chosen to explore the regulation of fatty acid biosynthesis and metabolism. Two cDNA libraries for each developmental stage were constructed and sequenced by the Illumina sequencing technology. Around 60 million RNA-seq reads were obtained for each developmental stage (Additional file 1:Table S1). After stringent quality control and data filtering, about 57.8 M, 55.7 M, and 57.6 M clean reads were generated for 5 DAF, 10 DAF and 20 DAF, respectively. A total of 25.53G data were further de novo assembled into 110,176 unigenes with an average length of 758 bp and an N50 of 1420 bp. Among of these unigenes, 22,492 unigenes were longer than 1 kb and account for 20.4% of the total unigenes. The length distribution of all unigenes was shown in Additional files 2 and 3: Figure S1 A and Table S2. These results revealed that the assembled data were qualified for further analyses.
Functional annotations of unigenes
For gene functional annotation, all assembled unigenes were aligned by BLAST search against the NR, NT, KO, SwissProt, Pfam, GO and KOG databases (e-value< e-5), which retrieved proteins with the highest sequences identities with the given unigene along with their functional annotations. Blast search showed 47.07% unigenes had significant match to genes in the NR database, followed by 37.51% in Swissport database, 34.66% in GO database, 34.37% in Pfam database, 26.10% in NT database, 21.16% in KOG database and 16.42% in KO database (Additional files 2 and 3: Figure S1 B and C, Table S2). The remaining unmatched unigenes could be attributable to the short sequence reads generated by the sequencing technology, or might be unique to P. frutescens, or the relatively short sequences lacked conserved functional domains.
To identify the species specificity, individual unigene was annotated based on the highest BLAST score against the NR database. Among higher plants, 39.8% unigenes had close homology to Sesamum indicum, then followed by Erythranthe guttata (10.4%), Brassica napus (5.9%), Hordeum vulgare (1.7%) and Vitis vinifera (1.7%) (Additional file 2: Figure S1 D). Further analysis indicated that 51.6% unigenes of the top hits showed very strong homology (E-value < 1.0e− 45), while 48.4% of the matched unigenes showed moderate homology with an E-value between 1.0e− 5 and 1.0e− 45 (Additional file 2: Figure S1 E). The similarity analysis showed that 51.2% unigenes had a similarity higher than 80%, 48.7% unigenes shared 40–80% similarity, and 0.1% unigenes were lower than 40% similarity (Additional file 2: Figure S1 F).
KOG and KEGG classification
Interestingly, some pathways are closely related to variations in oil content, such as fatty acid biosynthesis (97 unigenes), biosynthesis of unsaturated fatty acids (78 unigenes), α-linolenic acid metabolism (76 unigenes), fatty acid elongation (160 unigenes), glycerolipid metabolism (39 unigenes) and glycerophospholipid metabolism (56 unigenes). These unigenes will provide critical clues to identify and characterize key genes involving in UFA and TAG biosynthesis in P. frutescens seeds.
Analyses of differentially expressed genes at three seed development stages
Following the transcriptome assembly and annotation, clean reads obtained from each seed developing stage were individually mapped to determine the expression abundance as FPKM. Plotting expression fold change showed a high correlation of two biologically replicated sequencing runs as indicated by Pearson correlation (Additional file 4: Figure S2).
A total of 53 (32 up, 22 down), 653 (259 up, 394 down) and 1459 (742 up, 717 down) genes were differentially expressed in 10 DAF vs 5 DAF, 20 DAF vs 10 DAF, 20 DAF vs 5 DAF paired comparisons, respectively (log2 ratio ≥ 1 or ≤ − 1, FDR < 0.05) (Fig. 1c-f). Among all differentially expressed genes (DEGs), with the developmental process going on, the number of up-regulated genes was more than that of down-regulated genes. Differentially expressed genes will provide crucial cues to investigate the molecular mechanism of fatty acid synthesis and accumulation.
Identification and expression profiling of fatty acid biosynthesis genes
Finally, fatty acid synthesis is terminated by fatty acyl-ACP thioesterase (FATA, EC126.96.36.199) and palmitoyl/stearoyl-acyl carrier protein thioesterase (FATB, EC188.8.131.52) through moving the acyl group from ACP  . Interestingly, the expression of FATA (responsible for unsaturated FA production) was significantly increased from 5 DAF to 10 DAF, while the expression variation of FATB (for saturated FA production) was not observed during seed development. This was consist with higher plastid production of unsaturated than saturated FA in P. frutescens seed. In addition, one unigene encoding ω-6 fatty acid desaturase (FAD6, chloroplastic type), which catalyzes the formation of linolenic acid (C18:2), and one unigene encoding ω-7/8 fatty acid desaturase (FAD7/8, chloroplastic type), which catalyzes the formation of α-linolenic acid (C18:3), were identified and both of them exhibited an up-down-up expression pattern from 5 DAF to 20 DAF. Our results clearly indicated that linolenic acid and α-linolenic acid started to accumulate from 10 days after flowering, which was consistent with the lipid content measurement. Our results were also in agree with previous studies that most of the genes involving in the core fatty acid biosynthesis shared a similar temporal transcription pattern , suggesting the possibility that they were co-regulated and responsible for the higher oil accumulation in seeds. Free FA generated in the plastid were esterified to COA for triacylglycerol (TAG) biosynthesis by long-chain acyl-COA synthesis (LACs) at the plastid envelop. The expression of LACs peaked at 10 DAF suggested an increase in the flow of C16:0-COA, C18:0 COA or C18:1 COA towards TAG biosynthesis.
Identification and expression profiling of transcripts involved involved in TAG biosynthesis and metabolism
The biosynthesis of TAG starts with the acyl transfer from acyl-CoA to glycerol-3-phosphate (G3P) to generate lysophosphatidic acid (LPA) catalyzed by glycerol-3-phosphate acyltransferase (GPAT). Subsequently, LPA is dephosphorylated by lysophosphatidic acid acyltransferase (LPAT) and phophatidate phosphatase (PAP) to produce sn-1,2-diacylglycerol [25, 26]. In P. frutescens seeds, unigene GPAT, LPAT, and PAP have a temporal expression pattern of “down-up-down”, which was consistent with the expression pattern of genes involved in FA biosynthesis. The biosynthesis of TAG is terminated by diacylglycerol acyltransferase (DGAT), a rate-limiting enzyme in the Kennedy pathway, which transfers an acyl group from acyl-CoA to sn-3 of DAG. The transcription level of DGAT kept constantly from 5 DAF to 10 DAF, however it was significantly increased at 20 DAF (Additional file 7: Table S5). This result indicated that TAG assembly and accumulation through glycolysis pathway occurred in seed around 20 DAF. Previous studies also demonstrated that over expression of DGAT could improve the oil content in Arabidopsis, soybean and maize seeds. In an alternative metabolic pathway, DAG could be generated from the conversion of the lipid phosphatidylcholine (PC) to DAG, which catalyzed by phosphatidylcholine:diacylglycerol cholinephosphotransferase (PDCT) (EC: 2.7.8.*). The transcripts encoding of PDCT also showed a bell-shaped expression pattern. This expression pattern indicated that its potential role in providing DAG pool enriched with PUFA around 10 DAF, which was further incorporated into the accumulation of TAG by DAGT. Thus, any variation of PDCT probably affects directly or indirectly both the level of FA saturation and the assembly of TAG.
Though TAG biosynthesis was believed to occur mainly through the glycerol pathway as described above, an alternative pathway known as the acyl-CoA independent pathway has also been reported in some plants, in which phospholipid:diacylglycerol acyltransferase (PDAT) transfers the sn-2 acyl group from acyl-CoA to phospholipid and generates TAG. It is interesting to note that the expression level of PDAT at 10 DAF and 20 DAF was significantly higher than that in seed at 5 DAF (Fig. 7 and Additional file 7: Table S5). The different expression profile of PDAT and DGAT strongly suggested that the transcriptional regulation of genes in the reactions of TAG biosynthesis were under separated controls.
The oil accumulation is regulated by the dynamic balance between synthesis and breakdown of TAG. Catabolism of TAG is initialed by the action of triacylglycerol lipase (TAGL) that breakdowns the ester bonds and releasing free fatty acid . TAGL (c37957_gi) showed reduced expression (fold change = − 1.7) in 20 DAF seed than in 10 DAF seed. TAG catabolism proceeds in an opposite direction to the synthesis. Therefore, the suppression of TAG degradation would increase the accumulation of lipid content. Overall, identification of key genes involved in TAG biosynthesis and metabolism in our seed transcriptome helps to improve fatty acid and oil content in P. frutescens seeds.
Identification and expression profiling of α-linolenic acid metabolism and jasmonic acid biosynthesis genes
Although ALA is enriched in P. frutescens seed, the molecular mechanisms underlying the accumulation of in developing seed is still unclear. Our results revealed that levels of palmitic, oleic, and linoleic acid were higher in 5 DAF seeds, whereas oleic and linoleic acids levels were significantly decreased from 5 DAF to 25 DAF (Fig. 1b). Further analysis revealed that the accumulation of ALA was correlated with the expression of fatty acid desaturases 2 (FAD2) and FAD3. Previous studies have shown that microsomal FAD enzymes are the major contributors to seed ALA content in soybean  and Arabidopsis . Variation in the content of these fatty acids in developing seeds might be a result of differential activity of one or more desaturase enzymes. Therefore, it would be essential to study the genes involved in ALA content of P. frutescens seed varieties with specific emphasis on desaturase genes, in terms of copy numbers, allelic combination and transcriptional regulations as well as post-translational or post-translational regulation.
The biosynthesis of jasmonic acid in plant peroxisome requires the action of acyl-coenzyme A oxidase (ACX) through the octadecanoid pathway . Briefly, α-linolenic acid is oxygenated by lipoxigenase (LOX), and then converted to 12-oxo-phytodienoic acid (12-oxo-PDA) by the sequential action of allene oxide synthase (AOS) and allene oxide cyclase. Subsequently, JA is further catabolized to generate its volatile counterpart MeJA . Our results revealed that almost all genes encoding key enzymes involved in ALA metabolism in chloroplast were significantly down-regulated during the seed development process. There expression patterns extended the idea of suppressing ALA metabolism to increase its accumulation in mid-seed developmental stage.
Identification of transcription factors involved in oil biosynthesis and deposition
To validate the expression difference of identified TFs, about four TFs were selected for qRT-PCR analyses (Fig. 9b-e). The results of qRT-PCR confirmed that the transcriptome data. Because the main metabolic process in seeds is fatty acid and lipids synthesis, so the high expression level of these TFs might be involved in fatty acid and lipid synthesis. Of course, further studies will be performed to decipher their regulatory roles in oil synthesis. In summary, our results provide some valuable clues for understanding the molecular mechanism of fatty acid and lipids biosynthesis.
Understanding the basic molecular mechanisms of lipid biosynthesis and metabolism is crucial for developing genetic engineering approaches for enhancing the oil content in P. frutescens seed. Detailed genome information is essential and indispensable for our understanding. Therefore, in this study RNA-seq data were generated from three developmental stages of P. frutescens seed. Transcripts encoding key enzymes involved in the biosynthesis and metabolism of fatty acids and TAG were successfully identified and pathways were reconstructed. These findings would provide useful information regarding the oil accumulation of P. frutescens seed.
Our results showed that the major time period for unsaturation fatty acids accumulation in P. frutescens seed under our experimental conditions occurred between 5 and 15 DAF. However, a significant portion of the transcriptome was highly dynamic between 10 DAF and 20 DAF. Gene ontology and KEGG pathway enrichment analysis revealed that biological processes such as FA and TAG biosynthesis, regulation of α-linolenic acid metabolism, were upregulated. Our de novo assembled transcriptome for P. frutescens seed will serve as an important resource for future genetic and evolutionary researches (comparison between varieties, and so on) that focus on gene expression differences at particular developmental period.
Perilla frutescens var. crispa F. purpurea (red Perilla) were grown in the experiment garden of Chongqing Normal University, China, under the natural conditions. Blooming plants were observed daily at the same time and tagged, and the tagging dates were recorded as 0 day after flowering (0 DAF). Seeds at 5 DAF, 15 DAF and 25 DAF were harvested for oil content measurements. Based on the results of FA composition test, seeds at 5DAF, 10DAF and 20 DAF were selected as materials for comparative transcriptome analysis to explore the regulation of fatty acid synthesis and metabolism. Two biological repeat samples were celected for each developmental stage, frozen immediately in liquid nitrogen and stored at − 80 °C until further use.
Fatty acid composition determination
Seeds from each developmental stage were weighted and dried overnight at 60 °C, then were grounded, extracted with 1 mL of hexane for 1 h, centrifuged at 13,000 rpm for 10 min, and the upper suspensions were transferred to new tubes. This process was repeated for three times. To determine the profiles of fatty acids, extracted lipids were trans-methylated in 0.8 mL petroleum ether and 0.5 mL 5% H2SO4 (v/v, H2SO4: methanol) and the resulting fatty acids were analyzed using GC-MS method (GC-2010, plus instrument, Shimadzu, Japan) with a flame ionization detector on a DB-23 column (60 mm × 0.32 mm ID× 0.25 μm df, Agilent Technologies, Waldbronn, Germany) with the following parameters: column oven temperature 170 °C and flame ionization detector set as 280 °C. Fatty acid content was expressed as percentage of total fatty acids.
RNA extraction, library construction and sequencing
Total RNA was extracted from developing seeds at 5 DAF, 10 DAF and 20 DAF using TRIzol Reagent (Invitrogen, USA) with an additional DNAase I (QIAGEN) digestion step to remove any genomic DNA contamination according to the manufacturer’s directions. The purity and yield of total RNA was analyzed by the NanoDrop ND1000 spectrophotometer (Thermo Scientific, USA) and the Qubit Fluorimeter (Invitrogen, USA), respectively. The integrity was confirmed by the Aligent 2100 Bioanalyzer system (Agilent Technologies, USA). Samples with an RNA integrity number value greater than 8 were used for sequencing library preparation using Illumina®TruSeq™ RNA Sample Preparation Kit (Illumina Inc., San Diego, CA). Poly(A) mRNA was purified from 1 μg of total RNA using poly (T) oligo-attached magnetic beads according to the Illumina manufacturer’s instructions, and then fragmented by the Fragmentation Kit (Ambion, USA). Using these short fragments as templates, the first-strand cDNA was synthesized using ProtoScript II Reverse Transcriptase (Gibco, Life Technologies, USA) and random hexamers as primers. This step was followed by the second-strand cDNA synthesis using NEB second strand synthesis reaction buffer, DNA polymerase I and RNase H, The double stranded cDNA were purified using AMPure XP beads (Beckman Coulter, USA) and subjected to end repair process, adenylation and then ligated to Illumina multiplex barcode adapters. The adapter ligated cDNA was purified using AMPure XP beads and subjected to18 cycles of PCR to enrich the adapter-ligated fragments, which were further purified using AMPure XP beads. Sequencing libraries were initially quantified with a Qubit Fluorimeter (Thermo Fisher Scientific, USA) and diluted to a concentration of 1.5 ng/μL. The insert sizes were assessed by the Aligent 2100 Bioanalyzer system and then quantified by qPCR using the Kapa Library Quantification Kit (Kapa Biosystem, USA) (concentration > 2 nM). RNA sequencing was performed using a paired-end strategy (each end with 100 bases) on the Illumina HiSeq2000 platform at Biomaker Technology, Co., Ltd (Beijing China). The RNA-seq data was generated in FastQ format.
Data processing, assembly and functional annotation
Raw reads were trimmed to obtain high-quality reads by removing the adaptor sequences, low-quality tags and ambiguous inner regions. Gene functions were annotated by homology searching against NCBI NR, SwissPort, and KOG databases using the BlastX with a cutoff of E-value ≤10− 5. Proteins with the best hits to the unigenes were used for functional annotations. Gene Ontology annotation was performed by the Blast2GO program  and classified by WEGO (http://wego.genomics.org.cn/cgi-bin/wego/index.pl). Unigenes were also aligned to COG database to predict and classify potential functions. To further annotate their possible metabolic pathways, unigenes were mapped to KEGG database by using the single directional best hit (SBH) method on the KEGG Automatic Annotation Server (KAAS) online (http://www.genome.jp/tools/kaas/) (p < 0.05).
Transcription factor identification
To identify the transcription factors (TFs) represented in Perilla seed transcriptome, all assembled unigenes were searched against plant transcription factor database PlantTFDB (http://planttfdb.cbi.pku.edu.cn/) by BLAST with a cut-off of 1e− 5. Beased on the average of RPKM of genes across RNA-seq library replicates for a condition. Hierarchical clustering was performed using online Shinyheatmap server (http://shinyheatmap.com/). Before clustering, genes were filtered out that displayed low expression (< 5 RPKM) in all conditions. The average linkage method was used for cluster gerneration, with Euclidean distance as a similarity measure.
Time-course differentially gene expression analysis
Gene set association analyses for two pairs of samples, 10 DAF vs 5 DAF, and 20 DAF and 10 DAF, were performed to identify genes/ pathways involved in fatty acid biosynthesis and metabolism significantly changed during seed development. The normalized RPKM (fragments per kb per million reads) was used to calculate the expression abundance of unigenes between samples. The P-values were adjusted for multiple comparisons by hypergeometric test / Fisher’s exact test and the Benjamini and Hochberg false discovery rate correction (FDR ≤ 0.05). An absolute value of ∣log2 ratio∣ ≥ 1 was adopted as the cutoff to determine the significance of gene expression difference.
Validation of differentially expressed genes by qRT-PCR
qRT-PCR was performed to validate the results of RNA-seq analysis, 18 differentially expressed candidate genes involved in FA biosynthesis and metabolism were selected. Specific primers were designed using Primer 5.0 and were listed in Additional file 9: Table S6. Total RNA were extracted from seeds using TRIzol Reagent and treated with DNase to remove genome contaminations. The first-strand cDNA was synthesized using a RevertAid First Strand cDNA Synthesis kit (Fermentas, Vilnius, Lithuania). qRT-PCR was performed using a SYBR kit (SYBR Green I, Osaka, Japan) on a LightCycler 480 system (Roche, Basel, Switzerland). The amplification conditions were as follows: 95 °C for 1 min followed by 40 cycles of 95 °C for 10 s, and 62–68 °C for 30 s (depending on different genes). Three independent biological triplicates and two technique repeats were performed for each sample. The relative gene expression levels were normalized to inner controls β-actin and 18sRNA and calculated using 2-ΔΔT method  ANOVA analysis was performed using SPSS17.0 program (SPSS Inc., Chicago, USA). All data were represented as the means ± standard error (SE, n = 3).
Authors thank the Chongqing Engineering Research Center of Special Crop Resources for scientific advice.
This work was supported by grants from National Natural Science Foundation of China (31171588), Chongqing Science and Technology Commission (cstc2016shmszx80051), and The Program for Innovative Research Team in University, Chongqing (CXTDX201601018)..
Availability of data and materials
The sequence raw data from this study have been submitted to the NCBI Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under the BioProject ID PRJNA383438, PRJNA382769, PRJNA382879, PRJNA383439, PRJNA384884, PRJNA383437.
BNL, T Z and YJH designed the study, interpreted the data and wrote the manuscript. BNL, HYB and LG performed experimental work. YJH and JXL did the bioinformatics analysis. All authors read and approved the final manuscript.
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