Helin Tan

Key message In this manuscript, we disclosed the influence of light on the accumulation of storage reserves in B. napus embryos. 1. Light induced the gene expression in the developing embryos of B. napus. 2. Light promoted the starch synthesis in chloroplasts of B. napus embryos. 3. Light enhanced the metabolic activity of storage reserve synthesis in B. napus embryos. Abstract Light influences the accumulation of storage reserves in embryos, but the molecular mechanism was not fully understood. Here, we monitored the effects of light on reserve biosynthesis in Brassica napus by comparing embryos from siliques grown in normal light conditions to those that were shaded or masked (i.e., darkened completely). Masked embryos developed more slowly, weighed less, and contained fewer proteins and lipids than control embryos. They also had fewer and smaller oil bodies than control embryos and lacked chloroplasts, where starch grains are usually synthesized. The levels of most amino acids, carbohydrates, and fatty acids were higher in masked embryos than in control or shaded embryos, whereas the levels of these metabolites in the masked endosperms were lower than those in control and shaded endosperm. Transcriptome analysis indicated that genes involved in photosynthesis (42 genes), amino acid biosynthesis (51 genes), lipid metabolism (61 genes), and sugar transport (13 genes) were significantly repressed in masked embryos. Our results suggest that light contributes to reserve accumulation in embryos by inducing the expression of metabolic genes, thereby enhancing the biosynthesis of storage reserves.

Key message In this manuscript, we explored the key molecular networks for oil biosynthesis with the transcriptome and metabolome of B. napus embryo at different developmental stages. Abstract Brassica napus (B. napus) is an important oil crop worldwide, yet the molecular pathways involved in oil biosynthesis in seeds are not fully understood. In this study, we performed a combined investigation of the gene expression profiles and metabolite content in B. napus seeds at 21, 28 and 35 days after flowering (DAF), when seed oil biosynthesis takes place. The total triacylglycerol (TAG) content in seed embryos increased over the course of seed maturation, and was accompanied by changes in the fatty acid profile, an increase in lipid droplets, and a reduction in starch grains. Metabolome analysis showed that the total amino acid, free fatty acid and organic acid contents in seed embryos decreased during seed maturation. In total, the abundance of 76 metabolites was significantly different between 21 and 28 DAF, and 68 metabolites changed in abundance between 28 and 35 DAF. Transcriptome analysis showed that the set of genes differentially expressed between stages was significantly enriched in those related to lipid metabolism, transport, protein and RNA metabolism, development and signaling, covering most steps of plant lipid biosynthesis and metabolism. Importantly, the metabolite and gene expression profiles were closely correlated during seed development, especially those associated with TAG and fatty acid biosynthesis. Further, the expression of major carbohydrate metabolism-regulating genes was closely correlated with carbohydrate content during seed maturation. Our results provide novel insights into the regulation of oil biosynthesis in B. napus seeds and highlights the coordination of gene expression and metabolism in this process.

In this study, we analyzed the transcriptome and metabolite profile of the style to explore the essential metabolites and specific genes for pollen tube growth of B. napus in vivo.

The funiculus provides the sole channel of communication between the seed and the parent plant; however, little is known about its role in nutrient supply during seed maturation. Here, we investigated the dynamic metabolite profiles of the funiculus during seed maturation in Brassica napus. The funiculus was fully developed at 21 days after flowering (DAF), but the levels of nutrients, including carbohydrates, fatty acids, and amino acids, increased rapidly from 21 to 35 DAF. Orthogonal partial least squares discriminant analysis and correlation analysis identified 37 metabolites that correlated closely with seed fresh weight. To determine the influence of silique wall photosynthesis on the metabolites in the funiculus, we also covered the siliques of intact plants with aluminum foil; in these plants, the funiculus and silique wall had lower metabolite levels, compared with control. RNA-sequencing analysis of the funiculi in the dark-treated and light-exposed siliques showed that the expression of genes encoding nutrient transporters significantly increased in the funiculi in the dark-treated siliques. Furthermore, the transcripts encoding primary metabolic enzymes for amino acid synthesis, fatty acid synthesis and triacylglycerol assembly, and sucrose-starch metabolism, were also markedly up-regulated, despite the decline in metabolite levels of funiculi in the dark-treated silique. These results provide new insights into funiculus function in seed growth and synthesis of storage reserves in seeds, at the metabolic and transcriptional levels. The identification of these metabolites and genes also provides useful information for creating genetically enhanced oilseed crops with improved seed properties.

Canola (Brassica napus) is one of several important oil-producing crops, and the physiological processes, enzymes, and genes involved in oil synthesis in canola seeds have been well characterized. However, relatively little is known about the dynamic metabolic changes that occur during oil accumulation in seeds, as well as the mechanistic origins of metabolic changes. To explore the metabolic changes that occur during oil accumulation, we isolated metabolites from both seed and silique wall and identified and characterized them by using gas chromatography coupled with mass spectrometry (GC-MS). The results showed that a total of 443 metabolites were identified from four developmental stages. Dozens of these metabolites were differentially expressed during seed ripening, including 20 known to be involved in seed development. To investigate the contribution of tissue-specific carbon sources to the biosynthesis of these metabolites, we examined the metabolic changes of silique walls and seeds under three treatments: leaf-detachment (Ld), phloem-peeling (Pe), and selective silique darkening (Sd). Our study demonstrated that the oil content was independent of leaf photosynthesis and phloem transport during oil accumulation, but required the metabolic influx from the silique wall. Notably, Sd treatment resulted in seed senescence, which eventually led to a severe reduction of the oil content. Sd treatment also caused a significant accumulation of fatty acids (FA), organic acids and amino acids. Furthermore, an unexpected accumulation of sugar derivatives and organic acid was observed in the Pe- and Sd-treated seeds. Consistent with this, the expression of a subset of genes involved in FA metabolism, sugar and oil storage was significantly altered in Pe and Sd treated seeds. Taken together, our studies suggest the metabolite profiles of canola seeds dynamically varied during the course of oil accumulation, which may provide a new insight into the mechanisms of the oil accumulation at the metabolite level.

连翘既是传统的中药材, 又是优良的城市绿化树种, 具有重要的经济价值和生态价值. 但是连翘基因资源非常匮乏, 限制了其分子生物学和基因功能的研究. 本研究以连翘根、茎、叶、花和果实等器官的混合样品作为材料, 利用Illumina HiSeq^TM 2500测序平台对其进行转录组测序. 共获得23164327条干净数据(clean reads), 总碱基数为4678791021 bp. Clean reads经de novo组装后获得45112条unigenes. 进一步利用五大公共数据库进行同源比对, 注释了28699条unigenes. 其中, 473个基因参与了连翘次生物质的合成和代谢, 包括81个与苯丙氨酸和苯丙烷代谢相关的基因. 对这81个基因的分析表明, 有4个基因编码苯丙氨酸脱氨酶, 1个基因编码肉桂酸4-羟化酶, 2个基因编码4-香豆酰: 辅酶A连接酶. 这3个酶催化了连翘中主要药用活性物质苯乙醇苷和木脂素前体肉桂酸衍生物的生物合成. 此外, 还发现了2个松脂醇-落叶松树脂醇还原酶和1个开环异落叶松脂醇脱氢酶编码基因, 这2个酶是木脂素合成的关键酶. 最后, 分析了长度在1 kb以上的12721个unigenes的基因结构, 检测到3199个SSR位点, 并对其中40个位点进行了验证. 本研究不仅为连翘基因克隆和分子生物学研究提供了丰富的基础数据信息, 而且为连翘遗传多样性研究、指纹图谱构建和分子标记辅助选育奠定了分子基础. F. suspense is not only an important traditional Chinese medicine and but also an excellent urban greening tree species, thus has important economic and ecologic values. However, the lack of gene resources limits the molecular biology and gene functional studies in F. suspensa. In this study, the transcriptome of the mixed samples from root, stem, leaf, flower and fruit of F. suspensa was sequenced using the Illumina HiSeq^TM 2500 sequencing platform. After high through-put sequencing, a total of 23164327 clean reads with 4678791021 bp were obtained. The clean reads were then de novo assembled into 45112 unigenes, and 28699 unigenes were annotated by a similarity search against five public databases. Of these annotated unigenes, 473 genes were assigned to second metabolic pathway, including 81 genes associated with phenylalanine and phenylpropanoid metabolism. Further analysis of these 81 genes reveled that there were 4 genes encoding phenylalanine ammonia-lyase, 1 gene encoding cinnamate 4-hydroxylase and 2 genes encoding 4-coumarate: CoA ligase, respectively. These enzymes are involved in the biosynthesis of cinnamic acid derivatives, which are precursors of the mainly pharmaceutically active substances phenylethanoid glycosides and lignan in F. suspensa. In addition, we also identified 2 pinoresinol/lariciresinol reductase encoding genes and 1 secoisolariciresinol dehydrogenase encoding gene, which are the key genes in the lignan biosynthesis. Finally, a total of 3199 SSRs were identified from 12721 unigenes longer than 1 kb, and 40 of them were verified. This work not only provides many valuable basal data for gene cloning and molecular biology research, but also lays the foundation for genetic diversity analysis, finger printing construction and molecular marker assisted breeding in F. suspensa.