Plant Functional Genomics, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
Department of Viticulture, Szent István University, Villányi út 29-43, 1118 Budapest, Hungary.
BMC Genomics. 2020 Apr 9;21(1):290. doi: 10.1186/s12864-020-6666-1.
Jatropha curcas, a tropical shrub, is a promising biofuel crop, which produces seeds with high content of oil and protein. To better understand the maturation process of J. curcas seeds and to improve its agronomic performance, a two-step approach was performed in six different maturation stages of seeds: 1) generation of the entire transcriptome of J. curcas seeds using 454-Roche sequencing of a cDNA library, 2) comparison of transcriptional expression levels using a custom Agilent 8x60K oligonucleotide microarray.
A total of 793,875 high-quality reads were assembled into 19,382 unique full-length contigs, of which 13,507 could be annotated with Gene Ontology (GO) terms. Microarray data analysis identified 9111 probes (out of 57,842 probes), which were differentially expressed between the six maturation stages. The expression results were validated for 75 selected transcripts based on expression levels, predicted function, pathway, and length. Result from cluster analyses showed that transcripts associated with fatty acid, flavonoid, and phenylpropanoid biosynthesis were over-represented in the early stages, while those of lipid storage were over-represented in the late stages. Expression analyses of different maturation stages of J. curcas seed showed that most changes in transcript abundance occurred between the two last stages, suggesting that the timing of metabolic pathways during seed maturation in J. curcas occurs in late stages. The co-expression results showed that the hubs (CB5-D, CDR1, TT8, DFR, HVA22) with the highest number of edges, associated with fatty acid and flavonoid biosynthesis, are showing a decrease in their expression during seed maturation. Furthermore, seed development and hormone pathways are significantly well connected.
The obtained results revealed differentially expressed sequences (DESs) regulating important pathways related to seed maturation, which could contribute to the understanding of the complex regulatory network during seed maturation with the focus on lipid, flavonoid and phenylpropanoid biosynthesis. This study provides detailed information on transcriptional changes during J. curcas seed maturation and provides a starting point for a genomic survey of seed quality traits. The results highlighted specific genes and processes relevant to the molecular mechanisms involved in Jatropha seed maturation. These data can also be utilized regarding other Euphorbiaceae species.
麻疯树是一种热带灌木，是一种很有前途的生物燃料作物，其种子含有高含量的油和蛋白质。为了更好地了解麻疯树种子的成熟过程，并提高其农艺性能，采用两步法对种子的六个不同成熟阶段进行研究：1）使用 Roche 454 测序对 cDNA 文库进行测序，生成麻疯树种子的全转录组；2）使用定制的 Agilent 8x60K 寡核苷酸微阵列比较转录表达水平。
共组装出 793875 条高质量的读长，形成 19382 条全长的独特连续序列，其中 13507 条可被 Gene Ontology（GO）术语注释。微阵列数据分析在 6 个成熟阶段中鉴定出 9111 个探针（57842 个探针中的 9111 个探针）差异表达。根据表达水平、预测功能、途径和长度，对 75 个选定的转录本进行了验证。聚类分析结果表明，与脂肪酸、类黄酮和苯丙素生物合成相关的转录本在早期阶段表达量较高，而与脂质储存相关的转录本在晚期阶段表达量较高。麻疯树种子不同成熟阶段的表达分析表明，转录本丰度的大多数变化发生在最后两个阶段之间，这表明麻疯树种子成熟过程中代谢途径的时间发生在晚期阶段。共表达结果表明，具有最多边数（CB5-D、CDR1、TT8、DFR、HVA22）的枢纽基因与脂肪酸和类黄酮生物合成有关，其表达在种子成熟过程中呈下降趋势。此外，种子发育和激素途径的连接性很好。
本研究揭示了调控与种子成熟相关的重要途径的差异表达序列（DES），这有助于理解种子成熟过程中的复杂调控网络，重点关注脂质、类黄酮和苯丙素生物合成。本研究为麻疯树种子成熟过程中的转录变化提供了详细信息，并为种子质量性状的基因组调查提供了起点。研究结果突出了与麻疯树种子成熟相关的分子机制中特定基因和过程的重要性。这些数据也可用于其他大戟科物种。
