Differential lipid synthesis in the developing seeds of Jatropha and Vernicia: a comparative transcriptomic study
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ABSTRACT:
ORGANISM(S): Jatropha curcas Vernicia fordii
PROVIDER: GSE76386 | GEO | 2018/12/29
REPOSITORIES: GEO
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Project description:MicroRNAs or miRNAs are endogenously encoded small RNAs that play a key role in diverse plant biological processes. Jatropha curcas L. has received much attention as a potential oilseed crop for the production of renewable oil. Here, a sRNA library from mature seeds and three mRNA libraries, from three different stages of seed development, were generated by deep sequencing in order to identify and characterize miRNAs and pre-miRNAs of J. curcas. Computation analysis allowed the identification of 180 conserved miRNAs and 41 precursors (pre-miRNAs), as well as 16 novel pre-miRNAs. The predicted miRNA target genes are involved in a broad range of physiological functions, including cellular structure, nuclear function, translation, transport, hormone synthesis, defense and also lipid metabolism. Some of pre-miRNA and miRNA targets have different abundance among the three stages of seed development. A search for sequences that produce siRNA was performed indicating that J. curcas siRNAs play a role in nuclear functions, transport, catalytic process and diseases resistance. This study presents the first large scale identification of J. curcas miRNAs and their targets in mature seeds based on deep sequencing and contributes to understand the function of these miRNAs. microRNA identification in a mature seed library of Jatropha curcas by deep sequencing (Illumina HiSeq2000).
2016-09-06 | E-GEOD-50669 | biostudies-arrayexpress
Project description:MicroRNAs or miRNAs are endogenously encoded small RNAs that play a key role in diverse plant biological processes. Jatropha curcas L. has received much attention as a potential oilseed crop for the production of renewable oil. Here, a sRNA library from mature seeds and three mRNA libraries, from three different stages of seed development, were generated by deep sequencing in order to identify and characterize miRNAs and pre-miRNAs of J. curcas. Computation analysis allowed the identification of 180 conserved miRNAs and 41 precursors (pre-miRNAs), as well as 16 novel pre-miRNAs. The predicted miRNA target genes are involved in a broad range of physiological functions, including cellular structure, nuclear function, translation, transport, hormone synthesis, defense and also lipid metabolism. Some of pre-miRNA and miRNA targets have different abundance among the three stages of seed development. A search for sequences that produce siRNA was performed indicating that J. curcas siRNAs play a role in nuclear functions, transport, catalytic process and diseases resistance. This study presents the first large scale identification of J. curcas miRNAs and their targets in mature seeds based on deep sequencing and contributes to understand the function of these miRNAs.
2016-09-06 | GSE50669 | GEO
Project description:Jatropha curcas, a tropical shrub, is an attractive biofuel crop, which produces seeds with a high content of oil and protein. Most J. curcas accessions contain a range of toxins and anti-nutritional compounds, which are unfavorable for human consumption and animal feed. With the goal of better understanding the development of its seeds and to improve Jatropha`s agronomic performance, a two-step approach was performed: 1) generation of the entire transcriptome of six different developmental stages of J. curcas seeds using 454-Roche sequencing of a cDNA library, 2) comparison of transcriptional expression levels in six different developmental stages of seeds using a custom Agilent 8x60K oligonucleotide gene expression microarray. A total of 793,875 high quality reads with an average length of 358 bp were generated and assembled into 19,841 unique full-length contigs, of which 13,705 could be annotated with GO terms. Microarray data analysis identified a total of 9,111 contigs which were differentially expressed between the six developmental stages (based on P-value of < 1e-8). The microarray-based differential expression results were validated for 192 putative genes using high-throughput quantitative real-time PCR. Results from Gene Ontology (GO) and pathway enrichment analysis showed that the upstream biosynthesis pathways were relatively active among differentially expressed sequences (DESs) during seed development, such as starch and sucrose metabolism, glycolysis/gluconeogenesis, glycerophospholipid metabolism, amino sugar and nucleotide sugar metabolism. Further, DESs related to hormone and seed development, flavonoid biosynthesis-related pathways were over-represented. A pairwise comparison was used to discover particular seed maturation dependent patterns of gene expression. Genes related to fatty acid biosynthesis were over represented in early stage, while flavonoid biosynthesis in the late stage. The data provide a useful resources and references for the seed transcriptome of J. curcas and other related species with oil producing seeds. The identified transcripts related to seed development provide a starting point for further investigation into the molecular mechanisms underlying this process.
2018-05-31 | GSE109931 | GEO
Project description:We report the application of RNA-seq technology for highthroughput profiling of photosynthetic and non-photosynthetic seeds of Arabidopsis chlorophyll synthase mutant seeds. By generating over 21 GB of sequence data from these seeds, we showed that genes involved in oil accumulation in non-photosynthetic seeds were significantly induced compared to photosynthtic seeds. Additionally we found that genes involved in the plastidal oxidative pentos phosphate pathway were significantly upregulated in the non-photosynthetic seed opposite to photosynthetic seeds. Overall our RNA-seq analysis revealled the genes and pathway interaction underpinining oil accumulation in non-photosynthetic seeds.
2022-06-30 | GSE152614 | GEO
Project description:Differential lipid synthesis in the developing seeds of Jatropha and Vernicia: a comparative transcriptomic study
| PRJNA307164 | ENA
Project description:miRNA-sequencing of seeds in three developmental stages was performed to reveals gene regulation in relation to oil and fatty acid accumulation in sunflower
2020-06-02 | GSE151552 | GEO
Project description:This work present a large data set related to a non-target LC-MS/MS high-resolution metabolome analysis of the leaves and roots of Jatropha curcas. Besides its high protein contents, the seeds of J. curcas are also rich in oil, so the seeds are considered a potential source of raw material to produce biodiesel and a source of food for farm animals. The full exploitation of these potentials is hampered by the presence of a highly toxic class of diterpenoids, the phorbol esters (PE), both in the oil and in the seedcake derived from the extraction of the oil. The seeds are known to possess 6 different PE, and although their structures have been known for almost 30 years, the biosynthetic pathway of each one remains undetermined. However, there are indications that the enzyme casbene synthase is responsible for the first biosynthetic step. The leaves and roots of this species are also rich in several classes of diterpenes which by themselves have pharmacological potential not yet explored.
For our analysis, we used two genotypes that are contrasting regarding the contents of phorbol esters: One genotype has a high level of phorbol esters (HPE), while the other has low levels of phorbol esters in the seeds (LPE). We were able to detect a total of 2032 features and applied multivariate statistical methods, such as PCA and heatmap with hierarchical clustering to analyze and visualize the deposition pattern of metabolites, with a focus on terpenoids. Our analysis allowed us to several new findings regarding the synthesis of PE in J. curcas, such as that only in HPE genotypes roots are found diterpenes with the tigliane skeleton. In contrast, the LPE genotype has a higher concentration and diversity of sesquiterpenes. Taking into consideration the results of our previous proteome analysis of seeds, roots, and leaves and the metabolome data presented in the manuscript, we suggest that the absence of PE in the LPE genotype may be the result of the absence of the enzymes responsible for the final biosynthetic steps, which in turn lead to the accumulation of sesquiterpenes this genotype.
| MSV000092920 | MassIVE
Project description:RNA-sequencing (lncRNA,mRNA and circRNA) of seeds in three developmental stages was performed to reveals gene regulation in relation to oil and fatty acid accumulation in sunflower
2020-06-05 | GSE151778 | GEO
Project description:Identification of microRNAs and transcript targets in Jatropha seeds
| PRJNA218216 | ENA
Project description:Gene expression analysis by high-throughtput RNA-sequencing from roots of waterlogged jatropha (Jatropha curcas). Six leaf stage seedlings (~30 d.o.) were subjected to 24 h of soil waterlogging.
2014-11-05 | GSE57428 | GEO