Dataset Information

Identification of microRNAs and transcript targets in Jatropha seeds

ABSTRACT: 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.

ORGANISM(S): Jatropha curcas

PROVIDER: GSE50669 | GEO | 2016/09/06

SECONDARY ACCESSION(S): PRJNA218216

REPOSITORIES: GEO

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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.

Project description:Jatropha curcas L. is a potential biofuel plant. Application of exogenous cytokinin (6-benzyladenine, BA) on its inflorescence buds can significantly increase the number of female flowers, thereby improving seed yield. To investigate which genes and signal pathways are involved in the response to cytokinin in J. curcas inflorescence buds, we monitored transcriptional activity in inflorescences at 0, 3, 12, 24, and 48 h after BA treatment using a microarray. We detected 5,555 differentially expressed transcripts over the course of the experiment, which could be grouped into 12 distinct temporal expression patterns. We also identified 31 and 131 transcripts in J. curcas whose homologs in model plants function in flowering and phytohormonal signaling pathways, respectively. According to the transcriptional analysis of genes involved in flower development, we hypothesized that BA treatment delays floral organ formation by inhibiting the transcription of the A, B and E classes of floral organ-identity genes, which would allow more time to generate more floral primordia in inflorescence meristems, thereby enhancing inflorescence branching and significantly increasing flower number per inflorescence. BA treatment might also play an important role in maintaining the flowering signals by activating the transcription of GIGANTEA (GI) and inactivating the transcription of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and TERMINAL FLOWER 1b (TFL1b). In addition, exogenous cytokinin treatment could regulate the expression of genes involved in the metabolism and signaling of other phytohormones, indicating that cytokinin and other phytohormones jointly regulate flower development in J. curcas inflorescence buds. Our study provides a framework to better understand the molecular mechanisms underlying changes in flowering traits in response to cytokinin treatment in J. curcas inflorescence buds. The results provide valuable information related to the mechanisms of cross-talk among multiple phytohormone signaling pathways in woody plants. Gene expression of flower buds in response to BA was measured at 0h, 3h, 12h, 24h and 48h after 1mM 6-benzylaminopurine treatment. Three biological replicates were prepared for each time point.

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Identification of microRNAs and transcript targets in Jatropha seeds

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