Identification and characterization of long non-coding RNA (lncRNA) in the developing seeds of Jatropha curcas.
Ontology highlight
ABSTRACT:
SUBMITTER: Yan X
PROVIDER: S-EPMC7316758 | biostudies-literature | 2020 Jun
REPOSITORIES: biostudies-literature
Publications
Identification and characterization of long non-coding RNA (lncRNA) in the developing seeds of Jatropha curcas.
Yan Xihuan X Ma Lanqing L Yang MingFeng M
Scientific reports 20200625 1
Long non-coding RNAs (lncRNAs) play critical roles in plant development. However, the information of lncRNAs in Jatropha curcas remains largely unexplored. Thus, an attempt has been made in J. curcas to identify 1,850 lncRNAs based on deep sequencing of developing seeds at three typical stages. About ten percent lncRNAs (196 lncRNAs) were differentially expressed lncRNAs during seed developing process. Together with reverse transcription quantitative real-time PCR, the lncRNA expression analyses ...[more]
Similar Datasets
Project description:MicroRNAs (miRNAs) are endogenously short noncoding regulatory RNAs implicated in plant development and physiology. Nine small RNA (sRNA) libraries from three typical seed developmental stages (young, intermediate, and mature) were generated by deep sequencing to identify the miRNAs of J. curcas, a potential oilseed crop for the production of renewable oil. Strict criteria were adopted to identify 93 high confidence miRNAs including 48 conserved miRNAs and 45 novel miRNAs. Target genes of these miRNAs were involved in a broad range of physiological functions, including gene expression regulation, primary & secondary metabolism, growth & development, signal transduction, and stress response. About one third (29 out of 93) miRNAs showed significant changes in expression levels during the seed developmental process, indicating that the miRNAs might regulate its targets by their changes of transcription levels in seed development. However, most miRNAs were found differentially expressed in the late stage of seed development, suggesting that miRNAs play more important roles in the stage when seed accumulating organic matters and suffering dehydration stress. This study presents the first large scale identification of high confidence miRNAs in the developing seeds of J. curcas.
| S-EPMC6418140 | biostudies-literature
Project description:BACKGROUND: Physic nut (Jatropha curcas L.) is an oilseed plant species with high potential utility as a biofuel. Furthermore, following recent sequencing of its genome and the availability of expressed sequence tag (EST) libraries, it is a valuable model plant for studying carbon assimilation in endosperms of oilseed plants. There have been several transcriptomic analyses of developing physic nut seeds using ESTs, but they have provided limited information on the accumulation of stored resources in the seeds. METHODOLOGY/PRINCIPAL FINDINGS: We applied next-generation Illumina sequencing technology to analyze global gene expression profiles of developing physic nut seeds 14, 19, 25, 29, 35, 41, and 45 days after pollination (DAP). The acquired profiles reveal the key genes, and their expression timeframes, involved in major metabolic processes including: carbon flow, starch metabolism, and synthesis of storage lipids and proteins in the developing seeds. The main period of storage reserves synthesis in the seeds appears to be 29-41 DAP, and the fatty acid composition of the developing seeds is consistent with relative expression levels of different isoforms of acyl-ACP thioesterase and fatty acid desaturase genes. Several transcription factor genes whose expression coincides with storage reserve deposition correspond to those known to regulate the process in Arabidopsis. CONCLUSIONS/SIGNIFICANCE: The results will facilitate searches for genes that influence de novo lipid synthesis, accumulation and their regulatory networks in developing physic nut seeds, and other oil seeds. Thus, they will be helpful in attempts to modify these plants for efficient biofuel production.
| S-EPMC3344900 | biostudies-literature
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:BackgroundJatropha curcas L. is promoted as an important non-edible biodiesel crop worldwide. Jatropha oil, which is a triacylglycerol, can be directly blended with petro-diesel or transesterified with methanol and used as biodiesel. Genetic improvement in jatropha is needed to increase the seed yield, oil content, drought and pest resistance, and to modify oil composition so that it becomes a technically and economically preferred source for biodiesel production. However, genetic improvement efforts in jatropha could not take advantage of genetic engineering methods due to lack of cloned genes from this species. To overcome this hurdle, the current gene discovery project was initiated with an objective of isolating as many functional genes as possible from J. curcas by large scale sequencing of expressed sequence tags (ESTs).ResultsA normalized and full-length enriched cDNA library was constructed from developing seeds of J. curcas. The cDNA library contained about 1 × 10(6) clones and average insert size of the clones was 2.1 kb. Totally 12,084 ESTs were sequenced to average high quality read length of 576 bp. Contig analysis revealed 2258 contigs and 4751 singletons. Contig size ranged from 2-23 and there were 7333 ESTs in the contigs. This resulted in 7009 unigenes which were annotated by BLASTX. It showed 3982 unigenes with significant similarity to known genes and 2836 unigenes with significant similarity to genes of unknown, hypothetical and putative proteins. The remaining 191 unigenes which did not show similarity with any genes in the public database may encode for unique genes. Functional classification revealed unigenes related to broad range of cellular, molecular and biological functions. Among the 7009 unigenes, 6233 unigenes were identified to be potential full-length genes.ConclusionsThe high quality normalized cDNA library was constructed from developing seeds of J. curcas for the first time and 7009 unigenes coding for diverse biological functions including oil biosynthesis were identified. These genes will serve as invaluable genetic resource for crop improvement in jatropha to make it an ideal and profitable crop for biodiesel production.
| S-EPMC3091748 | biostudies-literature
Project description:MicroRNAs (miRNAs) are small noncoding RNAs that play crucial regulatory roles by targeting mRNAs for silencing. To identify miRNAs in Jatropha curcas L, a bioenergy crop, cDNA clones from two small RNA libraries of leaves and seeds were sequenced and analyzed using bioinformatic tools. Fifty-two putative miRNAs were found from the two libraries, among them six were identical to known miRNAs and 46 were novel. Differential expression patterns of 15 miRNAs in root, stem, leave, fruit and seed were detected using quantitative real-time PCR. Ten miRNAs were highly expressed in fruit or seed, implying that they may be involved in seed development or fatty acids synthesis in seed. Moreover, 28 targets of the isolated miRNAs were predicted from a jatropha cDNA library database. The miRNA target genes were predicted to encode a broad range of proteins. Sixteen targets had clear BLASTX hits to the Uniprot database and were associated with genes belonging to the three major gene ontology categories of biological process, cellular component, and molecular function. Four targets were identified for JcumiR004. By silencing JcumiR004 primary miRNA, expressions of the four target genes were up-regulated and oil composition were modulated significantly, indicating diverse functions of JcumiR004.
| S-EPMC3303143 | biostudies-literature
Project description:Jatropha curcas L. is a non-edible oilseed containing almost 40% of seed oil and is famous as the best source of raw material for biofuel production. J. curcas seeds contain three main tissues, such as inner integument, endosperm, and embryo. To best understand the physiological events related to specific tissues, it is important to perform the proteome analysis of these tissues. Previously we have explored the pattern of reserves deposition and tissue-specific biological pathways by analyzing the proteome of the inner integument and endosperm and organelles, such as plastids and gerontoplasts isolated from these tissues. The focus of the present study was to perform the proteomic analysis of embryo isolated from the mature seeds of J. curcas. This analysis resulted in the identification of 564 proteins of which 206 are not identified previously from any other tissue of this plant. The identified proteins were functionally classified using the MapMan classification system revealing various proteins involved in different functionalities. The proteins involved in transport functions and those with proteolytic activity were determined through the Transporter Classification Database (TCDB) and MEROPS database, respectively. In addition to identify a large number of proteins participating in various metabolic processes, we found several proteins involved in defense functions, such as the members of chaperones and the ubiquitin-proteasome system. Similarly, members of the legumin and vicilin family of seed storage proteins (SSPs) were identified which in addition to their storage function, are involved in defense. In addition, we have reported that proteases belonging to different mechanistic classes and are involved in diverse physiological functions. Last but not the least, several classes of transport-related proteins were identified that are discussed concerning their function in the transportation of different nutrients across the embryo. To the best of our knowledge, this study reported the highest number of proteins identified from the embryo of mature J. curcas seeds, most of which are essential for seed germination, reflecting the fact that many proteins required for germination are already present in the mature embryo.
| S-EPMC8971811 | biostudies-literature
Project description:According to IPCC Annual Report (AR-5), environmental impact assessment of any product prototype is recommended before its large-scale commercialization; however, no environmental profile analysis of any biodiesel prototype has been conducted in Pakistan. Therefore, objective of this study was to conduct a comprehensive life cycle assessment (LCA), water footprint and cumulative energy demand (CED) of biodiesel production from Jatropha curcas L. (JC) seeds oil in Pakistan. A cradle-to-gate LCA approach was applied for 400 liter (L) JC biodiesel produced in Pakistan. JC biodiesel production chain was divided into three stages i.e., 1). cultivation of JC crop 2). crude oil extraction from JC seeds and 3). crude oil conversion to biodiesel. Primary data for all the stages were acquired through questionnaire surveys, field visits and measurements in the field. Potential environmental impacts were calculated in SimaPro v.9.2 software using Eco-indicator 99 methodology. Results showed that crude oil extraction stage accounted for highest emissions (77%) to the overall environmental impact categories evaluated, followed by oil conversion stage (21%) and JC cultivation stage (02%), respectively. The three stages of JC biodiesel production chain are major contributor to ecotoxicity with a contribution of 57% to this impact category. Higher contribution to ecotoxicity was due to agrochemicals used in the JC cultivation. Similarly, fossil fuels impact category was responsible for 38% of overall environmental impacts. In addition, water footprint of JC biodiesel production chain was 2632.54 m3/reference unit. Cumulative energy required for 400L JC biodiesel production chain was 46745.70 MJ in Pakistan. Fossil diesel consumption, synthetic fertilizers use and purchased electricity were major hotspot sources to environmental burdens caused by JC biodiesel production in Pakistan. By performing sensitivity analysis at 20% reduction of the baseline values of fossil diesel used, synthetic fertilizers and purchased electricity, a marked decrease in environmental footprint was observed. It is highly recommended that use of renewable energy instead of fossil energy would provide environmental benefits such as lower greenhouse gases and other toxic emissions as compared to conventional petroleum fuels. It is also recommended that JC as a biofuel plant, has been reported to have many desired characteristics such as quick growth, easy cultivation, drought resistance, pest and insect resistance, and mainly great oil content in JC seeds (27-40%). Therefore, JC plant is highly recommended to Billion Tree Afforestation Project (BTAP) for plantation on wasteland because it has multipurpose benefits.
| S-EPMC8601503 | biostudies-literature
Project description:Jatropha curcas L. or the physic nut is a monoecious shrub belonging to the Euphorbiaceae family. The plant is an ideal feedstock for biodiesel production; oil-rich seed (37-42%), has a broad range of growth habitat such as arid, semi-arid and tropical and a relatively feasible process for conversion of crude oil into biodiesel. The major constraint affecting the success of large-scale J. curcas plantation is seed yield inconsistency. Numerous research projects conducted on J. curcas with integrated genetic, genomic and transcriptomic approaches have been applied on the leaf, apical meristem, flower, root and fruit tissues. However, to date, no genomics data of J. curcas shoot system are publicly available, despite its importance in understanding flowering, fruiting and seed set qualities targeted for yield improvement. Here, we present eighteen sets of shoot and inflorescence transcriptomes generated from J. curcas plants with contrasting yields. Raw reads of the RNA-seq data are found in NCBI?s Sequence Read Archive (SRA) database with the accession number SRP090662 (https://www.ncbi.nlm.nih.gov/sra/?term=SRP090662). This transcriptomic data could be integrated with the present genomic resources for in depth understanding of J. curcas reproductive system.
| S-EPMC6187019 | biostudies-literature
Project description:miRNAs are endogenous approx 22 nucleotide RNA which mediates transcriptional or Post-transcriptional gene regulation and play a critical role in diverse aspects of plant development. miRNA identification in wet lab have various constraints, it is time consuming and expensive. It also faces the limitation of identifying miRNAs expressed at specific time and/or at special conditions. Due to the nature of strong conservation of miRNA in plant species, the use of comparative genomics approach for expressed sequence tags (ESTs), Genome Survey Sequence (GSS) and structural feature criteria filter has paved the way toward the identification of conserved miRNAs from the plant species whose genomes are not yet available in public domain. To identify the novel miRNA from Jatropha curcas, a total of 46862 EST sequences and 1569 GSS were searched for homology to previously known viridiplantae 2502 mature miRNA. After predicting the RNA secondary structure, 24 new potential miRNA were identified in J. curcas. Using the newly identified miRNA sequences, a total of 78 potential target genes were identified for 3 miRNA families. Most of the miRNA targeted genes were predicted to encode transcription factors that regulate cell growth and development, signaling, and metabolism. These findings considerably broaden the scope of understanding the functions of miRNA in J. curcas.
| S-EPMC3657014 | biostudies-literature
Project description:Jatropha curcas has been widely studied at the molecular level due to its potential as an alternative source of fuel. Many of the reports till date on this plant have focussed mainly on genes contributing to the accumulation of oil in its seeds. A suppression subtractive hybridization strategy was employed to identify genes which are differentially expressed in the mid maturation stage of J. curcas seeds. Random expressed sequence tag sequencing of the cDNA subtraction library resulted in 385 contigs and 1,428 singletons, with 591 expressed sequence tags mapping for enzymes having catalytic roles in various metabolic pathways. Differences in transcript levels in early and mid-to-late maturation stages of seeds were also investigated using sequence information obtained from the cDNA subtraction library. Seven out of 12 transcripts having putative roles in central carbon metabolism were up regulated in early seed maturation stage while lipid metabolism related transcripts were detected at higher levels in the later stage of seed maturation. Interestingly, 4 of the transcripts revealed putative alternative splice variants that were specifically present or up regulated in the early or late maturation stage of the seeds. Transcript expression patterns from the current study using maturing seeds of J. curcas reveal a subtle balancing of oil accumulation and utilization, which may be influenced by their energy requirements.
| S-EPMC3988328 | biostudies-literature