Glycine max
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA285879 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2051070.fastq.gz | Fastqsanger.gz | |||
| SRR2051071.fastq.gz | Fastqsanger.gz | |||
| SRR2051072.fastq.gz | Fastqsanger.gz | |||
| SRR2051073.fastq.gz | Fastqsanger.gz |
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Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development. In soybean (Glycine max), an important edible oil crop, valuable lipids are synthesized and stored in the cotyledons during embryogenesis .This storage lipids are used as energy source of the emerging seeds, during the germination procces. Until now, there are no microRNAs related to lipid metabolism in soybean or any other plant. This work aims to describe the miRNAome of germinating seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus germinating seeds. A total of 183 familes were detected through a computational analysis of a large number of reads obtained from deep sequencing from two small RNA libraries of (i) pooled germintaing seeds stages and (ii) mature soybean seeds. We have found 39 new mirna precursors which produce 41 new mature forms. The present work also have identified isomiRNAs and mirnas offset (moRNAs). This work presents a comprehensive study of the miRNA transcriptome of soybean germinating seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in lipid consumption in development soybean seeds.
2015-05-25 | GSE38373 | GEO
Project description:RNA-seq was used to characterize gene expression in soybean from a wide range of tissues. The primary focus of the project was small RNAs, and the identification of microRNAs and phased siRNA-generating loci, but RNA-seq data were generated from the same samples. This project was supported by the United Soybean Board.
2020-05-09 | GSE150157 | GEO
Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development. In soybean (Glycine max), an important edible oil crop, valuable lipids are synthesized and stored in the cotyledons during embryogenesis .This storage lipids are used as energy source of the emerging seeds, during the germination procces. Until now, there are no microRNAs related to lipid metabolism in soybean or any other plant. This work aims to describe the miRNAome of germinating seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus germinating seeds. A total of 183 familes were detected through a computational analysis of a large number of reads obtained from deep sequencing from two small RNA libraries of (i) pooled germintaing seeds stages and (ii) mature soybean seeds. We have found 39 new mirna precursors which produce 41 new mature forms. The present work also have identified isomiRNAs and mirnas offset (moRNAs). This work presents a comprehensive study of the miRNA transcriptome of soybean germinating seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in lipid consumption in development soybean seeds. MicroRNA profiles in 2 different seed libraries (mature seeds and a pool of germinating seed stages) of Glycine max by deep sequencing (Illumina GAII).
2015-05-25 | E-GEOD-38373 | biostudies-arrayexpress
Project description:Small RNAs, including microRNAs and their targets, as well as phased secondary siRNAs, were characterized in the soybean genome by deep sequencing of small RNA libraries from a wide range of tissues. The mRNA targets of many of these small RNAs were also validated from many of the same tissues using PARE (Parallel Analysis of RNA Ends) libraries.
2014-12-01 | GSE58779 | GEO
Project description:Tropospheric ozone (O3) is a secondary air pollutant and anthropogenic greenhouse gas. Concentrations of tropospheric O3 have more than doubled since the Industrial Revolution, and are high enough to damage plant productivity. Soybean (Glycine max L. Merr.) is the worldâs most important legume crop and is sensitive to O3. Current ground-level O3 are estimated to reduce global soybean yields by 6% to 16%. In order to understand transcriptional mechanisms of yield loss in soybean, we examined the transcriptome of soybean flower and pod tissues exposed to elevated O3 using RNA-Sequencing.
2015-01-31 | E-MTAB-5226 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs (19–24 nt) that regulates de gene expression, mainly through mRNA targets cleavage and translation inhibition. In plants, miRNAs have been shown to play pivotal roles in a wide variety of metabolic and biological processes like plant growth, development, and response to biotic and abiotic stress. Soybean is one of the most important crops worldwide, due to the production of oil and its high protein content. The reproductive phase is considered the most important for the yield of soybean, which is mainly intended to produce the grains. The identification of miRNAs is not yet saturated in soybeans, and there are no studies linking them to the different floral organs. In this study, three different soybean floral whorls were used in the construction of sRNA libraries. The sequencing of petal, carpel and stamen libraries by the Solexa platform generated a total of 10,165,661 sequences. Subsequently analyses detected 200 miRNAs sequences, from those 41 were novel miRNAs never detected before, 80 were conserved soybean miRNAs, 31 were new antisense conserved soybean miRNAs and 46 soybean miRNAs isoforms. We also found a new miRNA conserved in other plant species, and finally one miRNA-sibling of a soybean conserved miRNA. Conserved and novel miRNAs were evaluated by RT-qPCR. We observed a differential expression across the three whorls for six miRNAs analyzed. A computational prediction of targets for miRNAs analyzed by RT-qPCR was performed. Many of the predicted targets have described functions related to the reproductive process in plants. In summary, the increased accumulation of specific and novel miRNAs in different whorls indicates that miRNAs are an important part of the regulatory network in soybean flower.
2018-05-25 | GSE69572 | GEO
Project description:Intercropping is a sustainable agricultural practice widely used around the world for enhancing resource use efficiency. However, short crops often grow in shade condition underneath the canopy of tall crops. Soybean is one of the most important oil crops and usually is planted in intercropping patterns. However, little is known about the acclimation responses of soybean leaves to shade in intercropping condition at the transcriptome level.
2013-07-11 | E-MTAB-4279 | biostudies-arrayexpress
Project description:RNA-seq of two soybean accessions under water deficit
2014-10-03 | E-MTAB-4352 | biostudies-arrayexpress
Project description:Background: Pollen, the male partner in the reproduction of flowering plants, comprises either two or three cells at maturity. The current knowledge of the pollen transcriptome is limited to the model plant Arabidopsis thaliana, which has tri-cellular pollen grains at maturity. Comparative studies on pollen of other genera, particularly crop plants, are needed to understand the pollen gene networks that are subject to functional and evolutionary conservation. In this study, we used the Affymetrix Soybean GeneChip® to perform transcriptional profiling on mature bi-cellular soybean pollen. Results: Compared to the sporophyte transcriptome, the soybean pollen transcriptome revealed a restricted and unique repertoire of genes, with a significantly greater proportion of specifically expressed genes than is found in the sporophyte tissue. Comparative analysis shows that, among the 37,500 soybean unique transcripts addressed in this study, 10,299 genes (27.46%) are expressed in pollen. Of the pollen-expressed genes, about 9,489 (92.13%) are also expressed in sporophytic tissues, and 810 (7.87%) are selectively expressed in pollen. Overall, the soybean pollen transcriptome shows an enrichment of transcription factors (mostly zinc finger family proteins), cell cycle-related transcripts, signal recognition receptors, ethylene responsive factors, chromatin remodeling factors, and members of the ubiquitin proteasome proteolytic pathway. Moreover, we identify several new pollen-specific candidate genes that might play a significant role in pollen biology. Conclusion: This is the first report of a soybean pollen transcriptional profile. These data extend our current knowledge regarding regulatory pathways that govern the gene regulation and development of pollen. We also demonstrate that pollen is a rich store of regulatory proteins that are essential and sufficient for de novo gene expression. A comparison between transcription factors up-regulated in soybean and those upregulated in Arabidopsis revealed some divergence in the numbers and kinds of regulatory proteins expressed in both species.
2009-03-26 | GSE12286 | GEO
Project description:Gene expression profiling implicates novel hormonal regulation of the floral initiation process in soybeans
| PRJNA108439 | ENA