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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Identifying conserved and novel miRNAs in germinating seeds of Glycine max using deep sequencing

ABSTRACT: 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).

ORGANISM(S): Glycine max

SUBMITTER: Rogerio Margis

PROVIDER: E-GEOD-38373 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Identifying conserved and novel miRNAs in germinating seeds of Glycine max using deep sequencing

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

Identifying conserved and novel miRNAs in developing seeds of Brassica napus using deep sequencing [small RNA-seq]

Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development and seed formation. In Brassica napus, an important edible oil crop, valuable lipids are synthesized and stored in specific seed tissues during embryogenesis. The miRNA transcriptome of B. napus is currently poorly characterized, especially at different seed developmental stages. This work aims to describe the miRNAome of developing seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus developing seeds. A total of 62 miRNA families were detected through a computational analysis of a large number of reads obtained from deep sequencing two small RNA and two RNA-seq libraries of (i) pooled immature developing stages and (ii) mature B. napus seeds. Among these miRNA families, 17 families are currently known to exist in B. napus; additionally, 32 families not reported in B. napus but conserved in other plant species were identified by alignment with known plant mature miRNAs. The contigs from the assembled mRNA-seq data allowed for a search for putative new precursors and led to the identification of 13 novel miRNA families. Differential expression between the libraries was determined through a statistical analysis of normalized miRNA reads and revealed several miRNAs and isomiRNAs that were more abundant during the developing stages. The predicted miRNA target genes encode a broad range of proteins related to seed development and energy storage. This work presents a comprehensive study of the miRNA transcriptome of B. napus seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in embryogenesis, seed maturation and lipid accumulation in B. napus. microRNA profiles in 2 different seed libraries (mature seeds and a pool of developing seed stages) of Brassica napus by deep sequencing (Illumina HiSeq2000).

2014-08-01 | E-GEOD-38019 | biostudies-arrayexpress

Identifying conserved and novel miRNAs in developing seeds of Brassica napus using deep sequencing [mRNA-seq]

Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development and seed formation. In Brassica napus, an important edible oil crop, valuable lipids are synthesized and stored in specific seed tissues during embryogenesis. The miRNA transcriptome of B. napus is currently poorly characterized, especially at different seed developmental stages. This work aims to describe the miRNAome of developing seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus developing seeds. A total of 62 miRNA families were detected through a computational analysis of a large number of reads obtained from deep sequencing two small RNA and two RNA-seq libraries of (i) pooled immature developing stages and (ii) mature B. napus seeds. Among these miRNA families, 17 families are currently known to exist in B. napus; additionally, 32 families not reported in B. napus but conserved in other plant species were identified by alignment with known plant mature miRNAs. The contigs from the assembled mRNA-seq data allowed for a search for putative new precursors and led to the identification of 13 novel miRNA families. Differential expression between the libraries was determined through a statistical analysis of normalized miRNA reads and revealed several miRNAs and isomiRNAs that were more abundant during the developing stages. The predicted miRNA target genes encode a broad range of proteins related to seed development and energy storage. This work presents a comprehensive study of the miRNA transcriptome of B. napus seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in embryogenesis, seed maturation and lipid accumulation in B. napus. RNA profiles in 2 different seed libraries (mature seeds and a pool of developing seed stages) of Brassica napus by deep sequencing (Illumina HiSeq2000).

2014-08-01 | E-GEOD-38018 | biostudies-arrayexpress

Circadian clock controlled gene expression in soybean seeds

Project description:Microarray expression profiling was used to identify genes expressed in developing soybean (Glycine max) seeds that are controlled by the circadian clock. Plants with developing seeds were entrained to 12hour light: 12 hour dark cycles and sampled in constant light conditions. Soybean seeds entrained to 12 hour-light:12 hour dark photocycles were harvested after 24 hours of constant light and temperature conditions. Timepoint 24h represents subjective dawn. To minimize developmental variation, flowers were marked as they opened and seeds were harvested from marked pods after 5 weeks. There are two replicate samples at each time point, and each sample consists of 8 seeds collected from three diffferent plants.

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Gene Expression Changes during embryo and seed maturation, quiescence and germination in soybean

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Detection and Characterization of Gene Expression Differences in Transgenic Glycine max Seeds with RNAseq

Project description:Transformation of Glycine max with seed-targeted expression vectors via Agrobacterium causes measurable unscripted gene expression changes in the seed transcriptome Overall design: mRNA was sequenced from three transgenic events expressing three different recombinant proteins in soybean seeds. Three plants were chosen from each as group replicates, and three seeds from each plant as individual biological replicates.

2015-10-06 | E-MTAB-4317 | biostudies-arrayexpress

Analysis of representative organ specific genes and promoters of rice using 3â ORF oriented long oligomer microarray

Project description:The profiling was conducted with the Rice 3'-Tiling Microarray designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). In this research, an array of 27,448 rice genes was used to elucidate the transcriptome of 7 tissues or organs of Oryza sativa L. cv. Dongjin including calli, regenerating calli, germinating seeds, leaves, roots, and flowers (before and after pollination) using a rice 3â² ORF tilling microarray. The ratio of standard deviation to the mean of microarray intensities was used to distinguish between organ-specific and constitutively expressed genes. Accordingly, the genes are classified into highly variable, variable, and constitutive groups. To isolate the organ-specific promoters, several genes were selected and validated in planta using reporter gene analysis. We found that the Os01g0702500, Os11g0211800, and Os01g0257300 promoters were active in the calli, germinating seeds, and roots, respectively. The Os08g0135500 promoter was shown to drive transgene expression in various organs of the mature flowers, such as the anther, lemma, and palea, whereas the Os03g0369100 promoter was only active in the anther. Lastly, the Os09g0553100 promoter induced high levels of reporter gene expression in all organs. The gene expression data from representative organs could put a frame work for large dataset collections and then subsequent profiling by subdivision of organ/tissues might be more efficient to find appropriate promoters. A total of 14 chips were used for microarray. Total RNAs were extracted from rice 7 tissues or organs of Oryza sativa L. cv. Dongjin including calli, regenerating calli, germinating seeds, leaves, roots, and flowers (before and after pollination. Experiments were duplicated.

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Soybean seed germination LC-MS/MS

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2016-09-12 | PXD004106 | Pride

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