Next generation sequencing reveals gene transcription activities and alternative splicing events in germinating barley embryos
Ontology highlight
ABSTRACT:
ORGANISM(S): Hordeum vulgare subsp. vulgare
PROVIDER: GSE66024 | GEO | 2016/02/18
SECONDARY ACCESSION(S): PRJNA275710
REPOSITORIES: GEO
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Project description:Seed germination triggers a transition of growth and metabolic activities from quiescent to active statuses. Germinating seeds is a good system to study many biological and biochemical processes including hormone metabolic activities and cell wall biosynthesis. Next generation sequence technology is used to study these processes. We have examined gene transcription activities and alternative splicing events in germinating embryos We dissected barley embryos from four barley varieties at 2 time points 24 h and 48 h
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Project description:A spatial resolved transcriptome for germinating barley grain was obtained for over 14,000 genes at 0, 1, 3 6 and 24 hours after imbibition. The spatial expression of a number of genes was validated using in-situ PCR, quantitative comparison to bulk RNA-seq reveal good correlations, despite the differences in the methodologies, and marker gene definition for tissues/clusters was consistent with previous gene specific studies. Targeted analysis of genes encoding aquaporins, crucial for water and ion movement during germination, revealed specific spatial expression patterns for gene members, and the tissue specific changes in gene members over time. Highly restricted spatial (and temporal) expression patterns were observed for genes encoding cell wall and transcription factors, e.g. one of the strongest expressed transcription factors was a bZIP family member that responds to germinating promoting Karrikin. It’s expression was restricted to the scutellum and the adjacent endosperm (0-3 HAI) and declined afterwards. Discovery-based bio-informatic approaches revealed thousands of genes displayed a spatially restricted pattern within tissues, with gene ontology revealing enriched categories such as auxin related functions of transport and response factors displaying distinct spatial expression patterns in tissues. This provides unprecedented spatial resolved cellular map for germination and specific genes to target for functional genomics to define cellular restricted processes in tissues during germination.
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Project description:Plant seeds prepare for germination already during seed maturation. We performed a detailed transcriptome analysis of barley grain maturation, desiccation and germination in two tissue fractions (endosperm/aleurone = e/a and embryo = em) using the Affymetrix barley1 chip. Experiment Overall Design: Barley developing and germinating seeds were harvested at different time points after flowering (developing) and imbibition (germinating). To further disseect the influence of different tissues, seeds were dissecte and tissues were analyzed individually.
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Project description:Genome-wide analysis was performed to assess the transcriptional landscape of germinating A. niger conidia using GeneChips. The metabolism of storage compounds during conidial germination was also examined and compared to the transcript levels from associated genes. The transcriptome of dormant conidia was shown to be highly differentiated from that of germinating conidia and major changes in response to environmental shift occurred within the first hour of germination. The breaking of dormancy was associated with increased transcript levels of genes involved in the biosynthesis of proteins, RNA turnover and respiratory metabolism. Increased transcript levels of genes involved in metabolism of nitrate and proline at the onset of germination implies their use as sources of nitrogen. Dormant conidia contained transcripts of genes involved in fermentation, gluconeogenesis and the glyoxylate cycle. The presence of such transcripts in dormant conidia may indicate the generation of energy from non-carbohydrate substrates during starvation-induced conidiation or for maintenance purposes during dormancy. The immediate onset of metabolism of internal storage compounds after the onset of germination, and the presence of transcripts of relevant genes, suggest that conidia are primed for the onset of germination.
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Project description:Genome-wide analysis was performed to assess the transcriptional landscape of germinating A. niger conidia using GeneChips. The metabolism of storage compounds during conidial germination was also examined and compared to the transcript levels from associated genes. The transcriptome of dormant conidia was shown to be highly differentiated from that of germinating conidia and major changes in response to environmental shift occurred within the first hour of germination. The breaking of dormancy was associated with increased transcript levels of genes involved in the biosynthesis of proteins, RNA turnover and respiratory metabolism. Increased transcript levels of genes involved in metabolism of nitrate and proline at the onset of germination implies their use as sources of nitrogen. Dormant conidia contained transcripts of genes involved in fermentation, gluconeogenesis and the glyoxylate cycle. The presence of such transcripts in dormant conidia may indicate the generation of energy from non-carbohydrate substrates during starvation-induced conidiation or for maintenance purposes during dormancy. The immediate onset of metabolism of internal storage compounds after the onset of germination, and the presence of transcripts of relevant genes, suggest that conidia are primed for the onset of germination. one biological replicate for each sample, each sample contained pooled RNA from three independent replicates
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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.
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