Ontology highlight
ABSTRACT:
PROVIDER: PRJNA636370 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11902032_1.fastq.gz | Fastqsanger.gz | |||
| SRR11902032_2.fastq.gz | Fastqsanger.gz | |||
| SRR11902033.fastq.gz | Fastqsanger.gz | |||
| SRR11902034_1.fastq.gz | Fastqsanger.gz | |||
| SRR11902034_2.fastq.gz | Fastqsanger.gz |
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2009-11-23 | E-GEOD-17943 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that play essential roles in plant growth and development. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling identified 150 high-confidence genes within 26 miRNA families. For 25 families, expression was verified by deep-sequencing of small RNA libraries that were prepared from an assortment of maize tissues. PCR-RACE amplification of 68 miRNA transcript precursors, representing 18 families conserved across several plant species, showed that splice variation and the use of alternative transcriptional start and stop sites is common within this class of genes. Comparison of sequence variation data from diverse maize inbred lines versus teosinte accessions suggest that the mature miRNAs are under strong purifying selection while the flanking sequences evolve equivalently to other genes. Since maize is derived from an ancient tetraploid, the effect of whole-genome duplication on miRNA evolution was examined. We found that, like protein-coding genes, duplicated miRNA genes underwent extensive gene-loss, with ~35% of duplicate homeologous miRNA genes retained. This number is higher than that observed with protein-coding genes. A search for putative miRNA targets indicated a bias towards genes in regulatory and metabolic pathways. As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes.
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Project description:Blanc Du bois grapes are gaining popularity in the South eastern US due to its distinctive flavor and disease tolerance characteristics. Berry composition at harvest is a major contributing factor of wine quality. Blanc Du bois grapes are harvested from EL-38 and EL-39 stages depending on the style of wine desired or harvested early to avoid rain nearing harvest. In the current study, gel-free proteome analysis was applied to investigate changes in enzymes, primary and secondary metabolism proteins during ripening and late ripe stage. Grape berries from EL-33, EL-34, EL-36, EL-38 and EL-39 were collected based on brix, acidity and density. Protein extracts from different berry stages were resolved by electrophoresis. Proteins were extracted from the gel as a single band, detained and subjected to proteolysis with sequencing grade trypsin. Trypsin digested peptides from different berry protein extracts were separated on a nano LC and the eluent was sprayed onto to a LTQ Orbitrap Velos mass spectrometer. The raw files were analyzed using Proteome Discoverer with Sequest and Mascot search nodes using Vitis species FASTA database (70,263 entries) and the data were further validated by Scaffold software. A total of 1091, 1131, 1078, 1042 and 1066 proteins were detected in EL-33, EL-34, EL-36, EL-38 and EL-39 of berries respectively. Statistical ANOVA analysis revealed 927 proteins present across the stages that are involved in various biochemical and metabolic pathways. Seventeen proteins including dihydroflavonol reductase, sucrose phosphate synthase, PR proteins increased more than three-fold between ripe and late ripe berry stages. Other proteins that increased during ripe and late ripe stage berries were alcohol dehydrogenase 1, anthocyanidin reductase, phospho-2-dehydro-3-deoxyheptonate aldolase, fatty acid hydroperoxide lyase, cinnamyl alcohol dehydrogenase, -isopiperitenol (-)-carveol and SAM-methyltransferases.
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