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| Status |
Public on Aug 01, 2014 |
| Title |
Identifying conserved and novel miRNAs in developing seeds of Brassica napus using deep sequencing [mRNA-seq] |
| Organism |
Brassica napus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
RNA profiles in 2 different seed libraries (mature seeds and a pool of developing seed stages) of Brassica napus by deep sequencing (Illumina HiSeq2000).
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| Contributor(s) |
Körbes AA, Guzman FF, Margis RR |
| Citation(s) |
23226347 |
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| Submission date |
May 17, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Rogerio Margis |
| E-mail(s) |
[email protected]
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| Organization name |
Universidade Federal do Rio Grande do Sul
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| Department |
Centro de Biotecnologia
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| Lab |
Laboratório de Genomas e Populações de Plantas - LGPP
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| Street address |
Av. Bento Goncalves 9500
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| City |
Porto Alegre |
| State/province |
RS |
| ZIP/Postal code |
91501-970 |
| Country |
Brazil |
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| Platforms (1) |
| GPL15579 |
Illumina HiSeq 2000 (Brassica napus) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE38020 |
Identification of miRNAs in developing seeds of Brassica napus |
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| Relations |
| BioProject |
PRJNA167107 |
| SRA |
SRP013235 |
