Identifying Conserved and Novel MicroRNAs in Developing Seeds of Brassica napus Using Deep Sequencing

Abstract

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. Members of 59 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 29 families not reported in B. napus but conserved in other plant species were identified by alignment with known plant mature miRNAs. Assembled mRNA-seq contigs allowed for a search of putative new precursors and led to the identification of 13 novel miRNA families. Analysis of miRNA population between libraries reveals that several miRNAs and isomiRNAs have different abundance in developing stages compared to mature seeds. The predicted miRNA target genes encode a broad range of proteins related to seed development and energy storage. This work presents a comparative study of the miRNA transcriptome of mature and developing B. napus seeds and provides a basis for future research on individual miRNAs and their functions in embryogenesis, seed maturation and lipid accumulation in B. napus.

Tight regulation of the interaction between Brassica napus and Sclerotinia sclerotiorum at the microRNA level

“…However, this number is only 92 for B. napus, although it is polyploidy with a much larger and more complex genome than these plants. This indicates that although an increasing number of B. napus miRNAs have been annotated (Buhtz et al 2008;Korbes et al 2012;Xu et al 2012a; wild-type except line #21, which showed retarded growth and more severely serrated leaves (Fig. 4b).…”

Recent transcriptomics advances and emerging applications in food science

“…The RNA-seq analysis of miRNA requires specialized protocols for preparation of libraries that allow capture of the short miRNA sequences from RNA samples [62]. Based on this idea, Illumina RNA-seq technology has been applied to study the miRNA fraction in the common bean [63] and rapeseed [64]. González-Ibeas et al used barcoding strategy to prepare 10 RNA libraries from different melon-plant tissues for further sequencing using Roche technology [65].…”

Emerging RNA-Seq Applications in Food Science

“…Similarly, Illumina RNA-Seq has been used for the study of different aspects in major food crops, such as for example the studies on rice including the investigation of seed development [39,40], the transcriptional response to nematode infection [41] and to drought stress [42]; differential gene expression between aleurone and starchy wheat endosperm [43]; and transcript profiling in maize [44], chickpea [45], and soybean [46]. Also, Illumina RNA-Seq technology has been applied to study the miRNA fraction in common bean [47] and rapeseed [48]. González-Ibeas et al used barcoding strategy to prepare 10 RNA libraries from different melon plant tissues for further sequencing using Roche technology [49].…”