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Transcriptome-wide identification and profiling of novel miRNAs involved in cold stress in Brassica oleracea
- 언어ENG
- URLhttps://db.koreascholar.com/Article/Detail/298269
Cabbage (Brassica oleracea) is one of the most important vegetable crops in the world. Yet, its sensitivity to cold stress, especially at the seedling stage, could limit the production. Until now, only, few studies about heritably durable cold tolerance were carried out in cabbage. Hence this study was done to characterize the transcriptome profiles of two cabbage genotypes with contrasting responses to cold stress using Illumina Hiseq short read (paired-end) sequencing technology. MicroRNAs (miRNAs) represent a class of short, non-coding, endogenous RNAs which play important roles in post-transcriptional regulation of gene expression. Thisstudy,wesoughttoprovideamorecomprehensivepredictionofB. oleracea cold responsive miRNAs based on high through put sequencing using two contrasting genotypes. The raw sequences were processed for removal of poor-quality and adaptor sequences. Then, the high quality unigenes (58,094) reads were applied for length filtering. Then, unigenes reads were used in a BLASTN search against of Rfam database and known miRNA database (miRBase 18.0) to removal of non-coding RNA’s and identifies conserved miRNA’s in B. oleracea. Further, novel reads were searched against B. oleracea genome. Their flanking sequences in the genome were used to predict their secondary structures, target prediction, and functional analysis. This is first report to identify novel miRNAs for cold stress through high throughput techniques. Our findings will provide an overview of potential miRNAs involved in cold stress, which may provide important clues on the function of miRNAs in from B. oleracea and other closely related Brassica species.
