High-throughput sequence analysis of small RNAs in skotomorphogenic seedlings of Brassica rapa ssp. rapa

• Published in: Gene 2014-09, Vol.548 (1), p.68-74
• Main Authors: Zhou, Bo, Fan, Pengzhen, Li, Yuhua
• Format: Article
• Language: English
• Subjects: Base Sequence; Brassica rapa; Brassica rapa - genetics; Conserved Sequence; Darkness; Gene Expression Regulation, Plant; High-Throughput Nucleotide Sequencing - methods; High-throughput sequencing; MicroRNA; MicroRNAs; RNA, Messenger - genetics; RNA, Plant - genetics; Seedlings - genetics; Seedlings - growth & development; Sequence Analysis, RNA - methods; Skotomorphogenesis; Turnip
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2014.07.010

Skotomorphogenic development is the process by which seedlings adapt to a stressful dark environment. Such metabolic responses to abiotic stresses in plants are known to be regulated in part by microRNAs (miRNAs); however, little is known about the involvement of miRNAs in the regulation of skotomorphogenesis. To identify miRNAs at the genome-wide level in skotomorphogenic seedlings of turnip (Brassica rapa subsp. rapa), an important worldwide root vegetable, we used Solexa sequencing to sequence a small RNA library from seedlings grown in the dark for 4days. Deep sequencing showed that the small RNAs (sRNAs) were predominantly 21 to 24 nucleotides long. Specifically, 13,319,035 reads produced 359,531 unique sRNAs including rRNA, tRNA, miRNA, small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), and unannotated sRNAs. Sequence analysis identified 96 conserved miRNAs belonging to 36 miRNA families and 576 novel miRNAs. qRT-PCR confirmed that the miRNAs were expressed during skotomorphogenesis similar to the trends shown by the Solexa sequencing results. A total of 2013 potential targets were predicted, and the targets of BrmiR157, BrmiR159 and BrmiR160 were proved to be regulated by miRNA-guided cleavage. These results show that specific regulatory miRNAs are present in skotomorphogenic seedlings of turnip and may play important roles in growth, development, and response to dark environment. •sRNAs unique to skotomorphogenic seedlings of turnip were identified.•We identified 96 miRNAs belonging to 36 conserved families and 576 novel miRNAs.•qRT-PCR confirmed the expression of miRNAs in skotomorophogenic seedlings.•Some miRNAs were induced to express in response to light or in different tissues.•miRNA-guided cleavage regulated predicted targets of miR157, miR159, miR160.