Abstract
MicroRNAs (miRNAs) are a class of endogenous, non-coding small RNAs that play an important role in transcriptional and post-transcriptional gene regulation. However, the sequence information and functions of miRNAs are still unexplored in Tulipa edulis. In this study, high-throughput sequencing was used to identify small RNAs in stolon formation stages (stage 1, 2, and 3) in T. edulis. A total of 12,890,912, 12,182,122, and 12,061,434 clean reads were obtained from stage 1, 2, and 3, respectively. Among the reads, 88 conserved miRNAs and 70 novel miRNAs were identified. Target prediction of 122 miRNAs resulted in 531 potential target genes. Nr, Swiss-Prot, GO, COG, and KEGG annotations revealed that these target genes participate in many biologic and metabolic processes. Moreover, qRT-PCR was performed to analyze the expression levels of the miRNAs and target genes in stolon formation. The results revealed that miRNAs play a key role in T. edulis stolon formation.
Highlights
IntroductionSince the first miRNA lin-4 was identified in Caenorhabditis elegans (Lee et al, 1993), more and more miRNAs, which play a pivotal role in post-transcriptional gene regulation, have been identified in plants and animals
Tulipa edulis is a perennial herb in the family Liliaceae and is an important medicinal plant in China
A similar result was reported in Arabidopsis thaliana and peanut (Rajagopalan et al, 2006; Chi et al, 2011)
Summary
Since the first miRNA lin-4 was identified in Caenorhabditis elegans (Lee et al, 1993), more and more miRNAs, which play a pivotal role in post-transcriptional gene regulation, have been identified in plants and animals. High-throughput sequencing has been successfully used to discover species-specific or lowly expressed miRNAs, such as those found in Aquilaria sinensis (Gao et al, 2012), Brachypodium (Zhang et al, 2009), and olive (Donaire et al, 2011). This powerful tool allows discovery of conserved and novel miRNAs in plant species without wholegenome data
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