Abstract
Phytochrome B (phyB), a member of the phytochrome family in rice, plays important roles in regulating a range of developmental processes and stress responses. However, little information about the mechanisms involved in the phyB-mediated light signaling pathway has been reported in rice. MicroRNAs (miRNAs) also perform important roles in plant development and stress responses. Thus, it is intriguing to explore the role of miRNAs in the phyB-mediated light signaling pathway in rice. In this study, comparative high-throughput sequencing and degradome analysis were used to identify candidate miRNAs and their targets that participate in the phyB-mediated light signaling pathway. A total of 720 known miRNAs, 704 novel miRNAs and 1957 target genes were identified from the fourth leaves of wild-type (WT) and phyB mutant rice at the five-leaf stage. Among them, 135 miRNAs showed differential expression, suggesting that the expression of these miRNAs is directly or indirectly under the control of phyB. In addition, 32 out of the 135 differentially expressed miRNAs were found to slice 70 genes in the rice genome. Analysis of these target genes showed that members of various transcription factor families constituted the largest proportion, indicating miRNAs are probably involved in the phyB-mediated light signaling pathway mainly by regulating the expression of transcription factors. Our results provide new clues for functional characterization of miRNAs in the phyB-mediated light signaling pathway, which should be helpful in comprehensively uncovering the molecular mechanisms of phytochrome-mediated photomorphogenesis and stress responses in plants.
Highlights
Light is a source of energy for photosynthesis, and a key environmental factor that affects plant growth and development
Small RNA Profiles of WT Rice and the Phytochrome B (phyB) Mutant To identify miRNAs involved in phyB-mediated light signaling, two independent small RNA libraries constructed with RNAs from the WT and phyB mutant leaves were sequenced
Adaptor sequences and low quality reads were removed and the remaining reads were aligned to the rice genome database, Rfam and Repeats database to filter out rRNA, tRNA, snoRNA, snRNA, other non-coding RNAs, and repeat sequences
Summary
Light is a source of energy for photosynthesis, and a key environmental factor that affects plant growth and development. To adapt to changing environments, plants perceive light signals through an array of photoreceptors to make appropriate adjustments (Chen et al, 2004; Franklin, 2009). Phytochrome (phy) is a kind of photoreceptor that mainly perceives and responds to the red and far-red light regions. Native phytochromes form homodimers and heterodimers, and exist in two reversible conformations under different light spectrums (Rockwell et al, 2006). Phytochromes are present as the red-light-absorbing form (Pr, biologically inactive) in the cytoplasm. Red light induces a conformation shift from Pr to the far-red-light-absorbing form (Pfr, biologically active) and promotes translocation of the Pfr form into the nucleus (Yamaguchi et al, 1999; Chen et al, 2005). Phytochromes interact with other nuclear proteins and trigger transcription cascades to regulate light responses
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