1) The relationships of miRNAs and their targets were also verif

1). The relationships of miRNAs and their targets were also verified for osa-miR156a and two genes encoding teosinte glume architecture 1 (TGA1) (Fig. S3). The MADS-box transcription 23 gene for osa-miR444b.2, a TCP TF gene (LOC_Os07g05720.1) for osa-miR319b, an expressed

protein gene (LOC_Os09g36650.1) for osa-miR159a.1, a gene encoding a putative protein (LOC_Os04g07260.1) for osa-miR319a-5p, and a gene encoding biopterin transport-related BT1 (LOC_Os03g58080.1) for osa-miR5148a were also confirmed, as shown in Fig. S2. It was noted that cleavage might occur upstream or downstream of the binding site instead of the commonly MDV3100 cost observed position. For example, the binding site of LOC_Os08g33488.1 (target of osa-miR444b.2) occurred between 311 and 331 bp; however, the cleavage

site occurred at about 360 bp, downstream of the binding site, which is consistent with Selleckchem Alectinib previous reports [30] and [31]. Quantitative RT-PCR was performed to determine the expression relationship between miRNAs and their corresponding targets, as shown in Fig. S4 and Table S4. In contrast to the lower expression of osa-miR156a in the rhizome, the expression levels of its targets, two TGA1s, were highly enriched in the rhizome compared with the AS. However, the expression of another target in the two tissues, SPL10, was similar to those of osa-miR156a. The transcripts of osa-miR319b and its target gene TCP were simultaneously

identified as highly enriched in rhizome compared with AS ( Fig. S2 and Fig. S4). These results indicated that miRNAs could be negatively or positively involved in the regulation of their targets at the post-transcriptional level. The development of high-throughput gene expression analyses, including deep sequencing techniques, has enabled the rapid profiling and investigation of the transcriptome. In O. longistaminata, genome-wide gene expression profiling has previously been performed using the Affymetrix rice microarray to identify tissue-specific genes, in particular genes related to rhizome development [8]. In this study, the comparative analysis of two small RNA libraries, one from ASs and one from rhizomes, indicated that some miRNAs were differentially expressed in the two tissues, and target gene predictions Tacrolimus (FK506) for these differentially expressed miRNAs suggested their roles in AS and rhizome development. MiRNAs play an important role in plant growth and development. To date, there are 592 miRNA sequences representing 713 mature miRNAs in the rice miRBase (http://www.mirbase.org/cgi-bin/mirna_summary. pl?org = osa). However, the miRNA transcriptome of wild rice, including O. longistaminata, is poorly characterized [32]. In the present study, 380 known rice miRNAs were identified in ASs and rhizomes, indicating that the majority of the identified rice miRNAs could be expressed in O. longistaminata.

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