All primers for real-time RT-PCR are listed in Table S1 and Table S2. To determine the miRNA cleavage sites in the target genes, RLM-RACE was performed using the SMARTer RACE cDNA Amplification Kit (Clontech, PT4096-2). First, total RNA was extracted from the two tissues and ligated with SMARTer II A oligonucleotide, and then the RNA was reverse transcribed using 10 × Universal Primer A Mix (UPM). PCR was then performed twice, using the UPM/gene-specific primer in the first reaction and the UPM/nested gene-specific primer in the second, according to the manufacturer’s instructions. The product was then gel-extracted and cloned ERK pathway inhibitor into

the PMD20-T Vector (Takara, Dalian, China) for sequencing. The primers for RLM-RACE are shown in Table S3. To investigate the small RNA expression profiles of O. longistaminata, two cDNA libraries of small RNAs, one from ASs and one from rhizomes, were sequenced. In total, 20,358,337 raw reads from ASs and 21,313,971 from rhizomes were produced. After HKI-272 datasheet elimination of low quality reads,

adaptors and contaminating sequences, 17,547,018 and 18,655,858 clean reads with lengths of 17 to 30 nt remained from the ASs and rhizomes, respectively. Of these reads, 4,866,476 and 6,517,161, respectively, were unique ( Table 1). The overall size distributions of the sequenced reads from the two libraries were very similar, with the 24 nt class being the most abundant ( Fig. 1). The unique sequences were mapped to the rice genome assembly using Bowtie [22]. As shown in Table 1, almost every category of RNAs, including miRNAs, siRNAs, rRNAs, snoRNAs, snRNAs, tRNAs, repeat-associated sRNAs, and degraded mRNAs, were detected in both tissues. Finally, 11,265 and 33,536 reads for ASs, and 12,997 and 40,126 reads for rhizomes were identified as known and predicted miRNA candidates, respectively, for analysis. All small RNA sequences were searched against the plant miRNA database to identify known, conserved and novel miRNAs in ASs and rhizomes, as described in Materials and methods. To reduce false-positive rates, only sequences with at least two detected

reads were designated as miRNA candidates. Of the 713 known rice miRNAs deposited in the miRBase database (Release 20, June 2013), Epothilone B (EPO906, Patupilone) 380 known rice miRNAs were identified as being expressed in ASs and rhizomes, including 340 miRNAs found in both tissues (Table 2). Among them, 21 and 19 known miRNAs were expressed exclusively in ASs and in rhizomes, respectively (Fig. 2, Tables 2, S4). The most highly tissue-specific miRNAs included osa-miRNA319a-3p and osa-miRNA529a in the rhizomes and osa-miRNA530-5p and osa-miRNA5073 in the ASs, indicating their roles in rhizome and AS growth. In the conserved and novel miRNAs 72 conserved miRNAs were expressed, including 53 miRNAs common to ASs and rhizomes. Seven and 12 miRNAs were expressed specifically in ASs and rhizomes, respectively (Table S5).