Characterization of expression patterns of small RNAs among various organs in Arabidopsis and rice based on 454 platform-generated high-throughput sequencing data

The advent of high-throughput sequencing (HTS) strengthened our capacity for small RNA (sRNA) discovery. Here, we did a transcriptome-wide survey of sRNAs, mainly focusing on the microRNAs, with organ-specific expression patterns in both Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). By using sRNA HTS data generated by 454 sequencing technology, four organs in Arabidopsis (i.e. six-day-old seedling, rosette leaf, flower and silique), and four in rice (shoot apex, leaf, root apex and inflorescence) were investigated. Chromosome-wide distribution patterns of the organ-specific sRNAs were obtained. We found that, in rice, the 21-nt (nucleotide) sRNAs occupy a large portion of the sRNA population highly expressed in inflorescences. In contrast, the sRNAs not expressed in rice floral organ are predominantly 24 nt in length. Through literature mining, ath-miR156d, ath-miR400, ath-miR822 and ath-miR824 were suggested to be involved in seedling development in Arabidopsis, and osa-miR169 induced by drought and high salinity was indicated to regulate leaf growth in rice.