Further identification of these differentially expressed miRNAs would allow better understanding of the regulatory mechanisms for tobacco response to topping. Moreover, since miRNAs are evolutionarily conserved across species, our results may become a useful resource for miRNA studies in other plants. To identify miRNAs involved in tobacco topping, two sRNA libraries were generated from tobacco roots before and after topping. The two libraries were sequenced by Solexa , yielding a total of 12,104,207 and 11,292,018 sRNA raw reads with lengths of 18 to 30nt and consisting of 3,633,398 and 3,084,102 unique sequences . After removing rRNA, tRNA, snRNA and snoRNA, a total of 9,979,127 and 9,351,526 small RNA sequences were obtained. This suggests that tobacco roots contain a large and diverse small RNA population. To further compare the average abundance of different sRNAs, we measured the ratio of redundant and unique sequences. After topping, the ratio of redundant and unique conserved miRNA sequences in tobacco roots decreased distinctly , which suggests that topping can decrease the abundance of conserved miRNA in tobacco roots. The size distribution of both unique and redundant reads was assessed . From the size distribution of reads, we found that the majority of small RNAs were in the range from 18 to 24nt, and there were two KU-0059436 distinct peaks around 21 and 24 nt in the two stages. So 21 and 24 nt small RNAs are the two major size classes, and this result was consistent with those of Arabidopsis and Oryza sativa . The reads of 24 nt small RNAs in tobacco roots after topping were markedly less than that in tobacco roots before topping, which suggests that 24 nt small RNAs have a critical role in the development of tobacco roots after topping. These observations indicated that the expression of miRNAs and siRNAs significantly altered after topping, suggesting that miRNAs and siRNAs could be involved in the extensive regulation of gene expression in response to topping in tobacco roots. The size distribution of all sRNAs annotated as miRNAs is summarized in Figure 2. LY2109761 Although the sRNAs annotated as miRNAs in the sizes of 18, 19, 20 and 21 nt all had about 93�C107 unique reads, the redundant reads of 18 and 19 nt group were surprisingly less than that of 20 and 21 nt group. 20 and 21 nt group had separately 172964 and 172225 redundant reads, which indicated that 20 and 21 nt group are the most abundant miRNA. MiRNAs provide global regulations both through posttranscriptional and translational regulation and chromatin modification. Identification of entire set of miRNAs and their targets will lay the foundation to unravel the complex miRNAs mediated regulatory networks controlling development and other physiological processes. Recently, a large number of miRNA have been found in various species.