Thiebaut et al. BMC Genomics 2012, 13:290 http://www.biomedcentral.com/1471-2164/13/290 in sorghum are highlighted. Thirty three new miRNAs had targets in sugarcane and 29 in sorghum. Targets annotated, as serine/threonine kinase, Myb protein, MADS-box, zinc finger protein-like were potentially regulated by different new miRNAs class I. In this set, targets annotated like AMP-binding protein were over- represented. This is a defense related protein that is involved in the regulation of defense response [53]. Next, sugarcane and sorghum identified targets were subjected to gene ontology analysis. We extracted the unique IDs of targets and compared them with GO anno- tations of S.bicolor gene models, and S.bicolor and sugar- cane TC annotations. The GO numbers of targets were subjected to agriGO toolkit [54]. Among the distribution of GO annotation of the targets, only miRNA class I tar- gets were represented in Figure 5. The most representative GO was the metabolic process (46,6%). The enrichment of this GO may be consistent with the fact that six libraries of sRNA were constructed from plants cultivated in vitro, which may have had their development accelerated by combination of plant hormones [55]. In addition, genes involved in immune system processes and cellular responses to stresses were present there, presumably due to the stress treatments. Page 9 of 14 Conservation of novel miRNAs in diverse plant species Flowering plants comprise approximately 250,000 species and originated around 200 million years ago [56]. Phylo- genetic analyses have recently resolved major relationships among angiosperm group using both molecular and mor- phological information [57,58]. The wide variability of the angiosperms allow their adaptation to diverse environ- mental conditions and also their domestication [59]. The estimate of divergence time, acquired using plastid exons and rDNA revealed that monocots and eudicots diverged about 150 million years ago [56]. Within monocots; rice, maize, sugarcane and sorghum (Poaceae family) originated approximately 60 million years ago [60]. Early in the radiation of eudicots plants, the Arabidopsis family (Brassicaceaea) diverged (~85 million years ago) [56]. Phylogenetic conservation analysis of novel miRNAs be- tween closely related species provides supporting evidence and has been used to annotate new miRNAs [61]. Based on miRCat pipeline we searched for the precursors of the novel sugarcane mature miRNAs candidates in two mono- cots (Oryza sativa and Zea mays) and Arabidopsis. We did not identified conserved precursors of new sugarcane miRNAs candidates in Arabidopsis. In rice, we identified 27 homologs of these mature miRNAs, while in maize, the Figure 5 Gene Ontology enriched terms of novel miRNA targets. Bars indicate the percentage of total annotated sorghum and sugarcane targets genes mapping to GO terms. Only putative targets arising new miRNAs class I were shown.