Our recent paper (Joshi et al., 2010
) describes the identification of sRNAs from root, seed, flower, and nodules. We are now analyzing data to add sRNAs from B. japonicum inoculated (0-48 HAI) soybean root hair samples and the corresponding stripped root tissues. This includes 30,250, 33,034 and 219,131 sRNA sequences that had unique genome hits in the mock inoculated root hair, inoculated root hair, and stripped root tissues, respectively. A total of 129 miRNAs were identified from root, seed, flower and nodules, including 42 miRNAs that matched previously identified soybean miRNAs or were conserved in other species. However, 87 novel miRNAs were identified. We also predicted the putative target genes of all identified miRNAs with computational methods and verified the predicted cleavage sites in vivo for a subset of these targets using the 5’ RACE method. Finally, we also studied the relationship between the miRNA and expression of the respective target genes by comparison to Solexa cDNA sequencing data. A genome browser was developed (http://digbio.missouri.edu/soybean_mirna/
) that allows direct comparison of miRNA and mRNA (from our transcriptome analysis) expression.