Figure 2

Results of miRNA prediction by sequence similarity and the existence of a stem-loop structure based on the draft Hessian fly genome sequence. A total of 2,130 loci were found to contain sequences identical or containing at most 3 mismatches differing from either known miRNAs from other insect species or Hessian fly miRNAs newly identified through deep sequencing in this research. Of the 2,130 sequences, 1,519 contained no flanking sequences that can form a stem-loop structure, and 52 sequences were truncated at ether the 5^′- or 3^′-end. The remaining 611 sequences were predicted to form a stem-loop structure that is characteristic of a pre-miRNA species, and therefore were likely to encode miRNAs. Of the 611 putative miRNAs, 92 were identical or very similar to known miRNAs from other insect species, and represented 73 families. The families averaged 1.3 genes with the largest family containing 5 members. The 519 newly identified putative miRNA genes represented 124 families. The families averaged 4.2 members, and the largest family contained 91 members.