smRNA target prediction for 21 smRNAs within the gene set of Symbiodinium microadriaticum. (A) 3 distinct animal-like target sites in the 3'UTR of genes exist that are characterized by seeds of lengths 6-8nt that display perfect complementary base pairing between the miRNA and mRNA sequence. Vertical dashes indicate Watson-Crick base pairing. The pie chart displays the relative frequency of these target sites in the 3'UTRs of 1,720 genes (from a set of 12,858 genes with available 3'UTRs). (B) 19 plant-like mRNA target sites were identified in the coding sequence and 3'UTRs of 51,917 genomic genes of Symbiodinium microadriaticum. Plant-like mRNA target sites are characterized by full-length complementary base pairing between a miRNA and its mRNA with only few mismatches (i.e. near-perfect). (C) Number of identified plant-like mRNA target sites (blue bars) in relation to number of mismatches allowed. Number of false positives in 1,000 randomly generated cohorts of small RNA sequences of length 22 nt (red bars) are displayed for comparison. A cutoff of 3 mismatches (mm) over the aligned smRNA and mRNA provides a False Positive Rate of about 1 in 5. (D) Enriched GO terms within the set of matching and annotated animal-like targets (n = 519, P < 0.05, 4,047 3' UTRs). (E) Enriched GO terms within the set of matching and annotated plant-like targets (n = 7, P < 0.05, 18,290 genes).
Baumgarten et al. BMC Genomics 2013 14:704 doi:10.1186/1471-2164-14-704