MicroRNAs of Worms and Flies Figure 2. miRNAs of nematode and fly model organisms conserved across species (59 and/or overall $70%). 73/139 C. elegans miRNAs share 59 end identities and/or $70% homology over sequence with miRNAs both in fly and humans. 13 C. elegans miRNAs currently appear to have sequence-related miRNAs limited to C. elegans, 14 miRNAs are shared by nematodes and flies, and 3 miRNAs are shared by nematodes and humans. For Drosophila, 54/152 miRNAs have 59 and/or $70% overall homology to nematode and human miRNAs. 15 D. melanogaster miRNAs have sequence-related sequences restricted to fly, 11 miRNAs appear present both in fly and nematodes and 29 in fly and humans. Names of family members cross species can be found in Tables 1–6 and sequence alignments in supporting datasets and Figure S1. Human miRNAs that have family members only in human are not included. It should be noted that the Venn diagram is inclusive showing miRNAs that have 59 and $70% overall conserved sequences as well as miRNAs with either 59 or $70% overall conserved sequences. Thus, miRNA totals in the diagram sections do not necessarily match those stated in the main text referring only to 59 sequence identity or only to $70% overall homology. Moreover, dme-miR-3, dme- miR-12 and dme-miR-318 are listed in both fly_nematode and fly_human groups but not in the fly_nematode_human group because their corresponding C. elegans and H. sapiens homologs are not cross related in sequence under our criteria. Similarly, dme-miR-3, dme-miR-12, dme-miR- 263a and dme-miR-318 are included in both fly_nematode and fly_human groups but not in the fly_nematode_human group when only 59 homology is considered (main text). doi:10.1371/journal.pone.0002818.g002 with hsa-miR-183, dme-miR-263b with hsa-miR-183, dme-miR- 306 with hsa-miR-873, and dme-miR-993 with hsa-miR-100*. miRNAs conserved among nematodes, flies and humans miRNAs that are conserved among nematodes, flies and humans are likely to regulate biological functions common between invertebrates and vertebrates. Thus, we had considerable interest in identifying miRNAs that are conserved in these three organisms. We found a total of 73 C. elegans miRNAs with identifiable sequence related counterparts shared by nematodes, flies and humans, summarized in Table 6, Venn diagram of Figure 2 and Figure S1. Limiting our relationship criteria to 59 end sequence identities, we identified 73 C. elegans miRNAs with 59 homologs in both flies and humans (Table 6, Figure S1). Some C. elegans miRNAs have conserved 59 ends either in flies or humans: 14 nematode miRNAs have 59 homologs in flies and 3 have 59 homologs in humans. 10 nematode miRNAs have similar 59 ends with other C. elegans miRNAs that have not yet been found among fly or human miRNAs. Using extended homology search criteria, we identified 16 C. elegans miRNAs that exhibit $70% sequence identity with both fly and human counterparts (Table 6, Figure S1). We found that 15 C. elegans miRNAs have $70% homologous counterparts in flies that are not found in the human genome, possibly lost during evolution PLoS ONE | www.plosone.org 19 July 2008 | Volume 3 | Issue 7 | e2818