miRNA comparison between FCDK and FCSH
FCDK and FCSH shared 91 miRNAs from 64 miRNA gene families (Figure 6a), including 78 known miRNAs from 53 families conserved in crustaceans and hexapods, and 13 miRNAs from 10 predicted families (MIR-fca1 to MIR-fca10) originated in the ancestor of FCDK and FCSH, since none of the miRNAs in the latter group were found in other collembolan genome data by the BLAST algorithm. Notably, seven known conserved miRNAs (MIR-bg5, MIR-927, MIR-3049, MIR-6012, MIR-971, MIR-11, and MIR-995a) were annotated in the sRNA data of FCSH but not in the sRNA or genomic data of FCDK. These miRNAs have probably been lost in FCDK.
By mapping miRNA precursors to the corresponding chromosomes, it was found that the locations of most shared miRNAs in FCDK and FCSH showed evolutionarily conserved synteny (Figure 6b). Only three F. candida -specific miRNAs (fca6-p1, fca6-p2 and fca4-p4) were located on different chromosomes of FCDK and FCSH.
It is of note that there were many more specific miRNAs in FCSH than in FCDK. Thirty-nine miRNAs from 15 predicted families (MIR-fcaSH-n1 to MIR-fcaSH-n15) were unique to FCSH, but only 9 miRNAs from 6 predicted families (MIR-fcaDK-n1 to MIR-fcaDK-n6) were unique to FCDK. We think that these miRNAs are strain specific since they could not be found in other collembolan genomes. Most FCDK-specific miRNA families had only one copy, with the exception of MIR-fcaDK-n3. However, many FCSH-specific miRNA families showed multiple duplications (Figure 6a) and tended to form clusters on chromosome 7 (Figure 6b). The remarkable differences in the miRNA distribution in FCSH and FCDK confirm that they have experienced independent evolutionary processes and evolved into different species.