Evolutionary and Expression Analysis of miR-#-5p and miR-#-3p at the miRNAs/isomiRs Levels

Figure 3

Examples of evolutionary patterns of different miRNAs. (a) Phylogenetic tree of let-7a. The tree is reconstructed using all the miRNA precursors, including multicopy pre-miRNAs. Multicopy pre-miRNAs are likely to be located in different clusters. (b) The phylogenetic tree of several members of mir-30 gene family (mir-30b, mir-30c, and mir-30d). The three members are split, and miR-30d shows a larger genetic distance with other members. (c) MJ networks of let-7a-3p, let-7-5p, and let-7-3p. Let-7a-3p is associated with nucleotide variation, although the other strand, let-7a-5p, is highly conserved. Similarly, let-7-5p from let-7 family also shows a simple network with several median vectors compared to let-7a-3p. Both let-7a-3p and let-7-3p show complex evolutionary networks with more median vectors. Members in let-7 gene family do not show clear module networks. The size of the circle shows the frequency of the miRNA haplotype (the specific miRNA sequence). (d) MJ networks of miR-30-5p and miR-30-3p from known miR-30b, miR-30c, and miR-30d sequences. Different miRNA members are likely to cluster together.

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