Supplementary Figure 7: Evolution of miRNA-2115 in the primate lineage.

(a) Phylogeny tree of upper primates (Bonobo excluded due to poor read sequence quality in region of interest). Star represents presence of miR-2115. I) Alignment of SPINK8 intron 3 - Grey represents agreement to consensus. Black represents disagreement to consensus. Lines indicate gaps compared to consensus. II) Sequence of miR-2115 in higher primates. Highlighting indicates disagreement to consensus. miR-2115 is predicted to be present in Orangutans but is absent in Gibbons. b) Intron 3 is significantly smaller in Gibbons than higher primates (~¼ the length) and more closely matches Intron 3 of mice. There is a ~7100 nucleotide section present in Hominidae but absent in Gibbons, likely arising from an insertion occurring in Hominidae after the divergence of Gibbons. This insertion likely carried miR-2115. There is a 367 nucleotide section directly downstream of miR-2115 present in Orangutans but not Great Apes, indicating it was lost in the Great Apes common ancestor after the divergence of Orangutans. There is a 1832 nucleotide section present only in Orangutans occurring after their divergence from the Great Apes. The great mobility in this intron is likely not due to transposable elements judging from the lack of inverted repeats in the area. (c) Expression of novel miRNAs that were not annotated in latest miRBase⁶⁷ across the samples. In this study, we found 36 of them expressed in prenatal brain samples. Of the expressed miRNAs, 31 of them were either human-specific or primate-specific, and 4 of them were specific expressed at GW15. Red dots indicate differentially expressed miRNAs between GW15-16 and GW19-20 by DEseq2.