Figure 9

Tracing the evolution of oni-miRNA-n780. (A) Syntheny block shows a high conservation among teleost genes. The origin of oni-miRNA-n780 paralogs is associated with extra rounds of genome duplication between in teleosts, since the lambrey presents only one copy of the miRNA cluster 29d/a and cichlids show three copies. In amphibians, reptiles and mammals, oni-miR-n780 paralog could have been lost, while the cluster 29b/a present in mammals or 29d/a present in amphibians might have emerged from a same ancestor paralogs found in lampreys. Syntheny blocks were obtained from Genomicus⁹⁵ and altered with homology data from Ensembl about oni-mir-n780 paralogs from other vertebrate species. (B) A manual check using the gene annotation in cichlids and the homology level among genes shows a high conservation of the synthetic block among the cichlid species. However, among M. zebra and N. brichardi there was an inversion of the genomic block. Each color represents a different gene and its transparency level represents the homology level (high homology/low transparency to low homology/high transparency). The oni-mir-n780 is represented by the red symbol in the center of the image. (C) A reconciled gene and species tree of oni-miR-n780 using RAxML and TreeBest to reconstructing the historical evolutive events among species. We found that the mir-29b from Apis mellifera is the closest common miRNA ancestor of oni-miR-n780. (D) Alignment of novel mir-n780 precursor sequences with homologs found in lamprey, amphibians and other teleost fish. Sequence similarity of oni-mir-n780 within all species is around 68.8%, although inside cichlid clade it has 100% of identity. The mature miRNA 3p is highly conserved, showing 95.2% of similarity among vertebrats and 100% of similarity when compared among cichlid fishes, B. belcheri, X. laevis, X. tropicalis and S. salar; by contrast the mature miRNA 5p form is more variable presenting 80.8% of similarity within vertebrates, but still highly conserved in the cichlid genomes where they show of 100% of identity. Another features include a G-to-A mutation in the seed region of the mature miRNA 5p sequences exclusively detected in cichlids, which might refer to a possible specific functional regulatory role of oni-miR-n780 in the genome of cichlids. Alignment data was retrieved from Geneious⁹⁶.