Vertebrate miRNA Family Evolution

The genome sequences of Ciona intestinalis, Branchiostoma floridae, Salmo salar, Danio rerio, Cyprinus carpio, Xenopus tropicalis, Anolis carolinensis, Gallus gallus, Ovis aries, Bos taurus, and Petromyzon marinus were downloaded from Ensembl (https://asia.ensembl.org/index.html). The miRNA sequences of all the other species except C. idella were downloaded from miRbase (https://www.mirbase.org/). The birth, death, and age of miRNA families were estimated based on a phylogenetic tree generated by RAxML(-m PROTGAMMAJTT -f a -# 100) [71 (link)] analysis from single-copy proteins. The birth, death, and age of miRNA families and the ancestral gene contents were assessed using the COUNT software [72 (link)] following the parsimony rule based on the miRNA families of each species. Branch lengths reflect evolutionary divergence times in million years (MY) inferred from timeTree (http://www.timetree.org/).