Figure 6.

This scheme shows the distribution of phylogenetically conserved miRNA gene clusters in selected bilaterian phyla from the MirGeneDB database. Species are listed on the left, with P. dumerilii shown at the bottom. The tree, next to the species names, reflects state of the art of the lophotrochozoan clade phylogeny, with the branching taken from Marlétaz et al. (2019). The names of the miRNA clusters are defined by the comprised miRNA genes, separated by underscores (_), and are listed at the top of the figure. Since the order of miRNA genes in genomic clusters can vary between different species, the nomenclature follows three hierarchical criteria: 1. The gene order in the P. dumerilii genome; 2. The most common arrangement in the analysed species 3. Alphabetical order, when the first two criteria cannot be fulfilled. When the same miRNA gene name is repeated in the cluster, it indicates the presence of multiple copies, with uncertain homology, of the correspondent gene family. If the cluster name ends with three dots (…) more copies of the last listed gene are present. The number of copies can vary between species. miRNA clusters are grouped and ordered according to their phylogenetic conservation, with the respective clades indicated just below the clusters. Here follows the description of the symbols. Full circle: the cluster listed above is present in the corresponding specie, with all genes included in the cluster. Empty circle: miRNA genes are found in the genome but not clustered together. Hyphen (−): corresponding miRNA genes are not found in the genome. Including when only one member of a two-gene cluster is missing. For clusters composed of three or more genes, there are three additional scenarios with respective symbols: 1. Hyphen followed by an empty half-circle: some miRNA genes are absent in the genome, while others are present but not clustered; 2. Circle half full: some miRNA genes are clustered, while others are not. 3. Hyphen followed by a full half-circle: some genes are clustered, while others are not present in the genome. Grey-filled circle: genes are not clustered but are found in the same genomic scaffold or chromosome. Circle with a filled center: indicates the presence of a cluster composed of gene copies with uncertain homology.