Large-scale analysis of microRNA evolution

Abstract

Background: In animals, microRNAs (miRNA) are important genetic regulators. Animal miRNAs appear to have expanded in conjunction with an escalation in complexity during early bilaterian evolution. Their small size and high-degree of similarity makes them challenging for phylogenetic approaches. Furthermore, genomic locations encoding miRNAs are not clearly defined in many species. A number of studies have looked at the evolution of individual miRNA families. However, we currently lack resources for large-scale analysis of miRNA evolution.

Results: We addressed some of these issues in order to analyse the evolution of miRNAs. We perform syntenic and phylogenetic analysis for miRNAs from 80 animal species. We present synteny maps, phylogenies and functional data for miRNAs across these species. These data represent the basis of our analyses and also act as a resource for the community.

Conclusions: We use these data to explore the distribution of miRNAs across phylogenetic space, characterise their birth and death, and examine functional relationships between miRNAs and other genes. These data confirm a number of previously reported findings on a larger scale and also offer novel insights into the evolution of the miRNA repertoire in animals, and it's genomic organization.

Figure 1

Evolutionary Distribution of miRNA Families. Phylogenetic tree representing miRNA family gains and losses. Branch width represents the number of miRNA families present among leaves of the branch, while the colour represents significant miRNA family loss (blue) or gain (red). For each of 408 miRNA families present at multiple loci it at least two species, we also build a graphical ‘glyph’. This glyph can be used to quickly assess presence, absence or expansion of families between clades. Each square represents a specific miRNA family. Squares are coloured as follows: white, indicates that this species does not contain a particular family, black indicates that this species contains at least 10 copies of miRNAs within that family. Copies between 1 and 10 are indicated as a rainbow gradient (red through violet). Groups of species are labelled according to the name of the evolutionary branch preceding them.

Figure 2

Evolution of miRNA families. For each node of the phylogenetic tree represented in Figure 1, a series of properties were assessed. Internal nodes are represented by black dots. Terminal nodes corresponding to high-coverage genomes are represented by red squares, while low-coverage genomes are represented by blue triangles. a) Cumulative number of miRNA families appearing at each node. b) Percentage of appearing miRNA families that are intronic per node. c) Percentage of appearing miRNA families that are part of miRNA clusters per node.

Figure 3

Normalised Cluster Length per Species. Cumulative plots of miRNA cluster size (in bp/genome size) per species, normalised by total genome length. Species are coloured according to the grouping shown in Figure 1 and listed in Additional file 1: Table S1; (a) clusters that contain only protein coding genes; (b) Mixed clusters containing both protein coding and miRNA genes; (c) Clusters containing only miRNA loci.

Figure 4

Examples of Synteny Block Structure. Example illustrations of the genomic organization of miRNA loci. Colours correspond to gene family. Intronic miRNA loci are indicated with the letter I inside their element, while protein coding genes are indicated by the letter P. Clusters are sorted alphabetically according to species name and the genomic coordinates of each block are indicated.