Pan-Genome miRNomics in Brachypodium

Abstract

Pan-genomes are efficient tools for the identification of conserved and varying genomic sequences within lineages of a species. Investigating genetic variations might lead to the discovery of genes present in a subset of lineages, which might contribute into beneficial agronomic traits such as stress resistance or yield. The content of varying genomic regions in the pan-genome could include protein-coding genes as well as microRNA(miRNAs), small non-coding RNAs playing key roles in the regulation of gene expression. In this study, we performed in silico miRNA identification from the genomic sequences of 54 lineages of Brachypodium distachyon, aiming to explore varying miRNA contents and their functional interactions. A total of 115 miRNA families were identified in 54 lineages, 56 of which were found to be present in all lineages. The miRNA families were classified based on their conservation among lineages and potential mRNA targets were identified. Obtaining information about regulatory mechanisms stemming from these miRNAs offers strong potential to provide a better insight into the complex traits that were potentially present in some lineages. Future work could lead us to introduce these traits to different lineages or other economically important plant species in order to promote their survival in different environmental conditions.

Keywords: Brachypodium; microRNA; pan-genome.

Figure 1

The distribution of miRNA families across lineages. The x-axis shows 115 miRNA families identified in 54 Brachypodium lineages, shown in y-axis. Conservation of miRNA families among lineages increased along the x-axis and miRNA families were classified into four groups based on this conservation: Rare miRNA families (purple), moderately conserved miRNA families (pink), highly conserved miRNA families (orange) and common miRNA families (green). The total number of miRNA families identified in each lineage is also shown in parenthesis next to lineage names.

Figure 2

The number of precursor miRNA (pre-miRNA) sequences identified for each miRNA family in (a) rare miRNA family group, (b) moderately conserved miRNA families group, (c) highly conserved miRNA families group, and (d) common miRNA families group are shown. Each bar indicates both repetitive pre-miRNAs, defined as containing repetitive elements for more than half of their lengths, with the light shade of gray, and non-repetitive pre-miRNAs with the dark shade of gray.

Figure 3

Heatmap displaying the miRNA family commonality between lineages. Darker green cells represent higher numbers of common miRNAs shared between two lineages while darker purple represents fewer numbers of common miRNA families. The heatmap is not symmetrical; it should be read from y > x. For example, the extent of conservation between ABR2 and Uni2, defined as the ratio of common miRNA families between ABR2 and Uni2 over the number of total miRNA families in ABR2 by our approach, is given on the top right corner (indicated by a blue square), while the conservation between Uni2 and ABR2, the ratio over the total number of families in Uni2, is given on the bottom left (red square).

Figure 4

Gene Ontology analysis for biological processes for rare, moderately conserved, highly conserved and common miRNA family groups targets, combined and clustered. Predicted targets from five biological processes appear to be collectively targeted by all four miRNA groups.

Figure 5

(a) The number of miRNA families having multiple predicted targets were averaged across lineages. For simplicity, targets were considered within 11 bins of certain sizes as given. Most miRNA families seemed to target a minimum of 2 and maximum of 50 coding sequences, whereas only a few miRNA families targeted only one target or had more than 50 predicted targets. (b) The number of predicted targets of only one or multiple miRNA families were averaged across lineages. In contrast to miRNAs targeting multiple targets, each target appeared to be predominantly targeted by one miRNA family.