Implementation of a de novo genome-wide computational approach for updating Brachypodium miRNAs

Abstract

Plant microRNAs (miRNAs) are single-stranded 20-22 nt small RNAs (sRNA) that are produced from their own genes. We have developed a de novo genome-wide approach for the computational identification of novel plant miRNAs based on the integration of the complete genome sequence with sRNA libraries. It comprises three modules - the clustering module identifies genomic regions that have two closely-located unidirectional sRNA clusters, the mirplan module explores the secondary structure of the genomic regions, and the duplex module predicts miRNA/miRNA* duplexes. We applied our approach to the Brachypodium genome and publicly available sRNA libraries and predicted 102 miRNAs. Our results extend the list of known miRNAs with 58 novel miRNAs and define the genomic loci of all predicted miRNAs. Because this approach considers specific features of plant miRNAs, it can be employed for the analysis of the genome and sRNA libraries generated for plant species to achieve systematic miRNA discovery.

Addressing the Role of microRNAs in Reprogramming Leaf Growth during Drought Stress in Brachypodium distachyon

“…In the present study, we have used next-generation sequencing (NGS) technology to annotate and profile the expression of conserved and non-conserved miRNA and miRNA-like molecules during Brachypodium leaf development along the proximo–distal axis and compare miRNA expression along this axis during normal and severe drought conditions. Specifically, we have identified a total of 270 miRNA and miRNA-like genes, confirming 66 previous annotations (Unver and Budak, 2009; Wei et al, 2009; Zhang et al, 2009; Baev et al, 2011) and adding 28 additional loci from known miRNA families as well as 94 novel miRNA genes plus 82 siRNA-like miRNA loci. Differential expression analyses suggest that a number of miRNAs are involved in developmental reprogramming of leaf growth in response to drought.…”

“…While an increased density of miRNAs on chromosome 1 and chromosome 3 was reported previously (Baev et al, 2011), we observed no distinct clustering of miRNA genes across the five chromosomes (Figure 4). Notably, for two miRNA genes ( miR5198 , miR5201 ), we confirmed the genomic localization annotated in miRBase, but we propose a new miRNA:miRNA* duplex that corresponds to the most abundant sequences found in our library.…”

“…The miRBase directory (, Release 18) contains 142 Brachypodium miRNA loci producing 105 distinct mature miRNAs recovered from various recent studies (Unver and Budak, 2009; Wei et al, 2009; Zhang et al, 2009; Baev et al, 2011). Of these, less than one-third (39 of 142) were independently validated.…”

“…In previous studies, 142 miRNA loci producing 105 distinct mature miRNAs were annotated in Brachypodium distachyon (Unver and Budak, 2009; Wei et al, 2009; Zhang et al, 2009; Baev et al, 2011). Our data confirmed approximately half (66) of the current Brachypodium miRNA sequences deposited in miRBase () and extended the list of Brachypodium miRNA genes.…”

miRTour: Plant miRNA and target prediction tool

“…Plant miRNAs have been well characterized in several model systems for plant genomics such as Arabidopsis, Brachypodium, Oryza and Populus [1–6]. They are single-stranded 20–22 nt small RNAs that are endogenously produced from their own genes [2].…”