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.

Combined Analysis of MicroRNAs and Target Genes Revealed miR156-SPLs and miR172-AP2 Are Involved in a Delayed Flowering Phenomenon After Chromosome Doubling in Black Goji (Lycium ruthencium)

“…The continuous upgrading of high-throughput sequencing technology can achieve pivotal transcripts, which has become a broad-spectrum method for exploring plant biomolecules (Ma et al, 2015). The expression of miRNAs has been found to be altered in different plant growth and adverse circumstances, which helps shed light on plant internal mechanism from a new perspective (Ferdous et al, 2015;Muslu et al, 2021). We applied high-throughput sequencing to consider how chromosome doubling influences the florescence of L. ruthenicum at the miRNA level and eventually got the transcript and miRNA information of the autotetraploid and diploid ancestor.…”

Comparative Analysis of Coding and Non-Coding Features within Insect Tolerance Loci in Wheat with Their Homologs in Cereal Genomes

“…In the second step, mirMachine pipeline identifies the potential miRNA precursor sequences (premiRNAs) and fold them using RNAfold [51]. Potential premiRNA sequences are subjected to the following criteria: (1) no mismatches at Dicer cut sites, (2) no multi-branched loop at the hairpin with the mature miRNA sequence, (3) mature miRNA sequence could not be located at the head portion of the hairpin, (4) no more than four and six mismatches in miRNA and miRNA*, respectively [50,[52][53][54].…”