Abstract
MicroRNAs (miRNAs) are important factors for the post-transcriptional regulation of protein-coding genes in plants and animals. They are discovered either by sequencing small RNAs or computationally. We employed a sequence-homology-based computational approach to identify conserved miRNAs and their target genes in Persian (English) walnut, Juglans regia, and its North American wild relative, J. microcarpa. A total of 119 miRNA precursors (pre-miRNAs) were detected in the J. regia genome and 121 in the J. microcarpa genome and miRNA target genes were predicted and their functional annotations were performed in both genomes. In the J. regia genome, 325 different genes were targets; 87.08% were regulated by transcript cleavage and 12.92% by translation repression. In the J. microcarpa genome, 316 different genes were targets; 88.92% were regulated by transcript cleavage and 11.08% were regulated by translation repression. Totals of 1.3% and 2.0% of all resistance gene analogues (RGA) and 2.7% and 2.6% of all transcription factors (TFs) were regulated by miRNAs in the J. regia and J. microcarpa genomes, respectively. Juglans genomes evolved by a whole genome duplication (WGD) and consist of eight pairs of fractionated homoeologous chromosomes. Within each pair, the chromosome that has more genes with greater average transcription also harbors more pre-miRNAs and more target genes than its homoeologue. While only minor differences were detected in pre-miRNAs between the J. regia and J. microcarpa genomes, about one-third of the pre-miRNA loci were not conserved between homoeologous chromosome within each genome. Pre-miRNA and their corresponding target genes showed a tendency to be collocated within a subgenome.
Highlights
MicroRNAs are small, 20–24 nucleotides long non-coding RNAs, which play important roles in the post-transcriptional regulation of protein-coding genes [1]
Using mature plant miRNAs from miRBase release 21.0, 119 and 121 pre-miRNA loci were identified in the J. regia and J. microcarpa genomes, respectively
Since more miRNAs were correctly detected with miRBase release 21.0, the subsequent analyses were performed with results of miRNA prediction based on miRBase release 21.0
Summary
MicroRNAs (miRNAs) are small, 20–24 nucleotides (nt) long non-coding RNAs, which play important roles in the post-transcriptional regulation of protein-coding genes [1]. The first miRNA, lin-4, was discovered as a temporal regulator of larval differentiation in Caenorhabditis elegans [2], and thousands of additional miRNAs have been discovered since . Their regulatory roles in various biological processes have been uncovered in many animals and plants [1,2,3,4,5,6,7,8,9]. Pre-miRNAs are exported into the cytoplasm, where they are further processed by Dicer RNase III [13] while pre-miRNAs in plants are entirely processed by DCL1 in the nucleus [1]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
