Abstract
BackgroundMiRNAs (microRNA) are 18–24 nt endogenous noncoding RNAs that regulate gene expression at the post-transcriptional level, including tissue-specific, developmental timing and evolutionary conservation gene expression.ResultsThis study used high-throughput sequencing technology for the first time in Larix olgensis, predicted 78 miRNAs, including 12,229,003 reads sRNA, screened differentially expressed miRNAs. Predicting target genes was helpful for understanding the miRNA regulation function and obtained 333 corresponding target genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation were analysed, mostly including nucleic acid binding, plant hormone signal transduction, pantothenate and CoA biosynthesis, and cellulose synthase. This study will lay the foundation for clarifying the complex miRNA-mediated regulatory network for growth and development. In view of this, spatio-temporal expression of miR396, miR950, miR164, miR166 and miR160 were analysed in Larix olgensis during the growth stages of not lignified, beginning of lignification, and completely lignified in different tissues (root, stem, and leaf) by quantitative real-time PCR (qRT-PCR). There were differences in the expression of miRNAs in roots, stems and leaves in the same growth period. At 60 days, miR160, miR166 and miR396–2 exhibited the highest expression in leaves. At 120 days, most miRNAs in roots and stems decreased significantly. At 180 days, miRNAs were abundantly expressed in roots and stems. Meanwhile, analysis of the expression of miRNAs in leaves revealed that miR396–2 was reduced as time went on, whereas other miRNAs increased initially and then decreased. On the other hand, in the stems, miR166–1 was increase, whereas other miRNAs, especially miR160, miR164, miR396 and miR950–1, first decreased and then increased. Similarly, in the roots, miR950–2 first decreased and then increased, whereas other miRNAs exhibited a trend of continuous increase.ConclusionsThe present investigation included rapid isolation and identification of miRNAs in Larix olgensis through construction of a sRNA library using Solexa and predicted 78 novel miRNAs, which showed differential expression levels in different tissues and stages. These results provided a theoretical basis for further revealing the genetic regulation mechanism of miRNA in the growth and development of conifers and the verification of function in target genes.
Highlights
MiRNAs are 18–24 nt endogenous noncoding RNAs that regulate gene expression at the post-transcriptional level, including tissue-specific, developmental timing and evolutionary conservation gene expression
The proportion of the clean reads in the corresponding raw reads was more than 50% in the two samples, which suggested that the quality of the sequencing data was high
The Clusters of Orthologous Groups of proteins (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases contained the least annotation information. These results indicate that a miRNA target gene has the same miRNAs, whereas a miRNA does not necessarily have a single target gene, which demonstrates the complexity of miRNAs and their target gene regulatory network
Summary
MiRNAs (microRNA) are 18–24 nt endogenous noncoding RNAs that regulate gene expression at the post-transcriptional level, including tissue-specific, developmental timing and evolutionary conservation gene expression. MiRNAs are a class of endogenous single-stranded noncoding RNAs approximately 18–24 nt in length. Derived from single-stranded precursor RNAs that can form hairpin structures [1, 2], miRNAs regulate gene expression primarily at the post-transcriptional level [3]. As miRNAs are structurally conserved, bioinformatics methods can be used to predict miRNAs and their target genes. Numerous follow-up studies found that in higher plants, miRNA plays an important role at the post-transcriptional level by regulating its target mRNA through silencing or degrading mRNA [5,6,7]. The first miRNA in plants was identified in Arabidopsis in 2002 [8]
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