Discovery and profiling of microRNAs and their targets in Paulownia ‘Yuza 1’ plants via high-throughput sequencing and degradome analysis

Polyploid breeding is an effective method that has been used widely for the development of new varieties of plants. MicroRNAs (miRNAs) are a class of endogenous small RNAs that regulate gene expression at the post-transcriptional level. To understand the functions of miRNAs in autotetraploid and diploid Paulownia ‘Yuza 1’ plants, two small RNA libraries and two degradome sequencing libraries of the autotetraploid and the corresponding diploid plants were constructed and analyzed. A total of 49 conserved miRNAs that were grouped into 15 families, and 25 novel miRNAs were obtained from two sRNA libraries. Among these miRNAs, 28 were differentially expressed at a significant level in the autotetraploid relative to the diploid. Moreover, the miRNA target genes were identified by degradome sequencing and some of the differently expressed miRNAs and their target genes were validated by quantitative RT-PCR analysis. This study has provided valuable information on P. ‘Yuza 1’ miRNAs and their targets, which will enrich the Paulownia miRNA information resources and will contribute to our understanding of miRNA-mediated regulation in autotetraploid Paulownia plantlets.