High-throughput sequencing and degradome analysis reveal microRNA differential expression profiles and their targets in Paulownia fortunei

Paulownia fortunei (family Paulowniaceae) is an economically important tree species indigenous to China. Autotetraploid cultivars of P. fortunei have better growth and wood quality than their diploid counterparts. MicroRNAs (miRNAs) play vital regulatory roles in plant growth, development, and biotic and abiotic stress responses by direct cleavage of transcripts, translational repression, or chromatin modification. Although miRNAs have been identified in various plant species, no reports of miRNAs in P. fortunei have been published so far. To study the functions of miRNAs in the autotetraploid P. fortunei, four sequencing libraries from the autotetraploid and its corresponding diploid plants were constructed. 142 conserved miRNAs grouped into 41 families, and 38 novel miRNAs were obtained. Among these miRNAs, 58 were up-regulated and 30 were down-regulated in the autotetraploid relative to the diploid. MiRNA target genes were identified using a degradome sequencing approach and the differently expressed miRNAs and their target genes were validated by real time PCR analysis. To our knowledge, this is the first study to identify conserved and novel miRNAs and their potential targets from diploid and autotetraploid Paulownia plants using high-throughput sequencing and degradome analysis. Our results provide valuable information on P. fortunei miRNAs and their targets, and will help build a foundation for future studies of the biological functions of miRNA-mediated gene regulation in P. fortunei.