Combined Analysis of mRNAs and miRNAs to Identify Genes Related to Biological Characteristics of Autotetraploid Paulownia

Autopolyploid plants and their organs are larger than their corresponding diploid ancestors, and they attract considerable attention for plant breeding. Paulownia is a fast-growing tree. To identify genes related to the biological characteristics of tetraploid Paulownia, transcriptome and small RNA sequencing were used to identify the key gene expression regulation in tetraploid Paulownia fortunei and tetraploid P. tomentosa and their corresponding diploids. A total of 1977 common differentially expressed genes (DEGs) and 89 differentially expressed miRNAs (DEMs) (38 conserved and 51 novel) were obtained in tetraploid vs. diploid comparisons of the two Paulownia species, and 18 target genes were identified by target prediction. Finally, by analyzing the expression profiles of the DEGs and DEMs and their target genes, we discovered that Pau-miR169, Pau-miR408 and Pau-miR156 interacted with their target gene nuclear transcription factor Y subunit A-9 (NF-YA9), serine/threonine protein phosphatase (PP1) and s-adenosyl-methionine-sterol-c-methyltransfera—se (SAM:SMT) to regulate the abiotic stress tolerance and the timber quality of the tetraploid Paulownia. This study lays a molecular biology foundation for understanding autotetraploid Paulownia and will benefit future breeding work.