Genome-wide expression analysis of transcripts, microRNAs, and the degradome in Paulownia tomentosa under drought stress

Drought is one of the most devastating effects that severely reduce plant growth and development worldwide. In recent years, the availability of a reference Paulownia genome sequence has made it easier to explore gene expression, transcriptional regulation, and posttranscriptional regulation in Paulownia species. Here, we combined the analyses of the transcriptome, small RNAs, and degradome of Paulownia tomentosa seedlings to generate a comprehensive resource to describe the links between key regulatory miRNA-target gene pairs and drought stress. A total of 22,904 differentially expressed genes, 2073 differentially expressed miRNAs, and 198 target genes were identified by deep sequencing. Gene ontology function and KEGG pathway analyses of the differentially expressed genes and the target genes of the differentially expressed miRNAs revealed that momilactone A synthase, 14-3-3 protein, serine/threonine-protein kinase CTR1, and polyphenol oxidase, as well as alternative splicing, were associated directly or indirectly with drought stress in P. tomentosa. Our results will help to pave the way for further genomic studies, not only on P. tomentosa but also on other plants in family Paulowniaceae.