Integrated analysis of full-length transcriptome and secondary metabolism reveals novel regulation in Paulownia fortunei infected with phytoplasma

Abstract

Background: Paulownia witches' broom (PaWB) is a devastating disease caused by phytoplasma, which can lead to considerable economic losses. Previous studies have shown that 60 mg•L-1 methyl methane sulfonate (MMS) can restore infected Paulownia seedlings to healthy one. To improve the understanding of PaWB, we used single molecule real time (SMRT) sequencing, which can provide long sequences that can be effectively used to identify gene alternative splicing, obtain novel genes, improve gene annotations and comprehensive analysis of the metabolome. Results: Here, the first integrated analysis SMRT sequencing, the Illumina platforms, and high-performance liquid chromatography-mass spectrometry (HPLC-MS) to analyze changes in transcripts and metabolites in Paulownia fortunei. A total of 140,528 non redundant transcripts were identified, which supported 6,209 of novel gene loci that can enrich 70,223 annotation information of Paulownia fortunei （P. fortunei）genome. A total of 5,606 transcripts, 46 lncRNAs, 83 fusion transcripts, 597 transcription factors, and 57 metabolites were related indirectly or directly to PaWB. Subsequent analysis of the transcriptome and metabolome found trans-cinnamate 4-monooxygenase, caffeoyl-CoA-O methyltransferase, ferulic acid and peroxidase were up-regulated in Paulownia fortunei infected with phytoplasma. They were involved in flavonoid, phenylpropane and salicylic acid metabolism, which might be related to Paulownia-phytoplasma interaction. Conclusions: Our results will enrich the understanding of molecular mechanisms of PaWB. This study provides a foundation for better understanding the changes in gene expression, metabolites, and morphology of Paulownia fortunei with PaWB.