Transcriptome, microRNA, and degradome analyses of the gene expression of Paulownia with phytoplamsa

Abstract

BackgroundPaulownia witches’ broom (PaWB) is a fatal disease of Paulownia caused by a phytoplasma. In previous studies, we found that plants with PaWB symptoms would revert to a healthy morphology after methyl methane sulfonate (MMS) treatment. To completely understand the gene expression profiles of the Paulownia-phytoplasma interaction, three high-throughput sequencing technologies were used to investigate changes of gene expression and microRNAs (miRNAs) in healthy Paulownia tomentosa plantlets, PaWB-infected plantlets, and PaWB-infected plantlets treated with 60 mg · L−1 MMS.MethodsTranscriptome, miRNAs and degradome sequencing were performed to explore the global gene expression profiles in the process of Paulownia tomentosa with phytoplasma infection.ResultsA total of 98,714 all-unigenes, 62 conserved miRNAs, and 35 novel miRNAs were obtained, among which 902 differentially expressed genes (DEGs) and 24 miRNAs were found to be associated with PaWB disease. Subsequently, the target genes of these miRNAs were predicted by degradome sequencing. Interestingly, we found that 19 target genes of these differentially expressed miRNAs were among the 902 DEGs. The targets of pau-miR156g, pau-miR403, and pau-miR166c were significantly up-regulated in the P. tomentosa plantlets infected with phytoplasma. Interaction of miRNA -target genes mediated gene expression related to PaWB were identified.ConclusionsThe results elucidated the possible roles of the regulation of genes and miRNAs in the Paulownia-phytoplasma interaction, which will enrich our understanding of the mechanisms of PaWB disease in this plant.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2074-3) contains supplementary material, which is available to authorized users.

Comparative Analysis of MicroRNA Expression in Three Paulownia Species with Phytoplasma Infection

“…Reverse transcription and PCRs were performed to obtain sufficient single-stranded cDNA. The PCR procedure was conducted according to [23]. An Agilent 21.00 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and ABI StepOnePlus Real-Time PCR System (Life Technologies, Grand Isle, NY, USA) were used to determine the quality and yield, respectively.…”

“…The primers for the selected target genes were designed using the Beacon Designer software (version 7.7, Premier Biosoft International, Ltd., Palo Alto, CA, USA), and the specific stem-loop primers for the miRNAs were designed as reported previously [33]. The PCR amplifications conditions were according to [23]. The U6 snRNA and 18S rRNA served as the miRNA and target gene endogenous references, respectively.…”

“…The functions of miRNAs in PaWB have also been investigated, and some miRNAs and their target genes involved in metabolism pathways have been reported [18][19][20][21][22][23], but most of the reported miRNAs were obtained from de novo transcriptome assemblies and were putative genes, because the lengths of unigene sequences obtained by transcriptome assembly are shorter than the reads obtained from the Paulownia reference genome sequence. This implies that the annotation information may be incomplete and a lot of time and effort may be required to validate their functions in the processes associated with PaWB occurrence.…”

Transcriptome and Small RNA Sequencing Analysis Revealed Roles of PaWB-Related miRNAs and Genes in Paulownia fortunei

“…Previous studies about genes related to PaWB have been found, but the mechanisms were still unclear. To get a deeper understanding of the interaction between Paulownia and phytoplasmas, we compared the data obtained in this study with others [51,52]. The number and species of miRNAs or genes in the present study were different.…”

Long Non-Coding RNAs Responsive to Witches’ Broom Disease in Paulownia tomentosa

“…Rifampicin treatment can make PaWB-infected Paulownia recover to normal morphology [13]. Furthermore, the rapid development of 'omics' has allowed for the investigation of the transcriptomes [3,[14][15][16][17][18], microRNAs (miRNAs), degradomes [19][20][21][22], and proteomes [4,23] of Paulownia species, and the results have revealed changes after PaWB infection at transcriptional, post-transcriptional, and translational levels.…”