Abstract
Paulownia witches’ broom (PaWB) is an epidemic disease caused by phytoplasmas infection, which is responsible for large production and economic losses. The study of PaWB has made significant progress, but the specific molecular mechanisms associated with PaWB remain unclear. To clearly know the gene expression profiles of plantlets infected with phytoplasmas, in this study, we used high-throughput sequencing technology to generate an integrated analysis of the transcriptome and microRNAs (miRNAs) of Paulownia fortunei (seem.) Hemsl. plantlets, and to obtain a comprehensive resource for the relationship between vital miRNA-target gene pairs and PaWB. A total of 756 genes, and 45 conserved and 22 new miRNAs were identified associated with PaWB. In addition, 635 target genes were predicted for the 67 DERs (Differentially expressed miRNAs). An interaction network of these miRNAs and their target genes was constructed. Gene ontology (GO) and KEGG pathway analysis of these target genes indicated that genes encoding transcription factors (TFs), including auxin response factors (ARF), WRKY, NAC (NAM, ATAF1/2 and CUC2), and MYB (v-myb avian myeloblastosis viral oncogene homolog), and genes encoding superoxide dismutase (SOD), as well as alternative splicing were related directly or indirectly to PaWB. Our results shed light on the possible roles of genes and miRNAs in PaWB-infected plantlets, which will enhance the understanding of the PaWB mechanism in Paulownia plants.
Highlights
As an important member in Scrophulariaceae family, the genus Paulownia contains some fast growing tree species [1]
The availability of reference genome sequences makes the annotation of important genes, proteins, lncRNAs (LncRNAs are defined as having more than 200 nucleotides and little protein-coding potential, which are an important class of pervasive genes involved in a variety of biological functions [48,49].), metabolites, and miRNAs more precise compared with the transcriptome background, as well as providing meaningful insights into genome reorganization, gene evolution and comparative genomic analyses between multiple species [50]
Our results revealed the significant roles of miRNA-target gene pairs in response to Paulownia witches’ broom (PaWB) based on the interaction network, but further studies still need to be performed to explore their complex functions in Paulownia
Summary
As an important member in Scrophulariaceae family, the genus Paulownia contains some fast growing tree species [1]. The production of Paulownia would suffer severe or even fatal loss when it is infected with phytoplasmas [5]. Phytoplasmas are single-cell prokaryotic organisms without a cell wall, which can infect more than 1000 plant species such as jujube [6], Paulownia [7], mulberry [8], peanut [9] and sweet potato [10]. As obligate parasites, they live and multiply in the Forests 2018, 9, 397; doi:10.3390/f9070397 www.mdpi.com/journal/forests
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