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

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.

Bioinformatic Analysis of the BTB Gene Family in Paulownia fortunei and Functional Characterization in Response to Abiotic and Biotic Stresses

“…By comparing the miRNA and transcriptome before and after PaWB, 74 pf-miRNAs targeting 42 PfBTB s were found. We found that PfBTB14 , their target gene, was increased in diseased seedlings, while pf-miRNA159a and pf-miRNA159b-3p were downregulated in diseased seedlings [ 48 ]. Infected seedlings had increased pf-miRNA114 expression, and its PfBTB44 target gene had increased expression as well.…”

Paulownia Witches’ Broom Disease: A Comprehensive Review

“…Many differentially expressed genes (DEGs) among these samples were identified. Studies using the gene ortholog (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway databases indicated that these DEGs are involved in various pathways, including phytohormone biosynthesis, photosynthesis and plant-pathogen interaction [51][52][53][54][55][56][57][58].…”

Transcriptome Analysis of Cambium Tissue of Paulownia Collected during Winter and Spring

“…Transcriptome analyses from various tree species indicate that the putative role of gene families belonging to receptor kinases, transcription factors, and secondary wall biosynthesis are highly expressed in wood-forming cells [17][18][19][20][21]. At a molecular level, studies related to Paulownia gene expression profiling published in the last few years have primarily focused on drought tolerance and host-pathogen interactions [22][23][24][25]. Cambial development (the initiation and activity of the vascular cambium) leads to an accumulation of wood (secondary xylem tissue).…”