Transcriptome and Small RNA Sequencing Analysis Revealed Roles of PaWB-Related miRNAs and Genes in Paulownia fortunei
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 kno...
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doaj-7a446c2774564fac80184bb305d8651d2020-11-25T01:04:38ZengMDPI AGForests1999-49072018-07-019739710.3390/f9070397f9070397Transcriptome and Small RNA Sequencing Analysis Revealed Roles of PaWB-Related miRNAs and Genes in Paulownia fortuneiBingbing Li0Xiaoqiao Zhai1Yabing Cao2Hui Zhao3Zhe Wang4Haifang Liu5Guoqiang Fan6Institute of Paulownia, Henan Agricultural University, 95 Wenhua Road, Jinshui District, Zhengzhou 450002, ChinaForestry Academy of Henan, Zhengzhou 450002, ChinaInstitute of Paulownia, Henan Agricultural University, 95 Wenhua Road, Jinshui District, Zhengzhou 450002, ChinaInstitute of Paulownia, Henan Agricultural University, 95 Wenhua Road, Jinshui District, Zhengzhou 450002, ChinaInstitute of Paulownia, Henan Agricultural University, 95 Wenhua Road, Jinshui District, Zhengzhou 450002, ChinaInstitute of Paulownia, Henan Agricultural University, 95 Wenhua Road, Jinshui District, Zhengzhou 450002, ChinaInstitute of Paulownia, Henan Agricultural University, 95 Wenhua Road, Jinshui District, Zhengzhou 450002, ChinaPaulownia 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.http://www.mdpi.com/1999-4907/9/7/397Paulownia fortuneipaulownia witches’ broomtranscriptomemiRNAsalternative splicing |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Bingbing Li Xiaoqiao Zhai Yabing Cao Hui Zhao Zhe Wang Haifang Liu Guoqiang Fan |
spellingShingle |
Bingbing Li Xiaoqiao Zhai Yabing Cao Hui Zhao Zhe Wang Haifang Liu Guoqiang Fan Transcriptome and Small RNA Sequencing Analysis Revealed Roles of PaWB-Related miRNAs and Genes in Paulownia fortunei Forests Paulownia fortunei paulownia witches’ broom transcriptome miRNAs alternative splicing |
author_facet |
Bingbing Li Xiaoqiao Zhai Yabing Cao Hui Zhao Zhe Wang Haifang Liu Guoqiang Fan |
author_sort |
Bingbing Li |
title |
Transcriptome and Small RNA Sequencing Analysis Revealed Roles of PaWB-Related miRNAs and Genes in Paulownia fortunei |
title_short |
Transcriptome and Small RNA Sequencing Analysis Revealed Roles of PaWB-Related miRNAs and Genes in Paulownia fortunei |
title_full |
Transcriptome and Small RNA Sequencing Analysis Revealed Roles of PaWB-Related miRNAs and Genes in Paulownia fortunei |
title_fullStr |
Transcriptome and Small RNA Sequencing Analysis Revealed Roles of PaWB-Related miRNAs and Genes in Paulownia fortunei |
title_full_unstemmed |
Transcriptome and Small RNA Sequencing Analysis Revealed Roles of PaWB-Related miRNAs and Genes in Paulownia fortunei |
title_sort |
transcriptome and small rna sequencing analysis revealed roles of pawb-related mirnas and genes in paulownia fortunei |
publisher |
MDPI AG |
series |
Forests |
issn |
1999-4907 |
publishDate |
2018-07-01 |
description |
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. |
topic |
Paulownia fortunei paulownia witches’ broom transcriptome miRNAs alternative splicing |
url |
http://www.mdpi.com/1999-4907/9/7/397 |
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