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Genome-wide identification of candidate genes related to disease resistance and high biomass in tetraploid Paulownia

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Abstract

Polyploidization is an important feature of speciation that results from genome doubling. Tetraploid plants often have better physical characteristics than their diploid counterparts, and Paulownia is no exception. In our previous studies, several genes related to timber quality and abiotic stress resistance were identified in Paulownia tomentosa and Paulownia fortunei. However, the genes related to disease resistance and high biomass were not confirmed. In this study, small RNA and transcriptome sequencing were performed to analyze changes in microRNA (miRNA) and mRNA expression levels in tetraploid Paulownia tomentosa × Paulownia fortunei and Paulownia australis and their diploid counterparts. A total of 930 common differentially expressed genes and 66 (19 known and 47 novel) common differentially expressed miRNAs were detected in the two tetraploid vs. diploid comparisons. Twenty-two miRNA target genes were predicted, and the regulatory functions of the miRNA–target gene pairs were analyzed, of which the novel miR327- SGT1 HOMOLOG PROTEIN At5g65490 (PAU019930.1) and pau-miR2111a-MYB-RELATED TRANSCRIPTION FACTOR (PAU011118.1) interacting pairs were predicted to co-regulate disease resistance in tetraploid Paulownia. The pau-miR157i-SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 15 (PAU009402.1) and novel miR10-PUTATIVE PENTATRICOPEPTIDE REPEAT-CONTAINING PROTEIN At5g65820 (PAU012281.1) interacting pairs were predicted to co-regulate high biomass in tetraploid Paulownia. The expression trends of the miRNA and candidate target genes were validated by qRT-PCR. The results will help to accelerate genetic gain in Paulownia breeding programs to develop superior varieties.

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Acknowledgements

We would like to thank Margaret Biswas, PhD, from Liwen Bianji, Edanz Group China (www.liwenbianji.cn/ac), for editing the English text of this manuscript.

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  1. Xibing Cao and Xiaoqiao Zhai have contributed equally to this work.

Authors and Affiliations

  1. Institute of Paulownia, Henan Agricultural University, 95 Wenhua Road, Jinshui District, Zhengzhou, 450002, Henan, P.R. China

    Xibing Cao, Zhenli Zhao & Guoqiang Fan

  2. College of Forestry, Henan Agricultural University, 95 Wenhua Road, Jinshui District, Zhengzhou, 450002, P.R. China

    Xibing Cao, Enkai Xu, Zhenli Zhao & Guoqiang Fan

  3. Forestry Academy of Henan, Zhengzhou, P.R. China

    Xiaoqiao Zhai

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  1. Xibing Cao
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11738_2020_3160_MOESM1_ESM.7z

Supplementary file1 Online Resource 1: Table S1 Primers of DEGs and DEMs for qRT-PCR analysis. Online Resource 1: Table S2 Statistics of clean reads mapped to reference gene and genome. Online Resource 1: Table S3 The common expression DEGs in the two diploid and tetraploid paulownia species. Online Resource 1: Table S4 The DEGs matched to the alternative splicing event corresponding genes. Online Resource 1: Table S5 Classification of Paulownia’ RNAs of diploid and tetraploid libraries *: unannotated. Online Resource 1: Table S6 Known miRNA in the two tetraploid and diploid paulownias. Online Resource 1: Table S7 New miRNA in the two tetraploid and diploid paulownias. Online Resource 1: Table S8 Common expression known DEMs in the two tetraploid and diploid paulownias. Online Resource 1: Table S9 Common expression new DEMs in the two tetraploid and diploid paulownias (7Z 294 KB)

11738_2020_3160_MOESM2_ESM.7z

Supplementary file2 Online Resource 2:Figure S1 Correlation coefficients of the gene expression of duplicate samples. Online Resource 2: Figure S2 The DEGs in the two tetraploid and diploid paulownias. Online Resource 2: Figure S3 The number of alternative splicing events and their corresponding genes. Online Resource 2: Figure S4 The pictures of the RNA separation and spectrophotometer measurements results A: The picture of RNA separations of PA2 and PA4 with three biological replicates, B: The picture of RNA separations of PTF2 and PTF4 with three biological replicates, C: The results of RNA concentrations and qualities measurements of the two diploid and tetraploid paulownias. Online Resource 2:Figure S1 Correlation coefficients of the gene expression of duplicate samples. Online Resource 2: Figure S2 The DEGs in the two tetraploid and diploid paulownias. Online Resource 2: Figure S3 The number of alternative splicing events and their corresponding genes. Online Resource 2: Figure S4 The pictures of the RNA separation and spectrophotometer measurements results A: The picture of RNA separations of PA2 and PA4 with three biological replicates, B: The picture of RNA separations of PTF2 and PTF4 with three biological replicates, C: The results of RNA concentrations and qualities measurements of the two diploid and tetraploid paulownias. (7Z 195 KB)

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Cao, X., Zhai, X., Xu, E. et al. Genome-wide identification of candidate genes related to disease resistance and high biomass in tetraploid Paulownia. Acta Physiol Plant 42, 171 (2020). https://doi.org/10.1007/s11738-020-03160-7

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