Abstract
Drought is one of the most devastating effects that severely reduce plant growth and development worldwide. In recent years, the availability of a reference Paulownia genome sequence has made it easier to explore gene expression, transcriptional regulation, and posttranscriptional regulation in Paulownia species. Here, we combined the analyses of the transcriptome, small RNAs, and degradome of Paulownia tomentosa seedlings to generate a comprehensive resource to describe the links between key regulatory miRNA-target gene pairs and drought stress. A total of 22,904 differentially expressed genes, 2073 differentially expressed miRNAs, and 198 target genes were identified by deep sequencing. Gene ontology function and KEGG pathway analyses of the differentially expressed genes and the target genes of the differentially expressed miRNAs revealed that momilactone A synthase, 14-3-3 protein, serine/threonine-protein kinase CTR1, and polyphenol oxidase, as well as alternative splicing, were associated directly or indirectly with drought stress in P. tomentosa. Our results will help to pave the way for further genomic studies, not only on P. tomentosa but also on other plants in family Paulowniaceae.
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Acknowledgements
This study was funded by the Natural Science Foundation of Henan Province of China (Grant No. 162300410158) and the Distinguished Talents Foundation of Henan Province of China (Grant No. 174200510001).
Data archiving statement
All the sequencing data generated in this study is available from the SRA-Archive (http://www.ncbi.nlm.nih.gov/sra) of NCBI. The transcriptome, small RNA, and degradome sequencing raw data from this article have been deposited under Accession Nos. SRP031515, SRP116066, and SRP116267.
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Guoqiang Fan conceived, designed, and carried out the study. Haifang Liu wrote the manuscript. Zhenli Zhao revised the manuscript. Limin Wang, Minjie Deng, Xiaoqiao Zhai, and Yanpeng Dong provided suggestions on the experimental design and analyses. All authors read and approved the manuscript.
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Communicated by A. Brunner
Haifang Liu and Zhenli Zhao are co-first authors.
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Fig. S1
Correlation coefficients of the expression of duplicate samples. X-axis represents the logarithmic value of diploid (A) or tetraploid (B) expression, while Y-axis represents the logarithmic value of the corresponding duplicate samples. (GIF 31 kb)
Fig. S2
Cluster analysis of the inter and union DEGs in the PT4 vs. PT2, PT4T vs. PT2T, PT4T vs. PT4, and PT2T vs. PT2 comparisons. (GIF 294 kb)
Fig. S3
Gene Ontology of the DEGs in Comparison A, B, C, and D. (GIF 67 kb)
Fig. S4
Gene Ontology of the DEGs in Comparison E, F, G, and H. (GIF 75 kb)
Fig. S5
KEGG annotation for the DEGs in Comparison A, B, C, and D. (GIF 142 kb)
Fig. S6
KEGG annotation for the DEGs in Comparison E, F, G, and H. (GIF 145 kb)
Fig. S7
Number of conserved miRNA families. (GIF 30 kb)
Fig. S8
Nucleotide bias at each position in miRNAs among the four sRNA libraries. A, B, C, and D represent the libraries made from the samples in PT2, PT2T, PT4, and PT4T, respectively. (GIF 140 kb)
Fig. S9
The cluster chart of miRNAs’ expression; (A): Conserved miRNAs; (B): Novel miRNAs. (GIF 219 kb)
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Liu, H., Zhao, Z., Wang, L. et al. Genome-wide expression analysis of transcripts, microRNAs, and the degradome in Paulownia tomentosa under drought stress. Tree Genetics & Genomes 13, 128 (2017). https://doi.org/10.1007/s11295-017-1211-3
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DOI: https://doi.org/10.1007/s11295-017-1211-3