Abstract
Masson pine (Pinus massoniana) is primarily present in southwest of China, which are severely deficient in inorganic phosphate (Pi). Although some studies identified transcriptomic and proteomic responses to Pi deficiency in Masson pine seedlings, miRNAs and molecular responses in different tissues have not been well studied. To shed further light on the complex responses of Masson pine to Pi deficiency, a spatiotemporal experiment was performed to identify differentially expressed mRNAs and miRNAs under Pi deficiency. Spatiotemporal analyses of 72 RNA sequencing libraries provided a comprehensive overview of the dynamic responses of Masson pine to low-Pi stress. Differentially expressed gene analysis revealed several high-affinity phosphate transporter genes (PHT1-1, PHT1-4, PHT1-5 and PHT1-12) and a nitrate transporter gene (NRT), reflecting the crosstalk between nitrate and Pi homeostasis in plants. miRNA differential expression analysis identified several families that were associated with Pi deficiency, such as miR399. In addition, some other families were dramatically changed in response to Pi starvation, such as miR156, miR169, and some novel miRNAs. Integrated analysis of DE miRNAs and mRNAs indicated that “amino acid metabolism”, “energy metabolism” and “lipid metabolism” were most enriched under Pi deficiency. This study provided essential regulation information between miRNAs and target genes on the response of Masson pine seedlings to Pi deficiency, which will aid in further elucidation of the biological regulatory mechanisms of pines in response to low-Pi stress.
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Abbreviations
- P:
-
Phosphorus
- Pi:
-
Inorganic phosphate
- PHR1:
-
Phosphate starvation response1
- SPX:
-
SYG1/PHO81/XPR1
- PHO2:
-
Phosphate2
- PHTs:
-
Phosphate transporters
- PAPs:
-
Purple acid phosphatases
- DEGs:
-
Differentially expressed genes
- ERF:
-
Ethylene responsive factor
- PEPC:
-
Phosphoenolpyruvate carboxylase
- GDPDs:
-
Glycerophosphodiester phosphodiesterases
- SQD1:
-
UDP-sulfoquinovose synthase
- MGDs:
-
Monogalactosyldiacylglycerol synthases
- AP2 :
-
APETALA2
- RSA:
-
Root system architecture
- RPKM:
-
Reads per kilobase per million reads
- PCC:
-
Pearson correlation coefficient
- RT-qPCR:
-
Reverse transcription quantitative real-time polymerase chain reaction
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This study was funded by the National Key Research and Development Project, P. R. China (2017YFD0600302); National Natural Science Foundation of China (31660185); Science and Technology of Guizhou Province, P. R. China (20175788); Innovation Driven Development Special Fund of Guangxi, P. R. China (AA17204087-4); and the Post-National Key Research and Development Project, P. R. China (20185261).
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FF conceived, designed the experiments and wrote the paper. XS performed experiments. GD contributed reagents and materials, revised manuscript. ZZ performed experiments. JT collected data. All authors have read and approved the final manuscript.
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Figure S1
Length distribution of transcripts using next-generation sequencing. (A)Length distribution of Masson pine unigenes using next-generation sequencing. (B) miRNA length distribution of Masson pine.
Figure S2
Venn diagram of the unigenes annotated by four databases (KEGG, KOG, Nr and Swissprot).
Appendix A: Supplementary Data
Appendix A: Supplementary Data
Illumina reads of all samples have been submitted to the Sequence Read Archive at the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/sra) under Accession Number PRJNA641031.
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Fan, F., Shang, X., Ding, G. et al. Integrated mRNA and miRNA Expression Analyses of Pinus massoniana Roots and Shoots in Long-Term Response to Phosphate Deficiency. J Plant Growth Regul 41, 2949–2966 (2022). https://doi.org/10.1007/s00344-021-10486-0
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DOI: https://doi.org/10.1007/s00344-021-10486-0