Comparative Transcriptome Analysis of Sophora japonica (L.) Roots Reveals Key Pathways and Genes in Response to PEG-Induced Drought Stress under Different Nitrogen Conditions

Sophora japonica is a native leguminous tree species in China. The high stress tolerance contributes to its long lifespan of thousands of years. The lack of genomic resources greatly limits genetic studies on the stress responses of S. japonica. In this study, RNA-seq was conducted for S. japonica roots grown under short-term 20% polyethylene glycol (PEG) 6000-induced drought stress under normal N and N starvation conditions (1 and 0 mM NH4NO3, respectively). In each of the libraries, we generated more than 25 million clean reads, which were then de novo assembled to 46,852 unigenes with an average length of 1310.49 bp. In the differential expression analyses, more differentially expressed genes (DEGs) were found under drought with N starvation than under single stresses. The number of transcripts identified under N starvation and drought in S. japonica was nearly the same, but more upregulated genes were induced by drought, while more downregulated genes were induced by N starvation. Genes involved in phenylpropanoid biosynthesis and biosynthesis of amino acids pathways were upregulated according to KEGG enrichment analyses, irrespective of the stress treatments. Additionally, upregulated N metabolism genes were enriched upon drought, and downregulated photosynthesis genes were enriched under N starvation. We found 4,372 and 5,430 drought-responsive DEGs under normal N and N starvation conditions, respectively. N starvation may aggravate drought by downregulating transcripts in the carbon metabolism, ribosome, arginine biosynthesis pathway, oxidative phosphorylation and aminoacyl-tRNA biosynthesis pathways. We identified 78 genes related to N uptake and assimilation, 38 of which exhibited differential expression under stress. A total of 395 DEGs were categorized as transcription factors, of which AR2/ERF-ERF, WRKY, NAC, MYB, bHLH, C3H and C2C2-Dof families played key roles in drought and N starvation stresses. The transcriptome data obtained, and the genes identified facilitate our understanding of the mechanisms of S. japonica responses to drought and N starvation stresses and provide a molecular foundation for understanding the mechanisms of its long lifespan for breeding resistant varieties for greening.

Automated summary

Sophora japonica, a native leguminous tree species in China, exhibits high stress tolerance and long lifespan. RNA-seq analysis under drought and N starvation conditions revealed similar numbers of transcripts in S. japonica roots, with drought inducing more upregulated genes and N starvation inducing more downregulated genes. N starvation may aggravate drought stress by downregulating genes related to carbon metabolism, ribosome, arginine biosynthesis pathway, etc.