PlaASDB: a comprehensive database of plant alternative splicing events in response to stress

Abstract

Background: Alternative splicing (AS) is a co-transcriptional regulatory mechanism of plants in response to environmental stress. However, the role of AS in biotic and abiotic stress responses remains largely unknown. To speed up our understanding of plant AS patterns under different stress responses, development of informative and comprehensive plant AS databases is highly demanded.

Description: In this study, we first collected 3,255 RNA-seq data under biotic and abiotic stresses from two important model plants (Arabidopsis and rice). Then, we conducted AS event detection and gene expression analysis, and established a user-friendly plant AS database termed PlaASDB. By using representative samples from this highly integrated database resource, we compared AS patterns between Arabidopsis and rice under abiotic and biotic stresses, and further investigated the corresponding difference between AS and gene expression. Specifically, we found that differentially spliced genes (DSGs) and differentially expressed genes (DEG) share very limited overlapping under all kinds of stresses, suggesting that gene expression regulation and AS seemed to play independent roles in response to stresses. Compared with gene expression, Arabidopsis and rice were more inclined to have conserved AS patterns under stress conditions.

Conclusion: PlaASDB is a comprehensive plant-specific AS database that mainly integrates the AS and gene expression data of Arabidopsis and rice in stress response. Through large-scale comparative analyses, the global landscape of AS events in Arabidopsis and rice was observed. We believe that PlaASDB could help researchers understand the regulatory mechanisms of AS in plants under stresses more conveniently. PlaASDB is freely accessible at http://zzdlab.com/PlaASDB/ASDB/index.html .

Keywords: Alternative splicing; Arabidopsis; Plant; RNA-Seq data; Rice; Stress response.

Fig. 1

The work flow of PlaASDB. The stress-related RNA-Seq data of Arabidopsis and rice were collected and processed with a standardized pipeline. Then, the expression values of genes and transcripts were calculated, and AS events were identified uniformly by using ASTool. In addition, co-expression networks of genes were constructed, and the related annotation information was also collected

Fig. 2

A brief introduction of PlaASDB through an example (gene ID: AT1G01020). A Basic information about the example. B Database built-in gene browser. C PSI range of AS events under 1-aminocyclopropane-1-carboxylic acid (ACC) stress. D The basic information of the transcript sequence. E Information of domains detected from transcripts. F The average transcripts per million reads (TPM) values of the transcripts in each stress type. For each stress type, we removed the control samples, calculated the TPM values of the transcripts from multiple experiments using StringTie (v2.1.4), and then obtained the average TPM value as the expression level of each transcript

Fig. 3

Transcript abundance of Arabidopsis (A) and rice (B) under different stress conditions

Fig. 4

Alternative splicing (AS) events in Arabidopsis and rice under stress. A The proportion of four types of AS events in Arabidopsis and rice. B The GC content of the retained introns and the skipped exons in Arabidopsis and rice are compared. C Length distribution of genome-wide introns, exons, and four major kinds of AS events in Arabidopsis and rice (*** means P-value <0.01, * means P-value <0.05). All lengths were divided by the average length of the corresponding introns/exons in the whole genome for standardization. D Distribution in ASX_i types and their frequency in Arabidopsis (left) and rice (right). ASX_i stands for the remainder of the length of an intron or exon divided by 3. X_i ∈ {0,1,2}

Fig. 5

A Differential splicing events (DSE) between Arabidopsis (left) and rice (right) under different stresses. B Venn diagram analysis of up- and down-regulated differential splicing events under biotic and abiotic stresses in Arabidopsis (left) and rice (right). C Venn diagram of differentially expressed genes (DEGs) and differentially spliced genes (DSGs) in Arabidopsis under different stresses