The landscape of abiotic and biotic stress-responsive splice variants using RNA-seq datasets in hot pepper

1.Overview of the pepper transcriptomes used in this study.
2.Quality assessment of raw read preprocessing on 132 raw RNA-seq datasets from C. annuum infected with P. capsici, TMV-P2, Xag8ra, Xcv1, and Xcv3. (a-e) Quality scores of reads for P. capsici, TMV-P2, Xag8ra, Xcv1 and Xcv3, respectively. X-axis represents mean sequence quality (Phred score) and y-axis represents read counts. (f-j) Graphs for quality scores per position. The x-axis represents the position (bp), and the y-axis Phred score.
3.Principal components analysis (PCA) for RNA-seq datasets infected with biotic stressors in hot pepper. PCA plots with normalized data of (a) P. capsici; (b) TMV-P2; (c) Xag8ra; (d) Xcv1; (e) Xcv3.
4.Proportion of alternative splicing events detected in hot pepper under different conditions. The graphs indicate the number of alternative splicing events in response to biotic and abiotic stressors, tissues and signaling molecules. Blue, exon skipping (SE); yellow, intron retention (RI); light grey, mutually exclusive exons (MXE); green, alternative 5’ splice site (A5SS); pink, alternative 3’ splice site (A3SS).
5.Statistical summary of mapping rates
:Information about mapping rates for 425 RNA-seq datasets

6.Information of AS events results
: Information of AS events under environmental stressors, tissues, and signaling molecules.

7. The list of AS gene, DAS gene, and description of DAS gene
Sheet 1: AS gene listSheet 2: DAS gene listSheet 3: DAS gene descriptionSheet 4: AS type information of DAS gene

8.Distribution of AS types in DAS genes under four intersection set
Sheet 1 (Abio&Biotic&Tissue&Phytohormone): Distribution of AS types in DAS genes under ABTS intersection setSheet 2 (Abiotic&Biotic&Tissue): Distribution of AS types in DAS genes under ABT intersection setSheet3 (Abiotic&Tissue): Distribution of AS types in DAS genes under AT intersection setSheet4 (Biotic&Tissue): Distribution of AS types in DAS genes under BT intersection set

9.Code availability. zip
: 1. Annotated gene_filtering.pl - Filtering code of transcripts containing two or more annotated genes
: 2. Stop codon_filtering.pl - Filtering code of transcripts that didn't have a stop codon
: 3. AS_counting code.pl - code for counting the number of AS
: 4. DAS_gene_counting code.pl - code for counting the DAS genes