Fig 1.
Overview of RNA-seq data used for analyses and alternative splicing in four Drosophila species.
Top: Numbers of genes and exons detected and numbers of stages/tissues for each of four Drosophila species. Bottom: Numbers of total, constitutive, and alternatively spliced exons, as well as a breakdown of types of alternatively spliced exons, for each species. Proportions of different types of alternatively spliced exons are shown as pie charts to the right of the table.
Fig 2.
Gene expression and alternative splicing profiles across tissues and development.
Comparisons of % of total genes expressed (left panel), % annotated alternatively spliced exons expressed (middle panel), and % of total genes expressed that are annotated as alternatively spliced (right panel) for (A) post-embryonic tissues and (B) embryonic stages. Each row of each heatmap is scaled separately by Z-score. “pse” = D. pseudoobscura; “mir” = D. miranda; “alb” = D. albomicans; “nas” = D. nasuta; “sperm.” = spermatheca; “larva” = 3rd instar larva; “acc.” = accessory gland
Fig 3.
Alternative splicing (left column) and gene expression (right column) profiles for D. pseudoobscura. The R function prcomp was used to perform the PCAs. (A) PC1 (AS: 57.9% of the variance & GE: 50.1% of the variance) and PC2 (AS: 10.7% of the variance & GE: 12.4% of the variance). (B) PC2 and PC3 (AS: 4.5% of the variance & GE: 7.5% of the variance). “f” = female; “m” = male; “5.5” = mid stage 5; “5.9” = late stage 5; “8.9” = late stage 8; “carc” = carcass; “ov” = ovary; “sperm” = spermatheca; “larv” = 3rd instar larva; “test” = testis; “acc” = accessory gland
Fig 4.
Correlations of gene expression versus alternative splicing.
Spearman correlations based on gene expression (TPM) for orthologous genes in (A) adult tissues (n = 3,005) and (B) embryonic stages (n = 6,707) (mean of three replicates per sex/stage). Spearman correlations based on alternative splicing (Ψ) for orthologous exons (C) expressed in all species and annotated as alternatively spliced in at least one sample in adult tissues (n = 472) and (D) expressed in both species and annotated as alternatively spliced in at least one sample in embryonic stages (n = 1,122).
Fig 5.
Sex-biased splicing in D. pseudoobscura.
Comparisons of ΔΨ distributions are between males and females for whole body (top left), gonad (ovary and testis, top right), carcass (bottom left), and head (bottom right). The x-axis gives ΔΨ values and the y-axis shows the number of sex-biased exons. Red bars represent female-biased exons (Ψfemale− Ψmale > 0) and blue bars represent male-based exons (Ψmale− Ψfemale > 0).