Table 1.
Summary of RNA-seq based genome annotation for S. mediterranea.
Figure 1.
Validation of S. mediterranea transcript assemblies.
Transcript assembly for Smed-Smad-1 (CUFF.118389.0). Smed-Smad-1 encodes 4 exons which are supported by RNA-Seq reads (maroon) and an S. mediterranea mRNA sequence.
Figure 2.
Strain-specific transcript expression.
(A) Scatterplot of log2(1+FPKM) values for transcripts expressed in non-irradiated asexual (x-axis) and sexual (y-axis) animals. Biases in expression are categorized as follows: sexual-specific (red), sexual-biased (orange), unbiased (green), asexual-biased (blue) and asexual-specific (purple). The piechart (inset) shows the fraction of transcripts that fall into each category. (B) RT-PCR validation of strain-biased expression in sexual and asexual non-irradiated (−) and irradiated (+) samples; results are shown for 13 samples (Smed-actin used as a control).
Table 2.
Strain-specific patterns of GO category enrichment.
Figure 3.
Classification of alternative splicing events.
(A) Number of splicing events and genes detected for 5 classes of alternative splicing events: cassette exons, alternative 5′ splice sites, alternative 3′ splice sites, mutually exclusive exons and retained introns. (B) Percentage of each class of alternative splicing event shown in piechart. (C) Frame preservation in constitutively and alternatively spliced cassette exons; phase 2 and phase 1 exons are out-of-frame; phase 0 exons are in-frame. (D) RT-PCR validation of strain-specific alternative splicing events in non-irradiated (−) and irradiated (+) sexual and asexual animals. A cassette exon (CUFF.250649) is shown in top gel, while a retained intron (CUFF.62385) is shown in the bottom gel.
Figure 4.
Transcript expression profile of S. mediterranea neoblasts.
(A) Overlap in transcript expression between the X1 (blue), X2 (green) and Xins (red) cell populations displayed as Venn Diagrams. (B) Expression values (FPKM) for transcripts in the X1 (column 1), X2 (column 2) and Xins (column 3) cell populations (expressed as Z-scores) are shown in the heat map. Z-score colors range from yellow (above the mean) and blue (below the mean). (C) Overlap in expression between transcripts enriched in FACS generated X1 cells and transcripts classified as irradiation-sensitive in sexual and asexual strains. (D) GO category counts (x-axis) for 11 categories (y-axis) associated with transcripts enriched in X1 (blue) and Xins (red) cells. Category counts are signficantly different between X1 and Xins populations for all categories (p<0.0009; Chi-square). P-values were adjusted using the Bonferroni correction.
Table 3.
Number of genes and transcripts enriched in S.mediterranea and Human cell populations.