Fig 1.
Global transcriptomic profiles of S. japonicum in four different life stages.
RNA-Seq was performed on replicate samples of eggs (Egg), miracidia (Mir), sporocysts (Spo) and cercariae (Cer). (A) Four S. japonicum larval stages used for RNA-Seq. (B) PCA results. Each symbol indicates an individual sample. (C) Venn diagram showing differentially transcribed genes among the four life stages. Circles of different colors represent a set of genes transcribed in one stage, where the values represent the number of uniquely transcribed genes in one stage, or common transcribed genes between two, three or four life stages.
Fig 2.
Stage-specific genes (SSG) and stage-enriched genes (SEG) in the four larval stages.
(A) The number of SSG and SEG in each stage. (B) GO enrichment analysis based on the SSG and SEG in each stage. Gene ratio is the percentage of total SEG or SSG in the given GO term.
Fig 3.
Differential gene expression among the stage transitions.
Volcano plots showing differentially expressed genes (DEGs) in miracidium compared to egg (A), in sporocyst compared to miracidium (B), and in cercaria compared to sporocyst (C). Genes with p-value near 0 were adjusted to the p-value = 10−500. The dot line on the y axis refers to p-value = 0.05. The dotted lines on the x axis refer to fold change = -2 or 2.
Fig 4.
Clusters of genes based on time-course expression pattern.
Membership value was calculated using R package Mfuzz, which indicated the degree of membership of this gene for the corresponding cluster. The y-axes were scaled independently to emphasize the differences between clusters.
Fig 5.
(A) Heatmaps showing the relative gene expression of the eighteen stem cell markers in egg, miracidium, sporocyst and cercaria, as indicated. (B) Expression profiles of the nine stem cell markers in the four larval stages.
Fig 6.
Genome-wide identification, characterization, and expression patterns analysis of the papain gene family in S. japonicum.
(A) Phylogenetic relationship of papain. An un-rooted phylogenic tree was constructed in MEGA 7 using multiple alignments of S. japonicum and S. mansoni whole sequences data. (B) The motif composition and exon-intron structure of papain genes. For the motif pattern, the motifs, numbers 1–10, are displayed in different colored boxes. For the gene structure, green boxes indicate untranslated 5’- and 3’-regions; yellow boxes indicate exons; black lines indicate introns. (C) Synteny analysis of papain genes between S. japonicum and S. mansoni. Gray lines in the background show the collinear blocks within S. japonicum and S. mansoni genomes, while the red lines highlight the syntenic papain gene pairs. The tandem duplicated genes are marked in red. (D) Expression profiles of the papain genes at the four life stages.
Fig 7.
AS landscapes in S. japonicum larval stages.
(A) Number and percentage of AS events in S. japonicum eggs, miracidia, sporocysts and cercariae. (B) Proportions of different AS types detected in S. japonicum eggs, miracidia, sporocysts and cercariae. (C) The Venn diagram shows the overlap of AS genes in the four life stages. (D) Interactions between the five types of detected AS genes in the cercaria stage were visualized using an UpSet plot. (E) Venn diagram of the overlap of the DE and DAS genes between the eggs and miracidia stages. (F) An example of a gene (Sjc_0007531) displayed different SE at the eggs and miracidia stages.