Exploring the role of differential splicing of Pekin ducks resistant to DHAV-3 based on full-length transcriptome

Fig. 1. Overview of ONT data. (A) Distribution of ONT read lengths in 12 samples. (B) Number of isoforms identified per gene detected in the samples.

Fig. 2. Volcano plots of differentially expressed transcripts. (A) Volcano plots of differentially expressed transcripts of K0h vs Y0h. (B) Volcano plots of differentially expressed transcripts of K24h vs Y24h. (C) Volcano plots of differentially expressed transcripts of K24h vs K0h. (D) Volcano plots of differentially expressed transcripts of Y24h vs Y0h.

Fig. 3. Verification results of differentially expressed genes of RNA-seq and qPCR.

Fig. 4. TOP 10 GO pathways enriched by differentially expressed transcripts (A) K24h vs Y24h down-regulated differentially expressed transcripts. (B) K24h vs Y24h up-regulated differentially expressed transcripts.

Fig. 5. Ligand–receptor interactions of K24h vs Y24h. (A) Heatmap of the top 20 most active ligand–receptor pairs identified by BulkSignalR. Activity scores are row-normalised. Higher activity in the resistant group (K24) is seen for immune-related pairs. (B) Ligand-receptor network (green: ligand; red: receptor). Genes have been labeled for nodes with higher connectivity.

Fig. 6. Summary of alternative splicing analysis of transcripts. (A) AS events of K0h vs Y0h. (B) AS events of K24h vs Y24h.

Fig. 7. AS event of SELENOP of K0h vs Y0h. (A) The isoform structure of SELENOP. (B) Proportion and expression abundance of isoforms in different samples. (C) Result of sequences aligning. (D) 3D structure of SELENOP.

Fig. 8. AS event of DHX58 of K24h vs Y24h (A) The isoform structure of DHX58. (B) Proportion and expression abundance of isoforms of DHX58 in different samples. (C) Result of sequences aligning. (D) 3D structure of DHX58.

Fig. 9. AS event of PRPF8 of K24h vs Y24h. (A) The isoform structure of PRPF8. (B) Proportion and expression abundance of isoforms of PRPF8 in different samples. (C) Result of sequences aligning. (D) 3D structure of PRPF8.

Fig. 10. PPI network plot and enrichment results (A) The PPI network plot of K0h vs Y0h. (B) Enrichment results of genes that undergo isoform switching in the K0h vs Y0h comparison. (C) The PPI network plot of and K24h vs Y24h. (D) Enrichment results of genes that undergo isoform switching in the K24h vs Y24h comparison.

Fig. 11. The expression characteristics of DHX58 and XRCC5 isoform switching, including isoforms with significant changes in usage, gene expression levels in different groups, as well as isoform expression levels and isoform usage quantities.. (A) The isoform switch in DHX58. (B) The isoform switch in XRCC5. * P < 0.05.

Fig. 12. Identification, classification and functional characterization of lncRNAs. (A) Venn plot of lncRNA transcripts identified from CPC and CNCI. (B) The type of lncRNA, including antisense, sense-overlapping, intronic and lincRNA. (C) LncRNA-mRNA network. (D) GO enrichment of target genes.