Fig. 1

Summary of workflow and results for the prediction, curation, and annotation of NPC2-like proteins in the genomes of a Korean and Chinese isolate of Clonorchis sinensis. Initially, putative C. sinensis NPC2-like proteins were identified using BLASTp sequence homology searches against curated NPC2 proteins submitted to the SWISS-PROT database (step 1). Selected proteins with a reciprocal best match to NPC2-like proteins submitted to NCBI-nr database were then identified (step 2). Next, C. sinensis predicted proteins with a conserved myeloid differentiation factor-2 (MD-2)-related lipid-binding (ML) domain (PF02221) were identified using InterProScan (step 3). The intersect between NPC2 protein sequence homology and retention of a conserved ML domain was then used to select putative NPC2-like proteins. Reciprocal BLASTn sequence homology across gene regions was used to infer orthology and incomplete homologous sequences were complemented in both isolates of C. sinensis using BLAT and Exonerate (step 5). Phylogenetic relationships among identified C. sinensis NPC2-like protein-encoding genes was then determined by employing MACSE2, TrimAl and MrBayes (step 6). Last, all NPC2-like proteins identified were functionally annotated using SignalP-5.0, SWISS-PROT and InterProScan databases, as well as I-TASSER, to predict tertiary structures. Transcription in different development stages and adult tissues was inferred using HISAT2 and FeatureCounts (step 7). The number of Korean (blue) and Chinese (red) C. sinensis sequences retained in each step are indicated