Fig. 2.

nrEVE search identifies unreported endogenous bornavirus-like elements. (A) Schematic representation of the workflow to search for nrEVEs. We searched nrEVE candidates with four steps: pA-TSD search, PES search, pseudogene and simple repeat removal, and classification using the SVM. (B) Numbers of nrEVE candidates in each step, and as a percentage of those from the preceding step, of the workflow shown in A. (C) Phylogenetic tree of human EBLNs and extant bornavirus N genes. The tree was constructed based on nucleotide sequences using the maximum-likelihood method with 1,000 bootstrap replicates. Bootstrap values greater than 70% are indicated. Gray and blue dots next to the leaf nodes represent previously reported and unreported EBLNs, respectively. The scale bar shows nucleotide substitutions per site. (D) Protein sequence alignment showing similarity across hsEBLN-8, hsEBLN-7, and BoDV-1. The underlined sequences are the regions detected by a tBLASTn search with the BoDV-1 N protein as a query. <del+fs>, deletion causing a frameshift mutation; <in+fs>, insertion causing a frameshift mutation; X, termination codon. (E) Protein sequence alignment showing similarity between hsEBLN-9 and JCPV. Putative regions affected by frameshift mutations are indicated by arrows.