Additional file 1 of Genomic and phylogenetic characterization of ChPV2, a novel goat PV closely related to the Xi-PV1 species infecting bovines
Creators: name: Willemsen, Anouk
name: Boom, Alexander Van Den
name: Dietz, Julienne
name: Dagalp, Seval Bilge
name: Firat Dogan
name: Bravo, Ignacio G.
name: Ehrhardt, Anja
name: Ehrke-Schulz, Eric
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Genome organization of ChPV2; Upstream regulatory region, yellow; early genes, green late genes, blue, potential E4 gene and potential E1^E4 splicing patterns, ochre. Figure S2. Presence and position of putative regulatory elements within URR and early gene region of ChPV1 and ChPV2, E1- binding sites (E1BS) are marked by yellow boxes, E2- binding sites (E2BS) perfectly matching the E2BS consensus sequence are marked by red boxes, E2BS with 1 nucleotide mismatch to the E2BS consensus sequence are marked in orange. nucleotide positions of early genes and regulatory elements are depicted below or above the respective element. Figure S3. Maximum likelihood phylogenetic trees of the concatenated E1E2 and concatenated L2L1 nucleotide alignments of 377 PVs. Clade color codes highlight the different PV groups and recombinant taxa: red, Alpha-OmikronPVs; green, Beta-XiPVs; yellow, Lambda-MuPVs; blue, Delta-ZetaPVs; gray, a yet unclassified clade consisting of PVs infecting birds and turtles; aqua-blue, a yet unclassified clade consisting of PVs infecting Caniformia; orange, known recombinant PVs infecting Cetaceans; and pink, possible recombinant PVs. The position of ChPV2 is indicated with a red arrow. Values on branches correspond to ML bootstrap support values. Figure S4. Maximum likelihood phylogenetic trees of the concatenated E1E2 and concatenated L2L1 nucleotide alignments of 324 PVs. Clade color codes highlight the different PV groups: red, Alpha-OmikronPVs; green, Beta-XiPVs; yellow, Lambda-MuPVs; blue, Delta-ZetaPVs; and gray, a yet unclassified clade consisting of PVs infecting birds and turtles. The position of ChPV2 is indicated with a red arrow. Values on branches correspond to ML bootstrap support values. Figure S5. Maximum likelihood phylogenetic trees of the concatenated E1E2 and concatenated L2L1 amino acid alignments of 324 PVs. Clade color codes highlight the different PV groups: red, Alpha-OmikronPVs; green, Beta-XiPVs; yellow, Lambda-MuPVs; blue, Delta-ZetaPVs; and gray, a yet unclassified clade consisting of PVs infecting birds and turtles. The position of ChPV2 is indicated with a red arrow. Values on branches correspond to ML bootstrap support values. Figure S6. Maximum likelihood phylogenetic tree of the concatenated E1E2L2L1 amino acid alignments of 324 PVs. Clade color codes highlight the different PV groups: red, Alpha-OmikronPVs; green, Beta-XiPVs; yellow, Lambda-MuPVs; blue, Delta-ZetaPVs; and gray, a yet unclassified clade consisting of PVs infecting birds and turtles. The position of ChPV2 is indicated with a red arrow. Values on branches correspond to ML bootstrap support values. Figure S7. Maximum likelihood phylogenetic trees of E6 (A), E7 (B) and the concatenated E1E2L2L1 (C) amino acid alignments of 17 PVs. The taxa highlighted in blue contain both the E6 and E7 oncogenes in their genomes, while the other taxa contain only E7. The position of ChPV2 is indicated with a red arrow. Values on branches correspond to ML bootstrap support values. Figure S8. Macroscopic view of teat papilloma of a Damascus (Shami) goat, taken from (12). Table S1. Genome organization of ChPV2 presenting orf positions, orf length, GC content and amino acid content of encoded potential proteins and their molecular weight. Table S2. Nucleotide (nt) identity of ChPV2 genes with the respective genes of closely related PV types. Table S3. Amino acid (aa) identity of ChPV2 genes with the respective genes of closely related PV types. Table S4. Potential motifs and domains identified in amino acid sequences of ChPV2 proteins. Table S5. Potential regulatory elements identified throughout the ChPV2 genome, elements marked with a * have a mismatch to the published consensus sequence for the respective element. Table S6. List of PV genomes collected from PaVE (pave.niaid.nih.gov) plus ChPV2.