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Bovine papillomaviruses (BPVs) cause many benign and  malignant lesions in cattle and other animals. Twelve BPV types have been  identified so far, and several putative novel BPV types have been detected  based on the analysis of L1 gene fragments, generated by FAP59/64 and MY11/09  primers. Phylogenetic trees are important in studies that describe novel BPV  types. However, topological mistakes could be a problem in such studies.  Therefore, we made use of entropy to find phylogenetic informative regions in  the BPV L1 gene sequences from all 12 BPVs. Six data sets were created and  phylogenetically compared to each other using neighbor-joining and maximum  likelihood methods of phylogenetic tree reconstruction. We found two major  regions in the L1 gene, using an entropy-based approach, which selects regions  with low information complexity. More robust phylogenetic trees were obtained  with these regions, when compared to the ones obtained with FAP59/64 and  MY11/09 primers. More robust phylogenetic trees are important to accurately  position novel BPV types, subtypes and variants. We conclude that an  entropy-based approach is a good methodology for selecting regions of the L1  gene of BPVs that could be used to design more specific and sensitive  degenerate primers, for the development of improved diagnostic methods.

Entropy-based approach for selecting informative regions in the L1 gene of bovine papillomavirus for phylogenetic inference and primer design