The evolution of protein domain repertoires: Shedding light on the origins of the Herpesviridae family.

ABSTRACT: Herpesviruses (HVs, Family: Herpesviridae) have large genomes that encode hundreds of proteins. Apart from amino acid mutations, protein domain acquisitions, duplications and losses are also common modes of evolution. HV domain repertoires differ across species, and only a core set is shared among all species, aspect that raises a question: How have HV domain repertoires diverged while keeping some similarities? To answer such question, we used profile Hidden Markov Models (HMMs) to search for domains in all possible translated open reading frames (ORFs) of fully sequenced HV genomes. With at least 274 domains being identified, we built a matrix of domain counts per species, and applied a parsimony method to reconstruct the ancestral states of these domains along the HV phylogeny. I

SUBMITTER: Brito AF 

PROVIDER: S-EPMC7000910 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature