title: Endogenization of mouse mammary tumor virus (MMTV)-like elements in genomes of pikas (Ochotona sp.).
abstract: Despite the finding in European rabbit and other leporid genomes of the first ever described endogenous lentivirus and of a European rabbit exclusive endogenous gammaretrovirus, until now no exogenous retroviruses have been isolated in Lagomorpha species. Nevertheless, looking for the presence of endogenous retroviruses (ERVs) in the species genomes could lead to the discovery of retroviral lineages yet to be found in Lagomorpha. Different mammalian genomes harbor endogenous viral sequences phylogenetically close to the betaretrovirus mouse mammary tumor virus (MMTV), propelling us to look for such retroviral "fossil" in American pika (Ochotona princeps) and European rabbit (Oryctolagus cuniculus) genomes. By performing genomic mining using MMTV gag and LTR as query sequences, we found that such viral elements were absent from the European rabbit genome. Oppositely, significant matches were found in American pika, and more importantly, a nearly complete MMTV-like virus (Pika-BERV) was identified. Using Pika-BERV gag and LTR as templates, we found similar sequences endogenized in different pika (Ochotona sp.) species. The orthology of the LTR flanking region between some pika species supported shared ancestry of specific endogenous betaretroviruses, while in other pika species similar sequences, but not orthologous, should have resulted from independent insertions. Our study supports the possible existence of infecting exogenous betaretroviruses for a long term, after the divergence of Ochotonidae from Leporidae, but yet to be identified.
authors.affiliation: CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal. Electronic address: anamatos@ufl.edu.
authors.forename: Ana
authors.initials: A
authors.lastname: Lemos de Matos
authors.affiliation: CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.
authors.forename: Patrícia
authors.initials: P
authors.lastname: de Sousa-Pereira
authors.affiliation: Zoological Museum, Moscow State Lomonosov University, 125009, B. Nikitskaya 6, Moscow, Russia.
authors.forename: Andrey A
authors.initials: AA
authors.lastname: Lissovsky
authors.affiliation: CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.
authors.forename: Wessel
authors.initials: W
authors.lastname: van der Loo
authors.affiliation: CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal.
authors.forename: José
authors.initials: J
authors.lastname: Melo-Ferreira
authors.affiliation: Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore 169857, Singapore.
authors.forename: Jie
authors.initials: J
authors.lastname: Cui
authors.affiliation: CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; CITS - Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, 4585-116 Gandra, Portugal. Electronic address: pjesteves@cibio.up.pt.
authors.forename: Pedro J
authors.initials: PJ
authors.lastname: Esteves
mesh_terms: D000818:Animals; D020077:Endogenous Retroviruses / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D007793:Lagomorpha / Q000821:virology*; D008324:Mammary Tumor Virus, Mouse / Q000145:classification / Q000235:genetics*; D011817:Rabbits / Q000821:virology
keywords: Endogenous betaretrovirus (EnBV); Endogenous retrovirus (ERV); Mouse mammary tumor virus (MMTV); genomic mining; genus Ochotona