Andrews S. FastQC: A quality control tool for high throughput sequence data. 2010.

Bannert N, Hofmann H, Block A, Hohn O. HERVs new role in cancer: from accused perpetrators to cheerful protectors. Front Microbiol. 2018;9:178.

Article  PubMed  PubMed Central  Google Scholar 

Benachenhou F, Sperber GO, Bongcam-Rudloff E, Andersson G, Boeke JD, Blomberg J. Conserved structure and inferred evolutionary history of long terminal repeats (LTRs). Mobile DNA. 2013. https://doi.org/10.1186/1759-8753-4-5.

Article  PubMed  PubMed Central  Google Scholar 

Berry BT, Ghosh AK, Kumar DV, Spodick DA, Roy-Burman P. Structure and function of endogenous feline leukemia virus long terminal repeats and adjoining regions. J Virol. 1988;62:3631–41.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Boeke JD, Stoye JP. Retrotransposons, endogenous retroviruses, and the evolution of retroelements. In: Coffin JM, Hughes SH, Varmus HE, editors. Retroviruses. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 1997. p. 343–6.

Google Scholar 

Cassandri M, Smirnov A, Novelli F, Pitolli C, Agostini M, Malewicz M, Melino G, Raschella G. Zinc-finger proteins in health and disease. Cell Death Discov. 2017;3:17071.

Article  PubMed  PubMed Central  Google Scholar 

Chisholm PJ, Busch JW, Crowder DW. Effects of life history and ecology on virus evolutionary potential. Virus Res. 2019;265:1–9.

Article  CAS  PubMed  Google Scholar 

Chiu ES, Hoover EA, VandeWoude S. A retrospective examination of feline leukemia subgroup characterization: viral interference assays to deep sequencing. Viruses. 2018. https://doi.org/10.3390/v10010029.

Article  PubMed  PubMed Central  Google Scholar 

Chiu ES, McDonald CA, VandeWoude S. Endogenous feline leukemia virus (FeLV) siRNA transcription may interfere with exogenous FeLV infection. J Virol. 2021;95: e0007021.

Article  PubMed  Google Scholar 

Chiu ES, VandeWoude S. Endogenous retroviruses drive resistance and promotion of exogenous retroviral homologs. Ann Rev Anim Biosci. 2020;9:225.

Article  Google Scholar 

Chiu ES, VandeWoude S. Presence of endogenous viral elements negatively correlates with feline leukemia virus susceptibility in puma and domestic cat cells. J Virol. 2020;94:e01274-e1220.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Coffin JM, Garfinkel DJ, Kozak CA, Leung NJ, Luciw PA, Myers G, Pavlakis GN, Payne LN, Ruscetti S, Temin HM. Virion structure. In: Levy JA, editor. The retroviridae. New York: Plenum Press; 1992. p. 21–34.

Google Scholar 

Consortium I.H.G.S. Initial sequencing and analysis of the human genome. Nature. 2001;409:860–921.

Article  Google Scholar 

Denner J. Expression and function of endogenous retroviruses in the placenta. APMIS. 2016;124:31–43.

Article  CAS  PubMed  Google Scholar 

Dobin A, Davis CA, Schlesinger F, Derenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21.

Article  CAS  PubMed  Google Scholar 

Erbeck K, Gagne RB, Kraberger S, Chiu ES, Roelke-Parker M, VandeWoude S. Feline leukemia virus (FeLV) endogenous and exogenous recombination events result in multiple FeLV-B subtypes during natural infection. J Virol. 2021;10:179.

Google Scholar 

Frank JA, Feschotte C. Co-option of endogenous viral sequences for host cell function. Curr Opin Virol. 2017;25:81–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ghosh SK, Roy-Burman P, Faller DV. Long terminal repeat regions from exogenous but not endogenous feline leukemia viruses tranactivate cellular gene expression. J Virol. 2006;74:9742–8.

Article  Google Scholar 

Gogvadze E, Stukacheva E, Buzdin A, Sverdlov E. Human-specific modulation of transcriptional activity provided by endogenous retroviral insertions. J Virol. 2009;83:6098–105.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Grandi N, Tramontano E. Human endogenous retroviruses are ancient acquired elements still shaping innate immune responses. Front Immunol. 2018;9:2039.

Article  PubMed  PubMed Central  Google Scholar 

Holt MP, Shevach EM, Punkosdy GA. Endogenous mouse mammary tumor viruses (mtv): new roles for an old virus in cancer, infection, and immunity. Front Oncol. 2013;3:287.

Article  PubMed  PubMed Central  Google Scholar 

Hoover EA, Mullins JI, Chu HJ, Wasmoen TL. Development and testing of an inactivated feline leukemia virus vaccine. Semin Vet Med Surg Small Anim. 1995;10(4):238–43.

CAS  PubMed  Google Scholar 

Krueger, F., James, F., Ewels, P., Afyounian, E., Schuster-Boeckler, B., 2021. FlixKrueger/TrimGalore, 0.6.7 ed, Zenodo.

Li G, Davis BW, Raudsepp T, Pearks Wilkerson AJ, Mason VC, Ferguson-Smith M, O’Brien PC, Waters PD, Murphy WJ. Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution. Genome Res. 2013;23:1486–95.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li Y, Holland CA, Hartley JW, Hopkins N. Viral integration near c-myc in 10–20% of MCF 247-induced AKR lymphomas. Proc Natl Acad Sci. 1984;81:6808–11.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Luo GX, Taylor J. Template switching by reverse transcriptase during DNA synthesis. J Virol. 1990;64:4321–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Maldarelli F, Wu X, Su L, Simonetti FR, Shao W, Hill S, Spindler J, Ferris AL, Mellors JW, Kearney MF, Coffin JM, Hughes SH. Specific HIV integration sites are linked to clonal expansion and persistence of infected cells. Science. 2014;345:179–83.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Maston GA, Evans SK, Green MR. Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet. 2006;7:29–59.

Article  CAS  PubMed  Google Scholar 

McKenna MJ, Robinson E, Goodwin EH, Cornforth MN, Bailey SM. Telomeres and NextGen CO-FISH: directional genomic hybridization (Telo-dGH™). In: Songyang Z, editor. Methods in molecular biology. New York, NY: Humana Press; 2017. p. 103–12.

Google Scholar 

Medstrand PVDLL, Mager DL. Retroelement distributions in the human genome: variations associated with age and proximity to genes. Genome Res. 2002;12:1483–95.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mi H, Ebert D, Muruganujan A, Mills C, Albou LP, Mushayamaha T, Thomas PD. PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. Nucleic Acids Res. 2021;49:D394–403.

Article  CAS  PubMed  Google Scholar 

Murcia PR, Arnaud F, Palmarini M. The transdominant endogenous retrovirus enJS56A1 associates with and blocks intracellular trafficking of Jaagsiekte sheep retrovirus Gag. J Virol. 2007;81:1762–72.

Article  CAS  PubMed  Google Scholar 

Pennacchio LA, Bickmore W, Dean A, Nobrega MA, Bejerano G. Enhancers: five essential questions. Nat Rev Genet. 2013;14:288–95.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Powers JA, Chiu ES, Kraberger SJ, Roelke-Parker M, Lowery I, Erbeck K, Troyer R, Carver S, VandeWoude S. Feline leukemia virus disease outcomes in a domestic cat breeding colony: Relationship to endogenous FeLV and other chronic viral infections. J Virol. 2018. https://doi.org/10.1128/JVI.00649-18.

Article  PubMed  PubMed Central  Google Scholar 

Rasmussen HB. Interactions between exogenous and endogenous retroviruses. J Biomed Sci. 1997;4:1–8.

CAS  PubMed  Google Scholar 

Riedhammer C, Halbritter D, Weissert R. Peripheral blood mononuclear cells: isolation, freezing, thawing, and culture. In: Weissert R, editor. Multiple sclerosis methods in microbiology. New York: Humana Press; 2014.

Google Scholar 

Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.

Article  CAS  PubMed  Google Scholar 

Sanville B, Dolan MA, Wollenberg K, Yan Y, Martin C, Yeung ML, Strebel K, Buckler-White A, Kozak CA. Adaptive evolution of Mus Apobec3 includes retroviral insertion and positive selection at two clusters of residues flanking the substrate groove. PLoS Pathog. 2010;6: e1000974.

Article  PubMed  PubMed Central  Google Scholar 

Thompson PJ, Macfarlan TS, Lorincz MC. Long terminal repeats: from parasitic elements to building blocks of the transcriptional regulatory repertoire. Mol Cell. 2016;62:766–76.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Torres AN, Mathiason CK, Hoover EA. Re-examination of feline leukemia virus: host relationships using real-time PCR. Virology. 2005;332:272–83.

Article  CAS  PubMed