Endogenous Pararetroviral Sequences (EPRVs) from Whole-Genome Sequencing of Five Dioscorea (Yam) Species

This dataset comprises endogenous pararetroviral sequences (EPRVs) mined from 86 publicly available whole-genome sequencing libraries across five yam species (<i>Dioscorea rotundata, D. alata, D. praehensilis, D. abyssinica, and D. dumetorum</i>). The primary focus is on the white yam (<i>D. rotundata</i>), which hosts a complex diversity of EPRVs that complicate pathogen diagnostics and germplasm exchange.Sequences were identified using the CAULIFINDER pipeline, which targets the conserved Reverse Transcriptase/RNase H (RT/RNase H) domains of the <i>Caulimoviridae</i> family. Subsequent phylogenetic analyses revealed four major EPRV groups: Yendovirus, Badnavirus, Yam Endovirus 1, and a novel, previously uncharacterized Dioscovirus-like lineage.A key feature of this dataset is the identification of both fragmented EPRV insertions and complete, full-length viral genomes within the Yam Badnavirus and Dioscovirus-like clades. These include sequences resembling linearized circular episomal viruses and integrated forms flanked by host genomic sequences.<b>Potential Applications:</b><b>Viral Diagnostics:</b> Development of specific assays to differentiate harmful episomal viruses from endogenous EPRVs.<b>Evolutionary Virology:</b> Study of virus-host co-evolution, integration events, and potential reactivation mechanisms.<b>Yam Breeding:</b> Informing breeding programs by characterizing the "viral fossil record" within yam genomes to avoid unnecessary rejection of germplasm.<b>Genome Surveillance:</b> Serving as a reference for genome-wide surveillance in yam virology.<b>Key Species:</b> <i>Dioscorea rotundata</i> (White Yam), <i>Dioscorea alata</i> (Water Yam), <i>Dioscorea praehensilis</i>, <i>Dioscorea abyssinica</i>, <i>Dioscorea dumetorum</i> (Bitter Yam)